Citrus Sinensis ID: 041711

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210
Protein Sequence
MDAAQWYNAHLKVVHLSNDYIPDQDRNLSPGFYFIIQIFNTDELIHPQVRVRIPLNAQEHTFHLKLHEIFFEDSDQDSFLEDLRANLLSTQGLGECAQEILMKTILDEAKAAAHATPYDPECSLVAVGVQLEVVRVIETWEIAILEEGSGLILGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCTTTGSD
Secondary Structure (PSIPRED)
ccHHHHHHHHcEEEEcccccccccccccccHHHHHHHHcccccccccccEEcccccccccccccccccccccccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHccccccccccHHccccccHHHHHHccccEEEEEEcccccccccccccccccccccccEEEEEcccccccHHHHHHHHccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHEHEEccccccccccccccccEEEEEEEEcccccccccEEEEEEcccccccEEEEEEEEEEccccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHcccEEEEccccccccccccEEEHHHcccccEEEEccccccccHHHHHHHHHHcccccEEEEEccccccccc
Coil and Loop (DISEMBL)
MDAAQWYNAHLKVVHlsndyipdqdrnlspgFYFIIQIFntdelihpqvrvriplnaqehTFHLKLHEiffedsdqdSFLEDLRANLLSTQGLGECAQEILMKTILDEAkaaahatpydpecslVAVGVQLEVVRVIETWEIAILEegsglilgqERCVICLeefsegdevislqcshvhhrhCILKWLvtgnncptcrftlpctttgsd
Flexible Loop (DISEMBL)
MDAAQWYNAHLKVVHLSNDYIPDQDRNLSPGFYFIIQIFNTDELIHPQVRVRIPLNAQEHTFHLKLHEIFFEDSDQDSFLEDLRANLLSTQGLGECAQEILMKTILDEAKAAAHATPYDPECSLVAVGVQLEVVRVIETWEIAILeegsglilgqERCVICLEEFSEGDEVISLQCSHVHHRHCILKWlvtgnncptcrftlpctttgsd
Low Complexity Region (SEG)
MDAAQWYNAHLKVVHLSNDYIPDQDRNLSPGFYFIIQIFNTDELIHPQVRVRIPLNAQEHTFHLKLHEIFFEDSDQDSFLEDLRANLLSTQGLGECAQEILMKTILDEAKAAAHATPYDPECSLVAVGVQLEVVRVIETWEIAILEEGSGLILGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCTTTGSD
Disordered region (IsUnstruct)
****QWYNAHLKVVHLSNDYIPDQDRNLSPGFYFIIQIFNTDELIHPQVRVRIPLNAQEHTFHLKLHEIFFEDSDQDSFLEDLRANLLSTQGLGECAQEILMKTILDEAKAAAHATPYDPECSLVAVGVQLEVVRVIETWEIAILEEGSGLILGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCT*****
Disordered Region (DISOPRED)
****QWYNAHLKVVHL**************GFYFIIQIFNTDELI*************************FEDSDQDSFLEDLRANLLSTQGLGECAQEILMKT********************************I*TW***************ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCR***********
Disordered Region (DISEMBL)
MDAAQWYNAHLKVVHLSNDYIPDQDRNLSPGFYFIIQIFNTDELIHPQVRVRIPLNAQEHTFHLKLHEIFFEDSDQDSFLEDLRANLLSTQGLGECAQEILMKTILDEAKAAAHATPYDPECSLVAVGVQLEVVRVIETWEIAILEEGSGLILGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCTTTGSD
Disordered Region (DISPRO)
MDAAQWYNAHLKVVHLSNDYIPDQDRNLSPGFYFIIQIFNTDELIHPQVRVRIPLNAQEHTFHLKLHEIFFEDSDQDSFLEDLRANLLSTQGLGECAQEILMKTILDEAKAAAHAT***PECSLVAVGVQLEVVRVIETWEIAILEEGSGLILGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCT*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDAAQWYNAHLKVVHLSNDYIPDQDRNLSPGFYFIIQIFNTDELIHPQVRVRIPLNAQEHTFHLKLHEIFFEDSDQDSFLEDLRANLLSTQGLGECAQEILMKTILDEAKAAAHATPYDPECSLVAVGVQLEVVRVIETWEIAILEEGSGLILGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCTTTGSD
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	210	2.2.26 [Sep-21-2011]
Q8LPN7	328	E3 ubiquitin-protein liga	no	no	0.223	0.143	0.468	2e-09
P87139	372	Uncharacterized RING fing	yes	no	0.295	0.166	0.412	9e-09
P0CH30	338	E3 ubiquitin-protein liga	N/A	no	0.223	0.139	0.425	3e-08
Q5M974	156	E3 ubiquitin-protein liga	yes	no	0.223	0.301	0.510	7e-08
Q6GPV5	156	E3 ubiquitin-protein liga	N/A	no	0.223	0.301	0.510	8e-08
Q07G42	639	E3 ubiquitin-protein liga	no	no	0.2	0.065	0.452	1e-07
Q7T037	757	E3 ubiquitin-protein liga	N/A	no	0.2	0.055	0.452	1e-07
Q68DV7	783	E3 ubiquitin-protein liga	yes	no	0.214	0.057	0.488	2e-07
Q5NCP0	784	E3 ubiquitin-protein liga	yes	no	0.214	0.057	0.488	2e-07
Q9WTV7	600	E3 ubiquitin-protein liga	no	no	0.2	0.07	0.452	3e-07

>sp|Q8LPN7|RNG1L_ARATH E3 ubiquitin-protein ligase RING1-like OS=Arabidopsis thaliana GN=At3g19950 PE=2 SV=1

 Score = 62.4 bits (150), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 32/47 (68%)

Query: 157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP 203
           +C +C++EF +G +V  + C HV H+ C+L WL   N+CP CRF LP
Sbjct: 215 QCAVCMDEFEDGSDVKQMPCKHVFHQDCLLPWLELHNSCPVCRFELP 261

E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Promotes polyubiquitination of target proteins.
Arabidopsis thaliana (taxid: 3702)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|P87139|YDM9_SCHPO Uncharacterized RING finger protein C57A7.09 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC57A7.09 PE=1 SV=1

 Score = 60.1 bits (144), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 26/63 (41%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 142 IAILEEGSGLILGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNN-CPTCRF 200
           + +++E +        CVICLE F++GD+V++L C H  HR CI KW+V   + CPTC  
Sbjct: 305 VPLMDESTRRATFGVECVICLESFTKGDKVVALPCKHEFHRPCIAKWIVDYRHACPTCNT 364

Query: 201 TLP 203
            +P
Sbjct: 365 EVP 367

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

>sp|P0CH30|RING1_GOSHI E3 ubiquitin-protein ligase RING1 OS=Gossypium hirsutum GN=RING1 PE=2 SV=1

 Score = 58.5 bits (140), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 31/47 (65%)

Query: 157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP 203
           +C +C+++F EG E   + C H++H+ C+L WL   N+CP CR  LP
Sbjct: 223 QCAVCMDDFEEGTEAKQMPCKHLYHKDCLLPWLELHNSCPVCRHELP 269

E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Promotes polyubiquitination of target proteins.

Gossypium hirsutum (taxid: 3635)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q5M974|RN181_XENTR E3 ubiquitin-protein ligase RNF181 OS=Xenopus tropicalis GN=rnf181 PE=2 SV=1

 Score = 57.4 bits (137), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 29/47 (61%)

Query: 157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP 203
           +C +CL EF EG+ V  L C H+ H  CIL WL   N+CP CR  LP
Sbjct: 78  KCPVCLLEFEEGETVRQLPCEHLFHSSCILPWLGKTNSCPLCRHELP 124

E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

Xenopus tropicalis (taxid: 8364)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q6GPV5|RN181_XENLA E3 ubiquitin-protein ligase RNF181 OS=Xenopus laevis GN=rnf181 PE=2 SV=1

 Score = 57.4 bits (137), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 29/47 (61%)

Query: 157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP 203
           +C +CL EF EG+ V  L C H+ H  CIL WL   N+CP CR  LP
Sbjct: 78  KCPVCLLEFEEGETVRQLPCEHLFHSACILPWLGKTNSCPLCRHELP 124

E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

Xenopus laevis (taxid: 8355)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q07G42|RNF12_XENTR E3 ubiquitin-protein ligase RNF12 OS=Xenopus tropicalis GN=rnf12 PE=2 SV=1

 Score = 56.6 bits (135), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 19/42 (45%), Positives = 29/42 (69%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCR 199
           C +C+ E++EG+++  L CSH +H HCI +WL   + CP CR
Sbjct: 585 CSVCITEYTEGNKLRKLPCSHEYHVHCIDRWLSENSTCPICR 626

Acts as a E3 ubiquitin-protein ligase specific for ldb1, mediating ubiquitination and proteasome-dependent degradation of excess ldb1 in a RING-dependent manner. Does not degrade ldb1 bound to lhx1/lim1, nor lim1 itself and thus contributes to the establishment of proper ldb1-lhx1/lim1 stoichiometry and the formation of a ldb1-lhx1/lim1 complex. Interferes with Spemann organizer function and suppresses secondary axis formation induced by ldb1 and lhx1/lim1.

Xenopus tropicalis (taxid: 8364)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q7T037|RF12B_XENLA E3 ubiquitin-protein ligase RNF12-B OS=Xenopus laevis GN=rnf12-b PE=2 SV=1

 Score = 56.2 bits (134), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 19/42 (45%), Positives = 29/42 (69%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCR 199
           C +C+ E++EG+++  L CSH +H HCI +WL   + CP CR
Sbjct: 703 CSVCITEYTEGNKLRKLPCSHEYHIHCIDRWLSENSTCPICR 744

Acts as a E3 ubiquitin-protein ligase specific for ldb1, mediating ubiquitination and proteasome-dependent degradation of excess ldb1 in a RING-dependent manner. Does not degrade ldb1 bound to lhx1/lim1, nor lim1 itself and thus contributes to the establishment of proper ldb1-lhx1/lim1 stoichiometry and the formation of a ldb1-lhx1/lim1 complex. Interferes with Spemann organizer function and suppresses secondary axis formation induced by ldb1 and lhx1/lim1.

Xenopus laevis (taxid: 8355)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q68DV7|RNF43_HUMAN E3 ubiquitin-protein ligase RNF43 OS=Homo sapiens GN=RNF43 PE=1 SV=1

 Score = 56.2 bits (134), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 22/45 (48%), Positives = 27/45 (60%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTL 202
           C ICLEEFSEG E+  + C H  HR+C+  WL     CP C F +
Sbjct: 272 CAICLEEFSEGQELRVISCLHEFHRNCVDPWLHQHRTCPLCMFNI 316

Probable E3 ubiquitin-protein ligase. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates.

Homo sapiens (taxid: 9606)

>sp|Q5NCP0|RNF43_MOUSE E3 ubiquitin-protein ligase RNF43 OS=Mus musculus GN=Rnf43 PE=2 SV=1

 Score = 55.8 bits (133), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 22/45 (48%), Positives = 26/45 (57%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTL 202
           C ICLEEFSEG E+  + C H  HR C+  WL     CP C F +
Sbjct: 272 CAICLEEFSEGQELRVISCLHEFHRTCVDPWLYQHRTCPLCMFNI 316

Probable E3 ubiquitin-protein ligase. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates.

Mus musculus (taxid: 10090)

>sp|Q9WTV7|RNF12_MOUSE E3 ubiquitin-protein ligase RLIM OS=Mus musculus GN=Rlim PE=1 SV=2

 Score = 55.1 bits (131), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 19/42 (45%), Positives = 29/42 (69%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCR 199
           C +C+ E++EG+++  L CSH +H HCI +WL   + CP CR
Sbjct: 546 CSVCITEYTEGNKLRKLPCSHEYHVHCIDRWLSENSTCPICR 587

E3 ubiquitin-protein ligase. Acts as a negative coregulator for LIM homeodomain transcription factors by mediating the ubiquitination and subsequent degradation of LIM cofactors LDB1 and LDB2 and by mediating the recruitment the SIN3a/histone deacetylase corepressor complex. Ubiquitination and degradation of LIM cofactors LDB1 and LDB2 allows DNA-bound LIM homeodomain transcription factors to interact with other protein partners such as RLIM. Plays a role in telomere length-mediated growth suppression by mediating the ubiquitination and degradation of TERF1. Acts as an activator of random inactivation of X chromosome in the embryo, a stochastic process in which one X chromosome is inactivated to minimize sex-related dosage differences of X-encoded genes in somatic cells of female placental mammals.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	210
71420237	393	hypothetical protein [Trypanosoma cruzi	0.366	0.195	0.388	2e-09
449519727	226	PREDICTED: E3 ubiquitin-protein ligase R	0.709	0.659	0.3	3e-09
15221860	224	C3HC4-type RING finger domain-containing	0.233	0.218	0.530	3e-09
449465461	226	PREDICTED: E3 ubiquitin-protein ligase R	0.709	0.659	0.3	3e-09
3582320	310	hypothetical protein [Arabidopsis thalia	0.328	0.222	0.391	3e-09
145360461	293	RING/U-box domain-containing protein [Ar	0.328	0.235	0.391	4e-09
297850266	344	hypothetical protein ARALYDRAFT_889306 [	0.233	0.142	0.510	5e-09
71394219	319	hypothetical protein [Trypanosoma cruzi	0.366	0.241	0.376	6e-09
147784488	245	hypothetical protein VITISV_000265 [Viti	0.247	0.212	0.461	9e-09
15221862	106	RING/U-box domain-containing protein [Ar	0.228	0.452	0.562	1e-08

>gi|71420237|ref|XP_811415.1| hypothetical protein [Trypanosoma cruzi strain CL Brener] gi|70876077|gb|EAN89564.1| hypothetical protein, conserved [Trypanosoma cruzi]

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 33/85 (38%), Positives = 47/85 (55%), Gaps = 8/85 (9%)

Query: 127 VGVQLEVVRVIETWEIAILE------EGSGLILGQER--CVICLEEFSEGDEVISLQCSH 178
            G+ L+ +R ++    + L+      +GSG   G+ R  C ICLEEFS G  V+ + C H
Sbjct: 302 TGLPLQQIRGMKGVPYSNLKSKNETAKGSGNAPGEHREECAICLEEFSSGTLVLKIGCGH 361

Query: 179 VHHRHCILKWLVTGNNCPTCRFTLP 203
           V H  C++KW    N CP CRF +P
Sbjct: 362 VFHHGCLVKWFKESNRCPKCRFEIP 386

Source: Trypanosoma cruzi strain CL Brener

Species: Trypanosoma cruzi

Genus: Trypanosoma

Family: Trypanosomatidae

Order: Kinetoplastida

Superkingdom: Eukaryota

>gi|449519727|ref|XP_004166886.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like [Cucumis sativus]

 Score = 67.8 bits (164), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 48/160 (30%), Positives = 74/160 (46%), Gaps = 11/160 (6%)

Query: 53  IPLNAQEHTFHLKLHEIFFEDSDQDSFLEDLRANLLSTQGLGECAQEILMKTILDEAKAA 112
           IP +    T    L  +F        FL+    ++LS      C      +TIL  A + 
Sbjct: 67  IPCDVFFATASSILIAVFSGTGVAQDFLDTALPDVLSVAADIACNPLNAGRTILPLAVSV 126

Query: 113 AHATPYDP--ECSLVAVGVQLEVVRVIETWEIAI-------LEEGSGLILGQERCVICLE 163
              +PY+   E   V      +  + +   E+AI       ++ G  L++G+  C ICL+
Sbjct: 127 LVVSPYNERQEIGRVLRESSPQAFKTLPASEMAIEGLKNVEIDVGGELLIGE--CRICLD 184

Query: 164 EFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP 203
           E   G EV  L C+H++HR CI+KWL T + CP CR+ +P
Sbjct: 185 ELMNGMEVTRLPCAHLYHRDCIVKWLETSHLCPLCRYAMP 224

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15221860|ref|NP_173311.1| C3HC4-type RING finger domain-containing protein [Arabidopsis thaliana] gi|6730708|gb|AAF27103.1|AC011809_12 Hypothetical protein [Arabidopsis thaliana] gi|70905057|gb|AAZ14054.1| At1g18760 [Arabidopsis thaliana] gi|332191639|gb|AEE29760.1| C3HC4-type RING finger domain-containing protein [Arabidopsis thaliana]

 Score = 67.8 bits (164), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 26/49 (53%), Positives = 34/49 (69%)

Query: 156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPC 204
           ERC ICLEEF++G +V++L C H     C+L W  T ++CP CRF LPC
Sbjct: 173 ERCTICLEEFNDGTKVMTLPCGHEFDDECVLTWFETNHDCPLCRFKLPC 221

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449465461|ref|XP_004150446.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like [Cucumis sativus]

 Score = 67.8 bits (164), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 48/160 (30%), Positives = 74/160 (46%), Gaps = 11/160 (6%)

Query: 53  IPLNAQEHTFHLKLHEIFFEDSDQDSFLEDLRANLLSTQGLGECAQEILMKTILDEAKAA 112
           IP +    T    L  +F        FL+    ++LS      C      +TIL  A + 
Sbjct: 67  IPCDVFFATASSILIAVFSGTGVAQDFLDTAVPDVLSVAADIACNPLNAGRTILPLAVSV 126

Query: 113 AHATPYDP--ECSLVAVGVQLEVVRVIETWEIAI-------LEEGSGLILGQERCVICLE 163
              +PY+   E   V      +  + +   E+AI       ++ G  L++G+  C ICL+
Sbjct: 127 LVVSPYNERQEIGRVLRESSPQAFKTLPASEMAIEGLKKVEIDVGGELLIGE--CRICLD 184

Query: 164 EFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP 203
           E   G EV  L C+H++HR CI+KWL T + CP CR+ +P
Sbjct: 185 ELMNGMEVTRLPCAHLYHRDCIVKWLETSHLCPLCRYAMP 224

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|3582320|gb|AAC35217.1| hypothetical protein [Arabidopsis thaliana]

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 27/69 (39%), Positives = 39/69 (56%)

Query: 136 VIETWEIAILEEGSGLILGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNC 195
            +E+      ++ S ++   E C ICLEEF +G  +++L C H     C LKW  T ++C
Sbjct: 239 AVESLNRKTYKKASDVVGENEMCSICLEEFDDGRSIVALPCGHEFDDECALKWFETNHDC 298

Query: 196 PTCRFTLPC 204
           P CRF LPC
Sbjct: 299 PLCRFKLPC 307

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145360461|ref|NP_180545.2| RING/U-box domain-containing protein [Arabidopsis thaliana] gi|330253216|gb|AEC08310.1| RING/U-box domain-containing protein [Arabidopsis thaliana]

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 27/69 (39%), Positives = 39/69 (56%)

Query: 136 VIETWEIAILEEGSGLILGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNC 195
            +E+      ++ S ++   E C ICLEEF +G  +++L C H     C LKW  T ++C
Sbjct: 222 AVESLNRKTYKKASDVVGENEMCSICLEEFDDGRSIVALPCGHEFDDECALKWFETNHDC 281

Query: 196 PTCRFTLPC 204
           P CRF LPC
Sbjct: 282 PLCRFKLPC 290

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297850266|ref|XP_002893014.1| hypothetical protein ARALYDRAFT_889306 [Arabidopsis lyrata subsp. lyrata] gi|297338856|gb|EFH69273.1| hypothetical protein ARALYDRAFT_889306 [Arabidopsis lyrata subsp. lyrata]

 Score = 67.0 bits (162), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 25/49 (51%), Positives = 34/49 (69%)

Query: 156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPC 204
           ++C ICLEEF++G  V++L C H     C+LKW  T ++CP CRF LPC
Sbjct: 293 QKCTICLEEFNDGRRVVTLPCGHDFDDECVLKWFETNHDCPLCRFKLPC 341

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|71394219|ref|XP_802258.1| hypothetical protein [Trypanosoma cruzi strain CL Brener] gi|70860552|gb|EAN80812.1| hypothetical protein, conserved [Trypanosoma cruzi]

 Score = 66.6 bits (161), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 32/85 (37%), Positives = 47/85 (55%), Gaps = 8/85 (9%)

Query: 127 VGVQLEVVRVIETWEIAILE------EGSGLILGQER--CVICLEEFSEGDEVISLQCSH 178
            G+ L+ +R ++    + L+      +GSG   G+ R  C ICL+EFS G  V+ + C H
Sbjct: 228 TGLPLQQIRGMKGVPYSNLKSKKETVKGSGNASGEHREECAICLDEFSSGTLVLKIGCGH 287

Query: 179 VHHRHCILKWLVTGNNCPTCRFTLP 203
           V H  C++KW    N CP CRF +P
Sbjct: 288 VFHHGCLVKWFKESNRCPKCRFEIP 312

Source: Trypanosoma cruzi strain CL Brener

Species: Trypanosoma cruzi

Genus: Trypanosoma

Family: Trypanosomatidae

Order: Kinetoplastida

Superkingdom: Eukaryota

>gi|147784488|emb|CAN74950.1| hypothetical protein VITISV_000265 [Vitis vinifera]

 Score = 66.2 bits (160), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 24/52 (46%), Positives = 37/52 (71%)

Query: 156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCTTT 207
           ++C+ICLEEF+   EV  + CSHV+H+ CI++WL   + CP CRF +P  ++
Sbjct: 194 DKCIICLEEFATESEVSRMPCSHVYHKDCIIQWLERSHMCPLCRFKMPAISS 245

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15221862|ref|NP_173312.1| RING/U-box domain-containing protein [Arabidopsis thaliana] gi|332191640|gb|AEE29761.1| RING/U-box domain-containing protein [Arabidopsis thaliana]

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/48 (56%), Positives = 33/48 (68%)

Query: 156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP 203
           E C+ICLEEFSEG  V++L C H     C+LKW  T ++CP CRF LP
Sbjct: 57  EMCIICLEEFSEGRRVVTLPCGHDFDDECVLKWFETNHSCPLCRFKLP 104

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	210
TAIR|locus:2034939	224	AT1G18760 [Arabidopsis thalian	0.233	0.218	0.530	1.9e-12
TAIR|locus:2034934	106	AT1G18770 [Arabidopsis thalian	0.228	0.452	0.562	2.4e-12
TAIR|locus:2050522	180	AT2G44330 [Arabidopsis thalian	0.252	0.294	0.415	2.8e-12
TAIR|locus:2060699	293	AT2G29840 [Arabidopsis thalian	0.323	0.232	0.397	1.1e-11
TAIR|locus:2117701	213	AT4G18110 [Arabidopsis thalian	0.538	0.530	0.341	2.2e-11
TAIR|locus:2034924	325	AT1G18780 [Arabidopsis thalian	0.280	0.181	0.406	2.7e-11
TAIR|locus:2151241	283	SGR9 "SHOOT GRAVITROPISM 9" [A	0.238	0.176	0.54	7.9e-11
TAIR|locus:2092231	328	AT3G19950 [Arabidopsis thalian	0.223	0.143	0.468	1.3e-10
POMBASE|SPAC57A7.09	372	SPAC57A7.09 "human RNF family	0.295	0.166	0.412	2e-10
TAIR|locus:2177886	164	AT5G41450 [Arabidopsis thalian	0.395	0.506	0.388	5.2e-10

TAIR|locus:2034939 AT1G18760 [Arabidopsis thaliana (taxid:3702)]

 Score = 166 (63.5 bits), Expect = 1.9e-12, P = 1.9e-12
 Identities = 26/49 (53%), Positives = 34/49 (69%)

Query:   156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPC 204
             ERC ICLEEF++G +V++L C H     C+L W  T ++CP CRF LPC
Sbjct:   173 ERCTICLEEFNDGTKVMTLPCGHEFDDECVLTWFETNHDCPLCRFKLPC 221

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2034934 AT1G18770 [Arabidopsis thaliana (taxid:3702)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 27/48 (56%), Positives = 33/48 (68%)

Query:   156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP 203
             E C+ICLEEFSEG  V++L C H     C+LKW  T ++CP CRF LP
Sbjct:    57 EMCIICLEEFSEGRRVVTLPCGHDFDDECVLKWFETNHSCPLCRFKLP 104

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2050522 AT2G44330 [Arabidopsis thaliana (taxid:3702)]

 Score = 142 (55.0 bits), Expect = 2.8e-12, Sum P(2) = 2.8e-12
 Identities = 22/53 (41%), Positives = 32/53 (60%)

Query:   158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCTTTGSD 210
             C IC E+F  G+    L C+H++H  CI+ WL + N+CP CR  LP  ++  D
Sbjct:    96 CAICREDFVVGESARRLPCNHLYHNDCIIPWLTSHNSCPLCRVELPVASSEDD 148

GO:0005634 "nucleus" evidence=ISM

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

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

TAIR|locus:2060699 AT2G29840 [Arabidopsis thaliana (taxid:3702)]

 Score = 162 (62.1 bits), Expect = 1.1e-11, P = 1.1e-11
 Identities = 27/68 (39%), Positives = 39/68 (57%)

Query:   137 IETWEIAILEEGSGLILGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCP 196
             +E+      ++ S ++   E C ICLEEF +G  +++L C H     C LKW  T ++CP
Sbjct:   223 VESLNRKTYKKASDVVGENEMCSICLEEFDDGRSIVALPCGHEFDDECALKWFETNHDCP 282

Query:   197 TCRFTLPC 204
              CRF LPC
Sbjct:   283 LCRFKLPC 290

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2117701 AT4G18110 [Arabidopsis thaliana (taxid:3702)]

 Score = 156 (60.0 bits), Expect = 2.2e-11, P = 2.2e-11
 Identities = 41/120 (34%), Positives = 60/120 (50%)

Query:    85 ANLLSTQGLGECAQEILMKTILDEA-KAAAHATPYDPECSLVAVGVQLEVVRVIETW-EI 142
             AN+LS   + +  Q+ ++  I ++      H    + +  LV V V LE +     W  +
Sbjct:    82 ANVLSKSKINKWIQQSIVPKICEDLIDIRRHLEEEEKDGFLVEVEVVLETL--YSDWLRV 139

Query:   143 AILEEGSGLILGQERCVICLEEF-SEGDE--VISLQCSHVHHRHCILKWLVTGNNCPTCR 199
                +    LI  +E C+ICLEE  S G E  ++ L CSH  H+ CIL WL    +CPTCR
Sbjct:   140 NDYDSQGCLIPIEEECIICLEELASSGSERRIMKLLCSHSFHKDCILPWLRCKRSCPTCR 199

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2034924 AT1G18780 [Arabidopsis thaliana (taxid:3702)]

 Score = 160 (61.4 bits), Expect = 2.7e-11, P = 2.7e-11
 Identities = 24/59 (40%), Positives = 36/59 (61%)

Query:   146 EEGSGLILGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPC 204
             ++ SG++   + C ICLEEF +G  +++L C H     C+L+W V  + CP CR  LPC
Sbjct:   265 KKASGVVCENDVCTICLEEFDDGRSIVTLPCGHEFDEECVLEWFVRSHVCPLCRLELPC 323

GO:0005737 "cytoplasm" evidence=ISM

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

TAIR|locus:2151241 SGR9 "SHOOT GRAVITROPISM 9" [Arabidopsis thaliana (taxid:3702)]

 Score = 154 (59.3 bits), Expect = 7.9e-11, P = 7.9e-11
 Identities = 27/50 (54%), Positives = 30/50 (60%)

Query:   154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP 203
             G+  CVIC EE SEG +V  + C H  H  CIL WL   N CP CRF LP
Sbjct:   210 GEVECVICKEEMSEGRDVCEMPCQHFFHWKCILPWLSKKNTCPFCRFQLP 259

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

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

GO:0009501 "amyloplast" evidence=IDA

GO:0009630 "gravitropism" evidence=IMP

TAIR|locus:2092231 AT3G19950 [Arabidopsis thaliana (taxid:3702)]

 Score = 154 (59.3 bits), Expect = 1.3e-10, P = 1.3e-10
 Identities = 22/47 (46%), Positives = 32/47 (68%)

Query:   157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP 203
             +C +C++EF +G +V  + C HV H+ C+L WL   N+CP CRF LP
Sbjct:   215 QCAVCMDEFEDGSDVKQMPCKHVFHQDCLLPWLELHNSCPVCRFELP 261

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

GO:0010200 "response to chitin" evidence=RCA

POMBASE|SPAC57A7.09 SPAC57A7.09 "human RNF family homolog" [Schizosaccharomyces pombe (taxid:4896)]

 Score = 150 (57.9 bits), Expect = 2.0e-10, Sum P(2) = 2.0e-10
 Identities = 26/63 (41%), Positives = 39/63 (61%)

Query:   142 IAILEEGSGLILGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNN-CPTCRF 200
             + +++E +        CVICLE F++GD+V++L C H  HR CI KW+V   + CPTC  
Sbjct:   305 VPLMDESTRRATFGVECVICLESFTKGDKVVALPCKHEFHRPCIAKWIVDYRHACPTCNT 364

Query:   201 TLP 203
              +P
Sbjct:   365 EVP 367

GO:0000139 "Golgi membrane" evidence=IEA

GO:0000324 "fungal-type vacuole" evidence=IDA

GO:0005774 "vacuolar membrane" evidence=IEA

GO:0005794 "Golgi apparatus" evidence=IDA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=NAS

TAIR|locus:2177886 AT5G41450 [Arabidopsis thaliana (taxid:3702)]

 Score = 143 (55.4 bits), Expect = 5.2e-10, P = 5.2e-10
 Identities = 35/90 (38%), Positives = 46/90 (51%)

Query:   114 HATPYDPECSLVAVGVQLEVVRVIETWEIAILEEGSGLILGQERCVICLEEFSEGDEVIS 173
             H T   P+ + +AVG  +  +      E   ++EGS  I     C ICLEEF +G E+I 
Sbjct:    72 HVTLPQPQQN-IAVGY-MTWIHETTILEFKDIKEGSNKIF----CPICLEEFEDGHEIIR 125

Query:   174 LQ-CSHVHHRHCILKWLVTGNNCPTCRFTL 202
             +  C HV HR CI  WL     CP CR +L
Sbjct:   126 INMCRHVFHRFCIDPWLNQNLTCPNCRCSL 155

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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	210
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	2e-14
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	3e-11
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	1e-10
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	1e-09
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	9e-09
smart00184	40	smart00184, RING, Ring finger	4e-07
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	3e-05
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	8e-05
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	4e-04
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	5e-04
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	0.002

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

 Score = 64.3 bits (157), Expect = 2e-14
 Identities = 23/42 (54%), Positives = 29/42 (69%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCR 199
           C ICL+EF  G+EV+ L C HV H+ C+ KWL + N CP CR
Sbjct: 3   CPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCR 44

Length = 46

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

 Score = 61.5 bits (149), Expect = 3e-11
 Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT-GNNCPTCRFTLP 203
           C IC+  F + D +  L C H  H  C+ KWL+   N CP CR  +P
Sbjct: 326 CAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372

Length = 374

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

 Score = 55.5 bits (134), Expect = 1e-10
 Identities = 21/54 (38%), Positives = 26/54 (48%), Gaps = 10/54 (18%)

Query: 156 ERCVICLEEFSE--------GDE--VISLQCSHVHHRHCILKWLVTGNNCPTCR 199
           + C IC   F          GD+  V+  +C H  H HCI +WL T N CP CR
Sbjct: 20  DVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73

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

>gnl|CDD|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 = 51.7 bits (124), Expect = 1e-09
 Identities = 24/46 (52%), Positives = 28/46 (60%), Gaps = 3/46 (6%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNN-CPTCRFTL 202
           C ICLEEF   + V+ L C HV  R CI KWL +G N CP CR  +
Sbjct: 2   CPICLEEF--REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 49.4 bits (118), Expect = 9e-09
 Identities = 18/42 (42%), Positives = 23/42 (54%), Gaps = 2/42 (4%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCR 199
           C ICL+     D V+   C HV  R CIL++L   + CP CR
Sbjct: 5   CPICLDLLR--DPVVLTPCGHVFCRECILRYLKKKSKCPICR 44

Length = 45

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

 Score = 44.8 bits (106), Expect = 4e-07
 Identities = 21/42 (50%), Positives = 26/42 (61%), Gaps = 3/42 (7%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNN-CPTC 198
           C ICLEE+ +  + + L C H   R CI KWL +GNN CP C
Sbjct: 1   CPICLEEYLK--DPVILPCGHTFCRSCIRKWLESGNNTCPIC 40

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

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

 Score = 39.8 bits (93), Expect = 3e-05
 Identities = 21/42 (50%), Positives = 23/42 (54%), Gaps = 3/42 (7%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN-NCPTC 198
           C ICLEE    D V  L C H+    CIL WL +GN  CP C
Sbjct: 1   CPICLEEPK--DPVTILPCGHLFCSKCILSWLESGNVTCPLC 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|227521 COG5194, APC11, Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]

 Score = 39.8 bits (93), Expect = 8e-05
 Identities = 18/44 (40%), Positives = 22/44 (50%), Gaps = 2/44 (4%)

Query: 158 CVICLEEFSEGDE--VISLQCSHVHHRHCILKWLVTGNNCPTCR 199
           C  C    + GDE  V+   C+H  H HCI +WL T   CP  R
Sbjct: 34  CPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDR 77

Length = 88

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

 Score = 40.8 bits (95), Expect = 4e-04
 Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 10/77 (12%)

Query: 133  VVRVIETWEIAILEEGSGLILGQERCVICLEEFSEGDEVISLQ----CSHVHHRHCILKW 188
             + ++  W+  I E+ SG     E C IC       D  +  +    C +  H  C+ KW
Sbjct: 1451 FMDLLGLWKKNIDEKFSGH----EECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKW 1506

Query: 189  LVTG--NNCPTCRFTLP 203
              +   +NCP CR  + 
Sbjct: 1507 FASSARSNCPLCRSEIT 1523

Length = 1525

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

 Score = 37.5 bits (87), Expect = 5e-04
 Identities = 15/28 (53%), Positives = 17/28 (60%), Gaps = 3/28 (10%)

Query: 175 QCSHVHHRHCILKWLVTGNN---CPTCR 199
           +C H  H HCILKWL T  +   CP CR
Sbjct: 51  KCKHNFHMHCILKWLATETSKGLCPMCR 78

Apc11 is one of the subunits of the anaphase-promoting complex or cyclosome. The APC subunits are cullin family proteins with ubiquitin ligase activity. Polyubiquitination marks proteins for degradation by the 26S proteasome and is carried out by a cascade of enzymes that includes ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and is responsible for recruiting E2s to the APC and for mediating the subsequent transfer of ubiquitin to APC substrates in vivo. In Saccharomyces cerevisiae this RING-H2 finger protein defines the minimal ubiquitin ligase activity of the APC, and the integrity of the RING-H2 finger is essential for budding yeast cell viability. Length = 85

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

 Score = 38.4 bits (89), Expect = 0.002
 Identities = 17/55 (30%), Positives = 22/55 (40%), Gaps = 10/55 (18%)

Query: 158 CVICLEEFSEGDEVIS----------LQCSHVHHRHCILKWLVTGNNCPTCRFTL 202
           C IC++E    D              L C H+ H HC+  WL     CP CR  +
Sbjct: 290 CTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPV 344

Length = 491

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	210
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.88
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.63
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.47
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.41
PHA02929	238	N1R/p28-like protein; Provisional	99.4
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.2
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.16
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.15
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.13
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.11
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.11
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.11
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.1
PHA02926	242	zinc finger-like protein; Provisional	99.05
PF14634	44	zf-RING_5: zinc-RING finger domain	98.97
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.93
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.9
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.88
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.86
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.86
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.84
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.84
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.73
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.68
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.61
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.6
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.56
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.53
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.51
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.5
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.48
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.46
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.39
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.36
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.33
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.28
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.16
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.11
KOG4445	368	consensus Uncharacterized conserved protein, conta	98.1
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.09
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.03
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.92
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.68
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.68
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.55
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.48
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.35
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.23
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.18
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	97.14
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	97.07
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.05
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	96.96
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	96.91
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	96.86
COG5152	259	Uncharacterized conserved protein, contains RING a	96.84
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	96.8
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	96.69
PHA03096	284	p28-like protein; Provisional	96.67
KOG3039	303	consensus Uncharacterized conserved protein [Funct	96.57
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.56
PHA02825	162	LAP/PHD finger-like protein; Provisional	96.52
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.45
KOG2660	331	consensus Locus-specific chromosome binding protei	96.45
KOG1002	791	consensus Nucleotide excision repair protein RAD16	96.32
PHA02862	156	5L protein; Provisional	96.3
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.29
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	96.28
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	96.09
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.07
PF04641	260	Rtf2: Rtf2 RING-finger	95.86
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.84
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	95.7
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	95.69
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	95.48
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	95.44
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	95.36
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	95.19
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	95.06
COG5236	493	Uncharacterized conserved protein, contains RING Z	95.05
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	94.96
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	94.55
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	94.25
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	93.8
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	93.68
KOG1001	674	consensus Helicase-like transcription factor HLTF/	93.48
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	93.19
KOG1940	276	consensus Zn-finger protein [General function pred	93.07
KOG0298	1394	consensus DEAD box-containing helicase-like transc	93.04
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	93.03
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	92.56
KOG3899	381	consensus Uncharacterized conserved protein [Funct	92.21
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	92.15
COG5175	480	MOT2 Transcriptional repressor [Transcription]	92.05
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	91.62
COG5222	427	Uncharacterized conserved protein, contains RING Z	91.49
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	90.89
cd02127	118	PA_hPAP21_like PA_hPAP21_like: Protease-associated	90.79
KOG3002	299	consensus Zn finger protein [General function pred	90.63
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	90.11
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	89.0
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	88.95
KOG1609	323	consensus Protein involved in mRNA turnover and st	88.1
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	88.04
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	87.99
cd02123	153	PA_C_RZF_like PA_C-RZF_ like: Protease-associated	87.96
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	87.78
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	87.53
cd02125	127	PA_VSR PA_VSR: Protease-associated (PA) domain-con	87.47
KOG3053	293	consensus Uncharacterized conserved protein [Funct	87.1
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	86.18
cd02122	138	PA_GRAIL_like PA _GRAIL_like: Protease-associated	83.92
PF02757	9	YLP: YLP motif; InterPro: IPR004019 The YLP motif	82.66
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	82.03
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	81.65
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	81.17
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	80.8
cd02129	120	PA_hSPPL_like PA_hSPPL_like: Protease-associated d	80.72
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	80.56

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

Probab=99.88  E-value=1.6e-23  Score=182.85  Aligned_cols=173  Identities=19%  Similarity=0.281  Sum_probs=101.6

Q ss_pred             CCCCCCCCCCceeeeEEeeccCCCCCcceeeecccccchhhhhhhhhhhcccCCCchh--HH-HHHHHhhhhccCcChHH
Q 041711           21 IPDQDRNLSPGFYFIIQIFNTDELIHPQVRVRIPLNAQEHTFHLKLHEIFFEDSDQDS--FL-EDLRANLLSTQGLGECA   97 (210)
Q Consensus        21 ~~~~~~~~~~~fi~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~dd~~~~~--~~-~~l~~~ll~~~~l~~~~   97 (210)
                      .+|.....+.+|+++|+|..|+|..+       .++|||+||++   +|++++...+.  .. .+-....+..+.++...
T Consensus        70 ~~p~~~~~~~~~laLI~Rg~CsFe~K-------v~~AQ~aGfka---aIVynn~~~~~lv~~~~~~~~v~i~~~~vs~~~  139 (348)
T KOG4628|consen   70 NFPEHSTRSTSFLALIRRGGCSFEDK-------VLNAQRAGFKA---AIVYNNVGSEDLVAMASNPSKVDIHIVFVSVFS  139 (348)
T ss_pred             cCccCCCCCcceEEEEEccCCchHHH-------HhhcccccCce---EEEecCCCCchheeeccCCccceeEEEEEeeeh
Confidence            33566788899999999999999655       56999999999   66555443321  00 00001112222333333


Q ss_pred             HHHHHHHHHHHHHhc-----cccCCCCCCcc-------------------------------ccccCCCHHHHhhcccce
Q 041711           98 QEILMKTILDEAKAA-----AHATPYDPECS-------------------------------LVAVGVQLEVVRVIETWE  141 (210)
Q Consensus        98 ~e~l~~~v~~~~~~~-----~~~~~~~~~~~-------------------------------~~~~g~~~~~~~~l~~~~  141 (210)
                      .+.+.++.......-     ....+.++...                               ..-.++.+..++.+|...
T Consensus       140 ge~l~~~~~~~~~~~~~~~~~~~~~~ws~~~~~~i~~l~v~~il~~~f~i~~~~~~~~~r~~~~~~r~~k~~l~~~p~~~  219 (348)
T KOG4628|consen  140 GELLSSYAGRTEFECLLIPLGFDTSPWSILAISLISLLTVVAILVTCFFIYRIRRLIRARNRLRRNRLIKRLLKKLPVRT  219 (348)
T ss_pred             HHHHHHhhcccceeeeeccccccCCcchhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhhHHHHHhhCCcEE
Confidence            444433322211100     01111111100                               001122333444444433


Q ss_pred             eeeecccCccccCccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCC-CCCccCcCCCCCCC
Q 041711          142 IAILEEGSGLILGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN-NCPTCRFTLPCTTT  207 (210)
Q Consensus       142 ~~~~~~~~~~~~~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~-~CPlCR~~i~~~~~  207 (210)
                      +.   .+...... .+|+||||+|..|+++++|||+|.||..||++||...+ .||+||++++....
T Consensus       220 f~---~~~~~~~~-~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~~  282 (348)
T KOG4628|consen  220 FT---KGDDEDAT-DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDSG  282 (348)
T ss_pred             ec---cccccCCC-ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCCCC
Confidence            33   32222112 58999999999999999999999999999999999875 59999999966543

>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=1.3e-16  Score=100.40  Aligned_cols=44  Identities=55%  Similarity=1.311  Sum_probs=40.4

Q ss_pred             cccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccC
Q 041711          156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCR  199 (210)
Q Consensus       156 ~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR  199 (210)
                      ++|+||+++|..++.++.++|+|.||..||.+|++.+.+||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence            36999999999889999999999999999999999999999997

...

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

Probab=99.47  E-value=2.7e-14  Score=121.66  Aligned_cols=51  Identities=37%  Similarity=0.901  Sum_probs=47.3

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHh-cCCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLV-TGNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~-~~~~CPlCR~~i~~  204 (210)
                      .+-+|+|||+.|..++..++|||+|.||..|+++|+. .+..||+||.++|.
T Consensus       322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            4578999999999999999999999999999999999 67899999999975

>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=99.41  E-value=2.7e-13  Score=94.46  Aligned_cols=45  Identities=38%  Similarity=0.959  Sum_probs=35.8

Q ss_pred             ccccccccccccCC----------CeeEEeCCCCcccHHhHHHHHhcCCCCCccC
Q 041711          155 QERCVICLEEFSEG----------DEVISLQCSHVHHRHCILKWLVTGNNCPTCR  199 (210)
Q Consensus       155 ~~~C~ICle~~~~~----------~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR  199 (210)
                      ++.|+||++.|...          -.+...+|+|.||..||.+||..+.+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            44699999999421          2344449999999999999999999999998

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=99.40  E-value=2.3e-13  Score=114.40  Aligned_cols=74  Identities=23%  Similarity=0.398  Sum_probs=52.0

Q ss_pred             CCCHHHHhhcccceeeeecccCccccCccccccccccccCCCe----eEEe-CCCCcccHHhHHHHHhcCCCCCccCcCC
Q 041711          128 GVQLEVVRVIETWEIAILEEGSGLILGQERCVICLEEFSEGDE----VISL-QCSHVHHRHCILKWLVTGNNCPTCRFTL  202 (210)
Q Consensus       128 g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~C~ICle~~~~~~~----~~~L-pC~H~Fh~~CI~~Wl~~~~~CPlCR~~i  202 (210)
                      |...+.++.+|..........  ....+.+|+||++.+..++.    ..++ +|+|.||..||.+|+..+.+||+||.++
T Consensus       149 ~~~~~~i~~lp~vl~~~e~~~--~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~  226 (238)
T PHA02929        149 KNYKKFLKTIPSVLSEYEKLY--NRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPF  226 (238)
T ss_pred             chhHHHHHhcchhhhhhhhhh--cCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEe
Confidence            455566666666543211110  11245789999999876431    2344 8999999999999999999999999987


Q ss_pred             C
Q 041711          203 P  203 (210)
Q Consensus       203 ~  203 (210)
                      .
T Consensus       227 ~  227 (238)
T PHA02929        227 I  227 (238)
T ss_pred             e
Confidence            4

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

Probab=99.20  E-value=9e-12  Score=108.93  Aligned_cols=50  Identities=34%  Similarity=0.864  Sum_probs=43.2

Q ss_pred             Ccccccccccc-ccCC---------CeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEE-FSEG---------DEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~-~~~~---------~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      ++..|+||+++ |..+         ..+..|||||.||.+|+..|+.+.++||+||.++-
T Consensus       286 ~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~i  345 (491)
T COG5243         286 SDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVI  345 (491)
T ss_pred             CCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccc
Confidence            56789999999 5443         24678999999999999999999999999999963

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

Probab=99.16  E-value=1.9e-11  Score=103.84  Aligned_cols=49  Identities=31%  Similarity=0.767  Sum_probs=42.6

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      ....|.+||+..++   +..+||||.||+.||..|+..+..||+||..+...
T Consensus       238 a~~kC~LCLe~~~~---pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~ps  286 (293)
T KOG0317|consen  238 ATRKCSLCLENRSN---PSATPCGHIFCWSCILEWCSEKAECPLCREKFQPS  286 (293)
T ss_pred             CCCceEEEecCCCC---CCcCcCcchHHHHHHHHHHccccCCCcccccCCCc
Confidence            34679999999765   55789999999999999999999999999988543

>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=99.15  E-value=3e-11  Score=77.87  Aligned_cols=46  Identities=33%  Similarity=0.794  Sum_probs=38.9

Q ss_pred             ccccccccccccCCCeeEEeCCCCc-ccHHhHHHHHhcCCCCCccCcCCC
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHV-HHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~-Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      +..|.||++....   +..+||+|. ||..|+..|+..+..||+||++|.
T Consensus         2 ~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRD---VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSS---EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCCc---eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            4579999998653   667799999 999999999999999999999874

...

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

Probab=99.13  E-value=3.5e-11  Score=85.33  Aligned_cols=50  Identities=44%  Similarity=0.956  Sum_probs=40.1

Q ss_pred             CccccccccccccC--------CCe-eEEe-CCCCcccHHhHHHHHhc---CCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSE--------GDE-VISL-QCSHVHHRHCILKWLVT---GNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~--------~~~-~~~L-pC~H~Fh~~CI~~Wl~~---~~~CPlCR~~i~  203 (210)
                      +++.|.||...|..        |+. +.++ .|+|.||..||.+|++.   +..||+||++..
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~   82 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWK   82 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeee
Confidence            46789999999972        332 3344 89999999999999986   468999999864

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.11  E-value=5.9e-11  Score=96.38  Aligned_cols=48  Identities=29%  Similarity=0.759  Sum_probs=39.8

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhc----------------CCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT----------------GNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~----------------~~~CPlCR~~i~~  204 (210)
                      +..+|+||++.+.+   +++++|+|.||+.||..|+..                +..||+||..+..
T Consensus        17 ~~~~CpICld~~~d---PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~   80 (193)
T PLN03208         17 GDFDCNICLDQVRD---PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE   80 (193)
T ss_pred             CccCCccCCCcCCC---cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence            55789999998754   567899999999999999852                2479999999854

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

Probab=99.11  E-value=3.9e-11  Score=99.21  Aligned_cols=49  Identities=29%  Similarity=0.749  Sum_probs=41.2

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC---CCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG---NNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~---~~CPlCR~~i~~~  205 (210)
                      ...+|.|||+.-   +.++++.|||.||+.||.+||..+   +.||+||..|..+
T Consensus        46 ~~FdCNICLd~a---kdPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~   97 (230)
T KOG0823|consen   46 GFFDCNICLDLA---KDPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSID   97 (230)
T ss_pred             Cceeeeeecccc---CCCEEeecccceehHHHHHHHhhcCCCeeCCccccccccc
Confidence            567899999983   457778999999999999999874   5799999988544

>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=99.11  E-value=7.8e-11  Score=72.74  Aligned_cols=44  Identities=52%  Similarity=1.121  Sum_probs=36.4

Q ss_pred             ccccccccccCCCeeEEeCCCCcccHHhHHHHHhc-CCCCCccCcCC
Q 041711          157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT-GNNCPTCRFTL  202 (210)
Q Consensus       157 ~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~-~~~CPlCR~~i  202 (210)
                      +|+||++.+  .+.....+|+|.||..|+..|+.. +..||+||..+
T Consensus         1 ~C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEF--REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhh--hCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            499999998  233444479999999999999998 67899999764

>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=99.10  E-value=7e-11  Score=72.26  Aligned_cols=39  Identities=38%  Similarity=0.984  Sum_probs=33.1

Q ss_pred             cccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCcc
Q 041711          158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTC  198 (210)
Q Consensus       158 C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlC  198 (210)
                      |+||++.+.+  .++.++|||.||..|+.+|+..+..||+|
T Consensus         1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC--cCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence            8999999865  44677999999999999999998899998

>PHA02926 zinc finger-like protein; Provisional

Probab=99.05  E-value=1.1e-10  Score=96.21  Aligned_cols=51  Identities=31%  Similarity=0.633  Sum_probs=39.8

Q ss_pred             CccccccccccccCC-----CeeEEe-CCCCcccHHhHHHHHhcC------CCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEG-----DEVISL-QCSHVHHRHCILKWLVTG------NNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~-----~~~~~L-pC~H~Fh~~CI~~Wl~~~------~~CPlCR~~i~~  204 (210)
                      .+.+|+||||..-.+     ....+| +|+|.||..||..|...+      .+||+||..+..
T Consensus       169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~  231 (242)
T PHA02926        169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN  231 (242)
T ss_pred             CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence            457899999987432     224556 999999999999999863      469999998743

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.97  E-value=4.9e-10  Score=70.32  Aligned_cols=44  Identities=32%  Similarity=0.723  Sum_probs=38.3

Q ss_pred             ccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCc
Q 041711          157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRF  200 (210)
Q Consensus       157 ~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~  200 (210)
                      .|.||++.|.......+++|+|.||..|+..+......||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            49999999965566888899999999999999866679999985

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

Probab=98.93  E-value=8.9e-10  Score=68.54  Aligned_cols=38  Identities=37%  Similarity=0.911  Sum_probs=29.9

Q ss_pred             cccccccccCCCeeEEeCCCCcccHHhHHHHHhcC----CCCCcc
Q 041711          158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG----NNCPTC  198 (210)
Q Consensus       158 C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~----~~CPlC  198 (210)
                      |+||++.|.+   ++.|+|||.||..||..|.+..    ..||.|
T Consensus         1 CpiC~~~~~~---Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKD---PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SS---EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCC---ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            8999999975   7789999999999999999874    369988

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

Probab=98.90  E-value=7.4e-10  Score=88.27  Aligned_cols=51  Identities=39%  Similarity=0.772  Sum_probs=42.9

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      +...|+|||+.++... +..++|||+||..||...++....||+||..|..+
T Consensus       130 ~~~~CPiCl~~~sek~-~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k  180 (187)
T KOG0320|consen  130 GTYKCPICLDSVSEKV-PVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHK  180 (187)
T ss_pred             cccCCCceecchhhcc-ccccccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence            4578999999997633 34579999999999999999999999999877543

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

Probab=98.88  E-value=1.4e-09  Score=75.61  Aligned_cols=48  Identities=40%  Similarity=0.838  Sum_probs=37.2

Q ss_pred             ccccccccccc-----------CCCee-EEe-CCCCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          156 ERCVICLEEFS-----------EGDEV-ISL-QCSHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       156 ~~C~ICle~~~-----------~~~~~-~~L-pC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      +.|+||...|-           .+++. ..- .|+|.||..||.+||..+..||++|++..
T Consensus        21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~   81 (88)
T COG5194          21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWV   81 (88)
T ss_pred             chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeE
Confidence            45777766553           34433 333 79999999999999999999999999874

>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=98.86  E-value=1.3e-09  Score=67.06  Aligned_cols=39  Identities=49%  Similarity=1.111  Sum_probs=32.9

Q ss_pred             cccccccccCCCeeEEeCCCCcccHHhHHHHHh--cCCCCCcc
Q 041711          158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLV--TGNNCPTC  198 (210)
Q Consensus       158 C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~--~~~~CPlC  198 (210)
                      |+||++.+..  ....++|+|.||..|+..|+.  ....||+|
T Consensus         1 C~iC~~~~~~--~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFED--PVILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSS--EEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccC--CCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            8999999865  234679999999999999999  34689998

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

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

Probab=98.86  E-value=8.3e-10  Score=103.44  Aligned_cols=49  Identities=41%  Similarity=0.993  Sum_probs=44.0

Q ss_pred             CccccccccccccCCCe--eEEeCCCCcccHHhHHHHHhcCCCCCccCcCC
Q 041711          154 GQERCVICLEEFSEGDE--VISLQCSHVHHRHCILKWLVTGNNCPTCRFTL  202 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~--~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i  202 (210)
                      ....|.||+|++..+..  +..|+|+|.||..|+..|+.+..+||+||..+
T Consensus       290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~  340 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVL  340 (543)
T ss_pred             cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhh
Confidence            46789999999988654  67889999999999999999999999999954

>smart00184 RING Ring finger

Probab=98.84  E-value=2.8e-09  Score=63.43  Aligned_cols=38  Identities=50%  Similarity=1.168  Sum_probs=32.6

Q ss_pred             cccccccccCCCeeEEeCCCCcccHHhHHHHHh-cCCCCCcc
Q 041711          158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLV-TGNNCPTC  198 (210)
Q Consensus       158 C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~-~~~~CPlC  198 (210)
                      |+||++..   .....++|+|.||..|+..|+. .+..||+|
T Consensus         1 C~iC~~~~---~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEEL---KDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCC---CCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            78999883   4577789999999999999998 56689997

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)

>smart00504 Ubox Modified RING finger domain

Probab=98.84  E-value=2.9e-09  Score=71.29  Aligned_cols=45  Identities=27%  Similarity=0.440  Sum_probs=40.2

Q ss_pred             ccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       157 ~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      .|+||++.+.+   ++.++|||+|+..||.+|+..+.+||+|+.++..
T Consensus         3 ~Cpi~~~~~~~---Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~   47 (63)
T smart00504        3 LCPISLEVMKD---PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTH   47 (63)
T ss_pred             CCcCCCCcCCC---CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence            69999999876   5677999999999999999998899999998843

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

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

Probab=98.73  E-value=1.7e-09  Score=74.52  Aligned_cols=50  Identities=46%  Similarity=0.941  Sum_probs=39.2

Q ss_pred             CccccccccccccC--------CCe-eEEe-CCCCcccHHhHHHHHhcC---CCCCccCcCCC
Q 041711          154 GQERCVICLEEFSE--------GDE-VISL-QCSHVHHRHCILKWLVTG---NNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~--------~~~-~~~L-pC~H~Fh~~CI~~Wl~~~---~~CPlCR~~i~  203 (210)
                      ++++|.||.-.|..        |+. +.++ -|.|.||..||.+|+...   ..||+||+...
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            45689999999963        332 3344 799999999999999874   47999999763

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.68  E-value=1.2e-08  Score=91.59  Aligned_cols=48  Identities=31%  Similarity=0.587  Sum_probs=41.6

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      ....|+||++.|..   +++++|+|.||..||..|+.....||+||..+..
T Consensus        25 ~~l~C~IC~d~~~~---PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~   72 (397)
T TIGR00599        25 TSLRCHICKDFFDV---PVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQE   72 (397)
T ss_pred             cccCCCcCchhhhC---ccCCCCCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence            44689999999864   4567999999999999999988899999998754

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

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

Probab=98.61  E-value=3.1e-08  Score=61.83  Aligned_cols=38  Identities=37%  Similarity=0.810  Sum_probs=22.9

Q ss_pred             cccccccccCCC-eeEEeCCCCcccHHhHHHHHhcC----CCCC
Q 041711          158 CVICLEEFSEGD-EVISLQCSHVHHRHCILKWLVTG----NNCP  196 (210)
Q Consensus       158 C~ICle~~~~~~-~~~~LpC~H~Fh~~CI~~Wl~~~----~~CP  196 (210)
                      |+||.+ |...+ .+++|+|||+|+..|+.+++..+    -.||
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 75544 57888999999999999999854    2576

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

Probab=98.60  E-value=2.2e-08  Score=72.94  Aligned_cols=49  Identities=33%  Similarity=0.681  Sum_probs=37.5

Q ss_pred             Ccccccccccccc------------CCCeeEEe--CCCCcccHHhHHHHHhcCCCCCccCcCC
Q 041711          154 GQERCVICLEEFS------------EGDEVISL--QCSHVHHRHCILKWLVTGNNCPTCRFTL  202 (210)
Q Consensus       154 ~~~~C~ICle~~~------------~~~~~~~L--pC~H~Fh~~CI~~Wl~~~~~CPlCR~~i  202 (210)
                      .-+.|+||..-+-            ..++..+.  -|+|.||..||.+||+.+..||+|.++.
T Consensus        45 ~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW  107 (114)
T KOG2930|consen   45 VVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEW  107 (114)
T ss_pred             eechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence            3467999876552            12233333  7999999999999999999999997764

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

Probab=98.56  E-value=2.5e-08  Score=90.32  Aligned_cols=51  Identities=35%  Similarity=0.907  Sum_probs=40.3

Q ss_pred             CccccccccccccC---CCe-----------eEEeCCCCcccHHhHHHHHh-cCCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSE---GDE-----------VISLQCSHVHHRHCILKWLV-TGNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~---~~~-----------~~~LpC~H~Fh~~CI~~Wl~-~~~~CPlCR~~i~~  204 (210)
                      ....|+|||.++.-   +..           -+.+||.|.||..|+.+|+. .+-.||+||.++|.
T Consensus       570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             ccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            45689999999852   111           23349999999999999999 45699999999974

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

Probab=98.53  E-value=8.3e-08  Score=61.63  Aligned_cols=42  Identities=21%  Similarity=0.748  Sum_probs=33.2

Q ss_pred             ccccccccccCCCeeEEeCCC-----CcccHHhHHHHHhcC--CCCCccC
Q 041711          157 RCVICLEEFSEGDEVISLQCS-----HVHHRHCILKWLVTG--NNCPTCR  199 (210)
Q Consensus       157 ~C~ICle~~~~~~~~~~LpC~-----H~Fh~~CI~~Wl~~~--~~CPlCR  199 (210)
                      .|.||++ ...++...+.||.     |.+|..|+.+|+..+  .+||+|+
T Consensus         1 ~CrIC~~-~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHD-EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCC-CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4899999 3344556677885     899999999999765  4899995

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

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

Probab=98.51  E-value=3.5e-08  Score=85.81  Aligned_cols=46  Identities=39%  Similarity=0.722  Sum_probs=41.3

Q ss_pred             cccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       156 ~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      -.|.||.+.|..   ++++||+|.||.-||..+|+.++.||.|+.++.+
T Consensus        24 LRC~IC~eyf~i---p~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~E   69 (442)
T KOG0287|consen   24 LRCGICFEYFNI---PMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTE   69 (442)
T ss_pred             HHHhHHHHHhcC---ceeccccchHHHHHHHHHhccCCCCCceecccch
Confidence            469999999875   5677999999999999999999999999988754

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

Probab=98.50  E-value=5.3e-08  Score=82.14  Aligned_cols=47  Identities=30%  Similarity=0.683  Sum_probs=39.6

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHH-HHhcCC-CCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILK-WLVTGN-NCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~-Wl~~~~-~CPlCR~~i~  203 (210)
                      .+..|+||++....   +..++|||.||+.||.. |-.++. .||+||+.+-
T Consensus       214 ~d~kC~lC~e~~~~---ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~  262 (271)
T COG5574         214 ADYKCFLCLEEPEV---PSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVY  262 (271)
T ss_pred             cccceeeeecccCC---cccccccchhhHHHHHHHHHhhccccCchhhhhcc
Confidence            46789999998654   55789999999999999 887776 4999999773

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

Probab=98.48  E-value=6.5e-08  Score=93.18  Aligned_cols=50  Identities=32%  Similarity=0.830  Sum_probs=39.0

Q ss_pred             CccccccccccccCCC----eeEEeCCCCcccHHhHHHHHhc--CCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGD----EVISLQCSHVHHRHCILKWLVT--GNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~----~~~~LpC~H~Fh~~CI~~Wl~~--~~~CPlCR~~i~  203 (210)
                      +-++|+||+..+..-+    .-+.-.|+|.||..|+.+|+..  +.+||+||..++
T Consensus      1468 G~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1468 GHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             CcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            5678999999886212    1123369999999999999986  468999998875

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

Probab=98.46  E-value=7.6e-08  Score=87.68  Aligned_cols=47  Identities=34%  Similarity=0.729  Sum_probs=38.3

Q ss_pred             ccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC-----CCCCccCcCCCC
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG-----NNCPTCRFTLPC  204 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~-----~~CPlCR~~i~~  204 (210)
                      +..|+|||+....   +..+.|||+||..||..++...     ..||+||..|-.
T Consensus       186 ~~~CPICL~~~~~---p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~  237 (513)
T KOG2164|consen  186 DMQCPICLEPPSV---PVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL  237 (513)
T ss_pred             CCcCCcccCCCCc---ccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence            5689999998654   3455799999999999988764     479999998844

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

Probab=98.39  E-value=8.2e-08  Score=81.20  Aligned_cols=50  Identities=26%  Similarity=0.741  Sum_probs=41.8

Q ss_pred             CccccccccccccCCC-------eeEEeCCCCcccHHhHHHHHh--cCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGD-------EVISLQCSHVHHRHCILKWLV--TGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~-------~~~~LpC~H~Fh~~CI~~Wl~--~~~~CPlCR~~i~  203 (210)
                      ++..|+||-..+....       ....|.|+|+||..||.-|..  ++++||-|+..+.
T Consensus       223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd  281 (328)
T KOG1734|consen  223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD  281 (328)
T ss_pred             CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence            6778999998886543       567889999999999999975  4679999988763

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

Probab=98.36  E-value=2.1e-07  Score=79.61  Aligned_cols=46  Identities=33%  Similarity=0.505  Sum_probs=40.1

Q ss_pred             ccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      ...|-||-+.|..   +..++|||.||.-||...|..++.||+||.+..
T Consensus        25 ~lrC~IC~~~i~i---p~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~   70 (391)
T COG5432          25 MLRCRICDCRISI---PCETTCGHTFCSLCIRRHLGTQPFCPVCREDPC   70 (391)
T ss_pred             HHHhhhhhheeec---ceecccccchhHHHHHHHhcCCCCCccccccHH
Confidence            3579999998865   456699999999999999999999999998763

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

Probab=98.33  E-value=4.2e-07  Score=63.06  Aligned_cols=48  Identities=27%  Similarity=0.386  Sum_probs=37.7

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhc-CCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT-GNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~-~~~CPlCR~~i~~  204 (210)
                      +...|+|+.+-|.+   ++++++||+|...||..|+.. +.+||+|+.++..
T Consensus         3 ~~f~CpIt~~lM~d---PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~   51 (73)
T PF04564_consen    3 DEFLCPITGELMRD---PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE   51 (73)
T ss_dssp             GGGB-TTTSSB-SS---EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred             cccCCcCcCcHhhC---ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence            34579999999875   778899999999999999999 7899999998854

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 ....

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

Probab=98.28  E-value=1.3e-07  Score=65.16  Aligned_cols=49  Identities=22%  Similarity=0.645  Sum_probs=23.6

Q ss_pred             cccccccccccc-CCCeeEEe----CCCCcccHHhHHHHHhc----C-------CCCCccCcCCC
Q 041711          155 QERCVICLEEFS-EGDEVISL----QCSHVHHRHCILKWLVT----G-------NNCPTCRFTLP  203 (210)
Q Consensus       155 ~~~C~ICle~~~-~~~~~~~L----pC~H~Fh~~CI~~Wl~~----~-------~~CPlCR~~i~  203 (210)
                      +.+|.||++.+. .++.+...    .|+..||..|+.+||..    +       ..||.|+.+|.
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            357999999876 44433333    59999999999999975    1       13999999874

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

Probab=98.16  E-value=7.3e-07  Score=75.00  Aligned_cols=44  Identities=36%  Similarity=0.729  Sum_probs=38.2

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCc
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRF  200 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~  200 (210)
                      +...|+||++.|...   .+++|+|.||..|+..+....-.||.||.
T Consensus        12 ~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   12 EELTCPICLEYFREP---VLLPCGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             ccccChhhHHHhhcC---ccccccchHhHHHHHHhcCCCcCCcccCC
Confidence            456899999999875   67899999999999999985568999993

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

Probab=98.11  E-value=2e-06  Score=75.51  Aligned_cols=47  Identities=34%  Similarity=0.743  Sum_probs=39.6

Q ss_pred             CccccccccccccCCCeeEEeCCCCc-ccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHV-HHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~-Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      ...+|.|||.+-.   ...+|||.|. -|..|.+...-+.+.||+||+++.
T Consensus       289 ~gkeCVIClse~r---dt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~  336 (349)
T KOG4265|consen  289 SGKECVICLSESR---DTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIE  336 (349)
T ss_pred             CCCeeEEEecCCc---ceEEecchhhehhHhHHHHHHHhhcCCCccccchH
Confidence            4678999999854   3778999996 688899888777899999999984

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

Probab=98.10  E-value=9.2e-07  Score=75.94  Aligned_cols=53  Identities=28%  Similarity=0.666  Sum_probs=43.7

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhc-----------------------CCCCCccCcCCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT-----------------------GNNCPTCRFTLPCTT  206 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~-----------------------~~~CPlCR~~i~~~~  206 (210)
                      ....|+|||--|..++...+++|.|+||..|+.++|+.                       +..||+||..|-.+.
T Consensus       114 p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~  189 (368)
T KOG4445|consen  114 PNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEE  189 (368)
T ss_pred             CCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccc
Confidence            44679999999999998889999999999999887653                       124999999985543

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

Probab=98.09  E-value=1.2e-06  Score=78.70  Aligned_cols=48  Identities=29%  Similarity=0.937  Sum_probs=37.8

Q ss_pred             CccccccccccccCCC-eeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGD-EVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~-~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      +-.+|++|||.+...- .++.+.|.|.||..|+..|-  ..+||+||.-..
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            4568999999997643 23445899999999999994  468999997553

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

Probab=98.03  E-value=2.6e-06  Score=75.43  Aligned_cols=50  Identities=32%  Similarity=0.749  Sum_probs=39.0

Q ss_pred             CccccccccccccCCC----eeEEe-CCCCcccHHhHHHHHh--c-----CCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGD----EVISL-QCSHVHHRHCILKWLV--T-----GNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~----~~~~L-pC~H~Fh~~CI~~Wl~--~-----~~~CPlCR~~i~  203 (210)
                      .+..|.||++.+...-    ...+| +|.|.||..||..|..  +     .+.||.||....
T Consensus       160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~  221 (344)
T KOG1039|consen  160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS  221 (344)
T ss_pred             ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence            4678999999986533    13445 6999999999999984  3     367999998763

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

Probab=97.92  E-value=2e-06  Score=57.74  Aligned_cols=45  Identities=29%  Similarity=0.703  Sum_probs=22.9

Q ss_pred             cccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          156 ERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       156 ~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      -.|++|.+.+..   ++.| .|.|.||..||..-+.  ..||+|+.+...+
T Consensus         8 LrCs~C~~~l~~---pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~q   53 (65)
T PF14835_consen    8 LRCSICFDILKE---PVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQ   53 (65)
T ss_dssp             TS-SSS-S--SS----B---SSS--B-TTTGGGGTT--TB-SSS--B-S-S
T ss_pred             cCCcHHHHHhcC---CceeccCccHHHHHHhHHhcC--CCCCCcCChHHHH
Confidence            469999998754   4444 9999999999988544  3599999876444

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

Probab=97.68  E-value=7.8e-06  Score=77.89  Aligned_cols=49  Identities=20%  Similarity=0.446  Sum_probs=42.4

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTL  202 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i  202 (210)
                      ....|++|+..+.++......+|+|.||..||..|-....+||+||..+
T Consensus       122 ~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF  170 (1134)
T KOG0825|consen  122 VENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEF  170 (1134)
T ss_pred             hhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhh
Confidence            4567999999988766555668999999999999999999999999876

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

Probab=97.68  E-value=5.8e-06  Score=72.50  Aligned_cols=50  Identities=36%  Similarity=0.634  Sum_probs=39.2

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhc-CCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT-GNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~-~~~CPlCR~~i~~~  205 (210)
                      .+-.|+|||+.+..  .....-|.|.||..||..-|.. +++||.||..+-.+
T Consensus        42 ~~v~c~icl~llk~--tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Sk   92 (381)
T KOG0311|consen   42 IQVICPICLSLLKK--TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSK   92 (381)
T ss_pred             hhhccHHHHHHHHh--hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcccc
Confidence            34679999999864  1222379999999999999976 57999999987443

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

Probab=97.55  E-value=4e-05  Score=69.21  Aligned_cols=48  Identities=23%  Similarity=0.522  Sum_probs=41.9

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      .+..|.||+..+..   ++.+||||.||..||.+-+..+..||.||..+..
T Consensus        83 sef~c~vc~~~l~~---pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   83 SEFECCVCSRALYP---PVVTPCGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             chhhhhhhHhhcCC---CccccccccccHHHHHHHhccCCCCccccccccc
Confidence            56789999888765   6677999999999999999988999999998864

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

Probab=97.48  E-value=2.6e-05  Score=50.64  Aligned_cols=45  Identities=29%  Similarity=0.654  Sum_probs=32.2

Q ss_pred             ccccccccccccCCCeeEEe-CCCCc-ccHHhHHHHHh-cCCCCCccCcCCC
Q 041711          155 QERCVICLEEFSEGDEVISL-QCSHV-HHRHCILKWLV-TGNNCPTCRFTLP  203 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~L-pC~H~-Fh~~CI~~Wl~-~~~~CPlCR~~i~  203 (210)
                      .++|.||+|.-.+   . +| .|||. .|..|-.+-++ .+..||+||.+|.
T Consensus         7 ~dECTICye~pvd---s-VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    7 SDECTICYEHPVD---S-VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             ccceeeeccCcch---H-HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            3689999987432   1 44 89997 46667555444 6789999999873

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

Probab=97.35  E-value=5.5e-05  Score=72.17  Aligned_cols=48  Identities=21%  Similarity=0.641  Sum_probs=38.2

Q ss_pred             ccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC-CCCCccCcCCCCC
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG-NNCPTCRFTLPCT  205 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~-~~CPlCR~~i~~~  205 (210)
                      --.|+.|-..+.+   .++..|+|.||..||.+-+..+ +.||.|-..+...
T Consensus       643 ~LkCs~Cn~R~Kd---~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan  691 (698)
T KOG0978|consen  643 LLKCSVCNTRWKD---AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAN  691 (698)
T ss_pred             ceeCCCccCchhh---HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence            4579999866543   4456999999999999998764 7999999888543

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

Probab=97.23  E-value=0.00011  Score=65.48  Aligned_cols=46  Identities=30%  Similarity=0.723  Sum_probs=38.3

Q ss_pred             ccccccccccccCCC-eeEEeCCCCcccHHhHHHHHhcC--CCCCccCc
Q 041711          155 QERCVICLEEFSEGD-EVISLQCSHVHHRHCILKWLVTG--NNCPTCRF  200 (210)
Q Consensus       155 ~~~C~ICle~~~~~~-~~~~LpC~H~Fh~~CI~~Wl~~~--~~CPlCR~  200 (210)
                      +--|..|-+.+..+. ....|||.|+||..|....|.++  ++||-||.
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            456999999986543 56778999999999999999775  58999983

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

Probab=97.18  E-value=0.00018  Score=65.08  Aligned_cols=49  Identities=27%  Similarity=0.586  Sum_probs=40.9

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      ....|+||...+.+.-  ....|+|.||..|+..|+..+..||.|++.+..
T Consensus        20 ~~l~C~~C~~vl~~p~--~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~   68 (391)
T KOG0297|consen   20 ENLLCPICMSVLRDPV--QTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQ   68 (391)
T ss_pred             ccccCccccccccCCC--CCCCCCCcccccccchhhccCcCCcccccccch
Confidence            5578999999987532  125899999999999999999999999887743

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

Probab=97.14  E-value=0.00019  Score=55.28  Aligned_cols=36  Identities=19%  Similarity=0.541  Sum_probs=30.4

Q ss_pred             ccccccccccccCCCeeEEeCCC------CcccHHhHHHHHh
Q 041711          155 QERCVICLEEFSEGDEVISLQCS------HVHHRHCILKWLV  190 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~------H~Fh~~CI~~Wl~  190 (210)
                      ..+|+||++.+..++.++.++|+      |.||..|+.+|-.
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence            45899999999985667777886      9999999999943

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.

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=97.07  E-value=0.00035  Score=60.98  Aligned_cols=36  Identities=22%  Similarity=0.501  Sum_probs=28.1

Q ss_pred             CeeEEeCCCCcccHHhHHHHHhc-CCCCCccCcCCCC
Q 041711          169 DEVISLQCSHVHHRHCILKWLVT-GNNCPTCRFTLPC  204 (210)
Q Consensus       169 ~~~~~LpC~H~Fh~~CI~~Wl~~-~~~CPlCR~~i~~  204 (210)
                      -...+-+|||.||..||+..+.. ...||.|+.++..
T Consensus        19 ~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk   55 (309)
T TIGR00570        19 LKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRK   55 (309)
T ss_pred             cccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccch
Confidence            33445589999999999997655 4589999988754

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).

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

Probab=97.05  E-value=0.00039  Score=45.92  Aligned_cols=41  Identities=29%  Similarity=0.715  Sum_probs=28.3

Q ss_pred             ccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC--CCCCc
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG--NNCPT  197 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~--~~CPl  197 (210)
                      ...|+|.+..|.+  .++...|+|+|-...|..|++.+  ..||+
T Consensus        11 ~~~CPiT~~~~~~--PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   11 SLKCPITLQPFED--PVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             -SB-TTTSSB-SS--EEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             ccCCCCcCChhhC--CcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            4679999999864  45556999999999999999543  47998

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

Probab=96.96  E-value=0.00033  Score=62.33  Aligned_cols=31  Identities=29%  Similarity=0.914  Sum_probs=25.6

Q ss_pred             EeCCCCcccHHhHHHHHhcC---CCCCccCcCCC
Q 041711          173 SLQCSHVHHRHCILKWLVTG---NNCPTCRFTLP  203 (210)
Q Consensus       173 ~LpC~H~Fh~~CI~~Wl~~~---~~CPlCR~~i~  203 (210)
                      +-.|||+||..|+.+|+..-   +.||+||-.++
T Consensus        23 i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~   56 (465)
T KOG0827|consen   23 IGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQ   56 (465)
T ss_pred             ccchhhHHHHHHHHHHHccCCccCCCCceeeccc
Confidence            45699999999999999873   57999994443

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

Probab=96.91  E-value=0.0003  Score=62.87  Aligned_cols=47  Identities=32%  Similarity=0.762  Sum_probs=37.9

Q ss_pred             ccccccccccccCCCeeEEeCCCCcccHHhHHHHHhc--CCCCCccCcCCCC
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT--GNNCPTCRFTLPC  204 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~--~~~CPlCR~~i~~  204 (210)
                      -+.|-||-|.   +..+.+-||||..|..|+..|-..  ..+||.||..|-.
T Consensus       369 FeLCKICaen---dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKG  417 (563)
T KOG1785|consen  369 FELCKICAEN---DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKG  417 (563)
T ss_pred             HHHHHHhhcc---CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEecc
Confidence            3569999876   444666699999999999999844  5799999998843

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

Probab=96.86  E-value=0.0009  Score=55.69  Aligned_cols=46  Identities=26%  Similarity=0.668  Sum_probs=38.6

Q ss_pred             cccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC--------CCCCccCcCC
Q 041711          156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG--------NNCPTCRFTL  202 (210)
Q Consensus       156 ~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~--------~~CPlCR~~i  202 (210)
                      ..|..|-..+..|+.++ |.|-|.||+.|+..|-..-        -.||.|-++|
T Consensus        51 pNC~LC~t~La~gdt~R-LvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~ei  104 (299)
T KOG3970|consen   51 PNCRLCNTPLASGDTTR-LVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEI  104 (299)
T ss_pred             CCCceeCCccccCccee-ehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCcc
Confidence            46999999998888554 7799999999999997651        2599999988

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

Probab=96.84  E-value=0.00038  Score=56.84  Aligned_cols=43  Identities=21%  Similarity=0.603  Sum_probs=37.7

Q ss_pred             cccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcC
Q 041711          156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFT  201 (210)
Q Consensus       156 ~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~  201 (210)
                      ..|.||-++|..   +++..|||.||..|...-++....|-+|-..
T Consensus       197 F~C~iCKkdy~s---pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~  239 (259)
T COG5152         197 FLCGICKKDYES---PVVTECGHSFCSLCAIRKYQKGDECGVCGKA  239 (259)
T ss_pred             eeehhchhhccc---hhhhhcchhHHHHHHHHHhccCCcceecchh
Confidence            479999999965   6678999999999999988889999999654

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

Probab=96.80  E-value=0.00084  Score=68.10  Aligned_cols=52  Identities=29%  Similarity=0.662  Sum_probs=41.4

Q ss_pred             cCccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC----------CCCCccCcCCCC
Q 041711          153 LGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG----------NNCPTCRFTLPC  204 (210)
Q Consensus       153 ~~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~----------~~CPlCR~~i~~  204 (210)
                      +.++.|.||+.+--.......|.|+|.||..|...-|.++          -+||+|+.+|..
T Consensus      3484 D~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred             ccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence            3567899999886655667889999999999998766553          259999998853

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

Probab=96.69  E-value=0.0016  Score=55.60  Aligned_cols=48  Identities=21%  Similarity=0.432  Sum_probs=37.9

Q ss_pred             cCccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcC--CCCCccCcCCC
Q 041711          153 LGQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTG--NNCPTCRFTLP  203 (210)
Q Consensus       153 ~~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~--~~CPlCR~~i~  203 (210)
                      ..+.+|++|-+.-.   .+.+. +|+|.||..||..-+...  .+||.|-.+.+
T Consensus       237 t~~~~C~~Cg~~Pt---iP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  237 TSDTECPVCGEPPT---IPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cCCceeeccCCCCC---CCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            36788999987733   34455 899999999999877643  68999988875

>PHA03096 p28-like protein; Provisional

Probab=96.67  E-value=0.00085  Score=58.21  Aligned_cols=45  Identities=27%  Similarity=0.443  Sum_probs=33.7

Q ss_pred             cccccccccccCCC----eeEEe-CCCCcccHHhHHHHHhcC---CCCCccCc
Q 041711          156 ERCVICLEEFSEGD----EVISL-QCSHVHHRHCILKWLVTG---NNCPTCRF  200 (210)
Q Consensus       156 ~~C~ICle~~~~~~----~~~~L-pC~H~Fh~~CI~~Wl~~~---~~CPlCR~  200 (210)
                      ..|.||++......    .-..| .|.|.||..||..|...+   .+||.||.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            57999999886532    34566 799999999999999863   34555543

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.57  E-value=0.0024  Score=53.83  Aligned_cols=52  Identities=15%  Similarity=0.225  Sum_probs=46.1

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      ....|+||.+.+.+.-...+| ||||+|+.+|+.+.+..-..||+|-.++.+.
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdr  272 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDR  272 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCccc
Confidence            456899999999998888888 9999999999999999889999998877543

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

Probab=96.56  E-value=0.00068  Score=58.42  Aligned_cols=47  Identities=26%  Similarity=0.528  Sum_probs=40.2

Q ss_pred             ccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      ...|-||...|..   +++..|+|.||..|-..-++....|++|-+.+..
T Consensus       241 Pf~c~icr~~f~~---pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g  287 (313)
T KOG1813|consen  241 PFKCFICRKYFYR---PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG  287 (313)
T ss_pred             Ccccccccccccc---chhhcCCceeehhhhccccccCCcceeccccccc
Confidence            3459999999875   6678999999999999988888999999887643

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=96.52  E-value=0.0025  Score=50.35  Aligned_cols=46  Identities=24%  Similarity=0.680  Sum_probs=34.0

Q ss_pred             CccccccccccccCCCeeEEeCC--CC---cccHHhHHHHHhcC--CCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQC--SH---VHHRHCILKWLVTG--NNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC--~H---~Fh~~CI~~Wl~~~--~~CPlCR~~i~  203 (210)
                      .+..|-||.++-.  ..  .-||  +.   .-|..|+.+|+..+  .+|++|+++..
T Consensus         7 ~~~~CRIC~~~~~--~~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~   59 (162)
T PHA02825          7 MDKCCWICKDEYD--VV--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYN   59 (162)
T ss_pred             CCCeeEecCCCCC--Cc--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEE
Confidence            5568999998843  22  2355  44   55999999999875  58999998763

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

Probab=96.45  E-value=0.0016  Score=57.50  Aligned_cols=44  Identities=32%  Similarity=0.704  Sum_probs=32.9

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      ....|.||+++..+   ...+||||+=|  |...- +..++||+||+.|.
T Consensus       304 ~p~lcVVcl~e~~~---~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI~  347 (355)
T KOG1571|consen  304 QPDLCVVCLDEPKS---AVFVPCGHVCC--CTLCS-KHLPQCPVCRQRIR  347 (355)
T ss_pred             CCCceEEecCCccc---eeeecCCcEEE--chHHH-hhCCCCchhHHHHH
Confidence            45789999999654   66779999955  66553 33456999999873

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

Probab=96.45  E-value=0.00076  Score=58.91  Aligned_cols=48  Identities=25%  Similarity=0.642  Sum_probs=39.4

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      ...+|.+|-..|-+..  .+.-|-|.||..||...|.....||+|...|-
T Consensus        14 ~~itC~LC~GYliDAT--TI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih   61 (331)
T KOG2660|consen   14 PHITCRLCGGYLIDAT--TITECLHTFCKSCIVKYLEESKYCPTCDIVIH   61 (331)
T ss_pred             cceehhhccceeecch--hHHHHHHHHHHHHHHHHHHHhccCCccceecc
Confidence            4568999998886532  23369999999999999999999999987763

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

Probab=96.32  E-value=0.0018  Score=59.91  Aligned_cols=48  Identities=27%  Similarity=0.723  Sum_probs=37.8

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhc-----CCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT-----GNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~-----~~~CPlCR~~i~~  204 (210)
                      +..+|.+|-+.-   +......|.|.||..||..+...     +-+||+|.-.+.-
T Consensus       535 ~~~~C~lc~d~a---ed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Lsi  587 (791)
T KOG1002|consen  535 GEVECGLCHDPA---EDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSI  587 (791)
T ss_pred             CceeecccCChh---hhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccc
Confidence            567899998873   44566799999999999888754     3589999776643

>PHA02862 5L protein; Provisional

Probab=96.30  E-value=0.0032  Score=49.01  Aligned_cols=44  Identities=25%  Similarity=0.636  Sum_probs=33.4

Q ss_pred             cccccccccccCCCeeEEeCCC-----CcccHHhHHHHHhc--CCCCCccCcCCC
Q 041711          156 ERCVICLEEFSEGDEVISLQCS-----HVHHRHCILKWLVT--GNNCPTCRFTLP  203 (210)
Q Consensus       156 ~~C~ICle~~~~~~~~~~LpC~-----H~Fh~~CI~~Wl~~--~~~CPlCR~~i~  203 (210)
                      +.|-||+++-.+  .  .-||.     ..-|..|+.+|++.  +..||+|+.+..
T Consensus         3 diCWIC~~~~~e--~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~   53 (156)
T PHA02862          3 DICWICNDVCDE--R--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN   53 (156)
T ss_pred             CEEEEecCcCCC--C--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence            579999998432  2  24653     57899999999986  358999998763

>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=96.29  E-value=0.0017  Score=47.38  Aligned_cols=32  Identities=25%  Similarity=0.688  Sum_probs=26.4

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHH
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCIL  186 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~  186 (210)
                      +...|++|-..+.. ....+.||+|.||..|+.
T Consensus        77 ~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   77 ESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence            56789999999976 445566999999999975

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 [].

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

Probab=96.28  E-value=0.0033  Score=39.83  Aligned_cols=40  Identities=33%  Similarity=0.860  Sum_probs=27.4

Q ss_pred             cccccccccCCCeeEEeCCC-----CcccHHhHHHHHhc--CCCCCcc
Q 041711          158 CVICLEEFSEGDEVISLQCS-----HVHHRHCILKWLVT--GNNCPTC  198 (210)
Q Consensus       158 C~ICle~~~~~~~~~~LpC~-----H~Fh~~CI~~Wl~~--~~~CPlC  198 (210)
                      |-||++.-...+ ..+.||+     -.-|..|+.+|+..  +.+|++|
T Consensus         1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            779999877655 3445764     37799999999985  4579988

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

Probab=96.09  E-value=0.0031  Score=61.11  Aligned_cols=47  Identities=36%  Similarity=0.822  Sum_probs=36.5

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcC-C------CCCccCc
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTG-N------NCPTCRF  200 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~-~------~CPlCR~  200 (210)
                      +..+|.||++.+.....+=.- .|-|+||..||..|-... .      .||-|+.
T Consensus       190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs  244 (950)
T KOG1952|consen  190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS  244 (950)
T ss_pred             CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence            567899999999765543333 688999999999998752 1      4999983

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

Probab=96.07  E-value=0.0043  Score=39.48  Aligned_cols=45  Identities=33%  Similarity=0.728  Sum_probs=21.7

Q ss_pred             cccccccccCCC-eeEEeCCCCcccHHhHHHHHh-cCCCCCccCcCC
Q 041711          158 CVICLEEFSEGD-EVISLQCSHVHHRHCILKWLV-TGNNCPTCRFTL  202 (210)
Q Consensus       158 C~ICle~~~~~~-~~~~LpC~H~Fh~~CI~~Wl~-~~~~CPlCR~~i  202 (210)
                      |++|.+++...+ ...--+|++..|..|-..-+. ....||-||.+.
T Consensus         1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            789999994433 333336789999999777775 367899999863

>PF04641 Rtf2: Rtf2 RING-finger

Probab=95.86  E-value=0.011  Score=50.71  Aligned_cols=49  Identities=20%  Similarity=0.491  Sum_probs=40.7

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      ....|+|...+|......+.| ||||+|...++..-- ....||+|-.++.
T Consensus       112 ~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~  161 (260)
T PF04641_consen  112 GRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFT  161 (260)
T ss_pred             ceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccc
Confidence            567899999999766667777 999999999999973 3568999988875

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

Probab=95.84  E-value=0.005  Score=55.38  Aligned_cols=38  Identities=29%  Similarity=0.560  Sum_probs=31.3

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhc
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT  191 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~  191 (210)
                      .-..|.||+++.........+||+|+||..|...++..
T Consensus       183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~  220 (445)
T KOG1814|consen  183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTI  220 (445)
T ss_pred             hcccceeeehhhcCcceeeecccchHHHHHHHHHHHHH
Confidence            34679999999764456667799999999999999875

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

Probab=95.70  E-value=0.0033  Score=49.84  Aligned_cols=29  Identities=38%  Similarity=0.906  Sum_probs=26.6

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccH
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHR  182 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~  182 (210)
                      ...+|.||||+++.|+.+..|||-.+||+
T Consensus       176 dkGECvICLEdL~~GdtIARLPCLCIYHK  204 (205)
T KOG0801|consen  176 DKGECVICLEDLEAGDTIARLPCLCIYHK  204 (205)
T ss_pred             cCCcEEEEhhhccCCCceeccceEEEeec
Confidence            55689999999999999999999999996

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

Probab=95.69  E-value=0.002  Score=55.49  Aligned_cols=41  Identities=29%  Similarity=0.775  Sum_probs=30.1

Q ss_pred             ccccccccccccCCCeeEEeCCCCcc-cHHhHHHHHhcCCCCCccCcCC
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVH-HRHCILKWLVTGNNCPTCRFTL  202 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~F-h~~CI~~Wl~~~~~CPlCR~~i  202 (210)
                      ...|+||++.-   .....|+|||.- |..|-..    -..||+||+-|
T Consensus       300 ~~LC~ICmDaP---~DCvfLeCGHmVtCt~CGkr----m~eCPICRqyi  341 (350)
T KOG4275|consen  300 RRLCAICMDAP---RDCVFLECGHMVTCTKCGKR----MNECPICRQYI  341 (350)
T ss_pred             HHHHHHHhcCC---cceEEeecCcEEeehhhccc----cccCchHHHHH
Confidence            67899999874   347788999963 5556433    23899999865

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

Probab=95.48  E-value=0.042  Score=49.18  Aligned_cols=28  Identities=32%  Similarity=0.825  Sum_probs=23.2

Q ss_pred             CCCcccHHhHHHHHhcC-------------CCCCccCcCCC
Q 041711          176 CSHVHHRHCILKWLVTG-------------NNCPTCRFTLP  203 (210)
Q Consensus       176 C~H~Fh~~CI~~Wl~~~-------------~~CPlCR~~i~  203 (210)
                      |.-.+|.+|+.+|+..+             -.||+||..+.
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC  351 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC  351 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence            78889999999998653             24999999874

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

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

Probab=95.44  E-value=0.0081  Score=53.19  Aligned_cols=47  Identities=26%  Similarity=0.496  Sum_probs=39.0

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      ++..|+||+..--   ..+..||+|.-|..||.+.|.+.+.|=.|+..+.
T Consensus       421 Ed~lCpICyA~pi---~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~  467 (489)
T KOG4692|consen  421 EDNLCPICYAGPI---NAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVI  467 (489)
T ss_pred             ccccCcceecccc---hhhccCCCCchHHHHHHHHHhcCCeeeEecceee
Confidence            6778999986522   2344599999999999999999999999998775

>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=95.36  E-value=0.0074  Score=37.49  Aligned_cols=41  Identities=27%  Similarity=0.731  Sum_probs=23.5

Q ss_pred             cccccccccCCCeeEEeCCCCcccHHhHHHHHhcCC--CCCcc
Q 041711          158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN--NCPTC  198 (210)
Q Consensus       158 C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~--~CPlC  198 (210)
                      |.+|-+....|..-..-.|+=.+|..|+..+++.+.  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            677877776655332234888999999999998865  79987

; PDB: 3NW0_A 2CT0_A.

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

Probab=95.19  E-value=0.013  Score=47.18  Aligned_cols=52  Identities=25%  Similarity=0.613  Sum_probs=36.8

Q ss_pred             cccccccccccCCCe----eEEeCCCCcccHHhHHHHHhc----C-------CCCCccCcCCCCCCC
Q 041711          156 ERCVICLEEFSEGDE----VISLQCSHVHHRHCILKWLVT----G-------NNCPTCRFTLPCTTT  207 (210)
Q Consensus       156 ~~C~ICle~~~~~~~----~~~LpC~H~Fh~~CI~~Wl~~----~-------~~CPlCR~~i~~~~~  207 (210)
                      ..|.||+..--.|..    .-...|+.-||.-|+..||+.    +       ..||.|-.++.-+.+
T Consensus       166 ~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKmS  232 (234)
T KOG3268|consen  166 GACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKMS  232 (234)
T ss_pred             hcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeecc
Confidence            458888765444432    223479999999999999975    1       249999998865544

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

Probab=95.06  E-value=0.02  Score=50.26  Aligned_cols=44  Identities=25%  Similarity=0.582  Sum_probs=35.8

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCCCCCccCc
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTCRF  200 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~~CPlCR~  200 (210)
                      ....|++|+....+..   ++ .=|-+||..||-.++...+.||+=-.
T Consensus       299 ~~~~CpvClk~r~Npt---vl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~  343 (357)
T KOG0826|consen  299 DREVCPVCLKKRQNPT---VLEVSGYVFCYPCIFSYVVNYGHCPVTGY  343 (357)
T ss_pred             ccccChhHHhccCCCc---eEEecceEEeHHHHHHHHHhcCCCCccCC
Confidence            5678999999876532   44 45999999999999999999998543

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

Probab=95.05  E-value=0.023  Score=50.33  Aligned_cols=47  Identities=23%  Similarity=0.502  Sum_probs=36.9

Q ss_pred             cCccccccccccccCCCeeEEeCCCCcccHHhHHH--HHhcCCCCCccCcCC
Q 041711          153 LGQERCVICLEEFSEGDEVISLQCSHVHHRHCILK--WLVTGNNCPTCRFTL  202 (210)
Q Consensus       153 ~~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~--Wl~~~~~CPlCR~~i  202 (210)
                      ++...|.||-+.+.   ...++||+|.-|-.|..+  .|..++.||+||...
T Consensus        59 Een~~C~ICA~~~T---Ys~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~  107 (493)
T COG5236          59 EENMNCQICAGSTT---YSARYPCGHQICHACAVRLRALYMQKGCPLCRTET  107 (493)
T ss_pred             cccceeEEecCCce---EEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence            35678999988753   355779999999999854  455688999999864

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

Probab=94.96  E-value=0.0013  Score=58.69  Aligned_cols=50  Identities=32%  Similarity=0.702  Sum_probs=43.0

Q ss_pred             ccccccccccccCC-CeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          155 QERCVICLEEFSEG-DEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       155 ~~~C~ICle~~~~~-~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      ...|+||.+.+... +.+..+-|+|.+|..|+.+||..+..||.||+.++.
T Consensus       196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~  246 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPK  246 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhh
Confidence            35799999998765 456667899999999999999999999999998864

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

Probab=94.55  E-value=0.015  Score=36.70  Aligned_cols=33  Identities=30%  Similarity=0.699  Sum_probs=23.7

Q ss_pred             EeCCC-CcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          173 SLQCS-HVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       173 ~LpC~-H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      .+.|+ |+.|..|+...|.....||+|..++|..
T Consensus        15 Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen   15 LIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK   48 (50)
T ss_dssp             EEE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred             eeeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence            44785 9999999999999999999999999875

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.

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

Probab=94.25  E-value=0.037  Score=49.89  Aligned_cols=32  Identities=41%  Similarity=0.906  Sum_probs=26.1

Q ss_pred             eeEEeCCCCcccHHhHHHHHhcC--CCCCccCcC
Q 041711          170 EVISLQCSHVHHRHCILKWLVTG--NNCPTCRFT  201 (210)
Q Consensus       170 ~~~~LpC~H~Fh~~CI~~Wl~~~--~~CPlCR~~  201 (210)
                      .+..+.|+|.|-..||.+||-++  ..||.|...
T Consensus        21 r~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~k   54 (463)
T KOG1645|consen   21 RIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGK   54 (463)
T ss_pred             EEeeecccccccHHHHHHHHhhhhhhhCcccCCh
Confidence            45667999999999999999642  479999753

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

Probab=93.80  E-value=0.038  Score=53.91  Aligned_cols=44  Identities=25%  Similarity=0.668  Sum_probs=33.0

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTL  202 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i  202 (210)
                      +...|..|--.+.-  ..+...|+|.||.+|..   .....||-|+...
T Consensus       839 q~skCs~C~~~Ldl--P~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  839 QVSKCSACEGTLDL--PFVHFLCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeeeecccCCcccc--ceeeeecccHHHHHhhc---cCcccCCccchhh
Confidence            44689999887654  23334899999999998   4456899998743

>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=93.68  E-value=0.072  Score=42.19  Aligned_cols=33  Identities=24%  Similarity=0.618  Sum_probs=21.8

Q ss_pred             ccccccccccccCCCeeEEeCC------------C-CcccHHhHHHHHh
Q 041711          155 QERCVICLEEFSEGDEVISLQC------------S-HVHHRHCILKWLV  190 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC------------~-H~Fh~~CI~~Wl~  190 (210)
                      +..|+||||---+   .+.|-|            + -.-|..|+++.-+
T Consensus         2 d~~CpICme~PHN---AVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    2 DVTCPICMEHPHN---AVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CccCceeccCCCc---eEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence            4579999987433   334444            2 3458899999854

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

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

Probab=93.48  E-value=0.03  Score=54.17  Aligned_cols=44  Identities=30%  Similarity=0.636  Sum_probs=35.9

Q ss_pred             cccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC--CCCCccCcCCC
Q 041711          156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG--NNCPTCRFTLP  203 (210)
Q Consensus       156 ~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~--~~CPlCR~~i~  203 (210)
                      ..|.||++    -+...+.+|+|.||..|+..-+...  ..||+||..+.
T Consensus       455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~  500 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLK  500 (674)
T ss_pred             cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHH
Confidence            68999999    2456677999999999999988763  36999998663

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

Probab=93.19  E-value=0.043  Score=53.77  Aligned_cols=37  Identities=22%  Similarity=0.569  Sum_probs=29.5

Q ss_pred             cCccccccccccccCCCeeEEeCCCCcccHHhHHHHHh
Q 041711          153 LGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLV  190 (210)
Q Consensus       153 ~~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~  190 (210)
                      +.++.|.+|.-.+.. +.-.+.||+|.||+.|+.+-..
T Consensus       815 ep~d~C~~C~~~ll~-~pF~vf~CgH~FH~~Cl~~~v~  851 (911)
T KOG2034|consen  815 EPQDSCDHCGRPLLI-KPFYVFPCGHCFHRDCLIRHVL  851 (911)
T ss_pred             cCccchHHhcchhhc-CcceeeeccchHHHHHHHHHHH
Confidence            367789999988875 3456669999999999977643

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

Probab=93.07  E-value=0.05  Score=46.97  Aligned_cols=45  Identities=29%  Similarity=0.609  Sum_probs=38.1

Q ss_pred             cccccccccccCCC-eeEEeCCCCcccHHhHHHHHhcCCCCCccCc
Q 041711          156 ERCVICLEEFSEGD-EVISLQCSHVHHRHCILKWLVTGNNCPTCRF  200 (210)
Q Consensus       156 ~~C~ICle~~~~~~-~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~  200 (210)
                      ..|+||.+.+.... .+..++|+|.-|..|.......+-+||+|..
T Consensus       159 ~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  159 FNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             CCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence            45999999987665 4567799999999999988877789999977

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

Probab=93.04  E-value=0.034  Score=56.36  Aligned_cols=47  Identities=28%  Similarity=0.584  Sum_probs=38.6

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTL  202 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i  202 (210)
                      +...|.||++.+...  ..+..|+|.+|..|...|+..+..||+|+...
T Consensus      1152 ~~~~c~ic~dil~~~--~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi~ 1198 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQ--GGIAGCGHEPCCRCDELWLYASSRCPICKSIK 1198 (1394)
T ss_pred             cccchHHHHHHHHhc--CCeeeechhHhhhHHHHHHHHhccCcchhhhh
Confidence            345799999998731  22557999999999999999999999998543

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

Probab=93.03  E-value=0.043  Score=47.87  Aligned_cols=42  Identities=21%  Similarity=0.378  Sum_probs=28.6

Q ss_pred             ccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCC
Q 041711          157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTL  202 (210)
Q Consensus       157 ~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i  202 (210)
                      .|.-|--.+..  .-|.+||+|+||.+|...  ..-+.||.|-.+|
T Consensus        92 fCd~Cd~PI~I--YGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen   92 FCDRCDFPIAI--YGRMIPCKHVFCLECARS--DSDKICPLCDDRV  133 (389)
T ss_pred             eecccCCccee--eecccccchhhhhhhhhc--CccccCcCcccHH
Confidence            46666544432  345669999999999643  2246899997665

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=92.56  E-value=0.078  Score=34.60  Aligned_cols=46  Identities=26%  Similarity=0.527  Sum_probs=32.3

Q ss_pred             cccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCCCC
Q 041711          156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCTT  206 (210)
Q Consensus       156 ~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~~  206 (210)
                      ..|..|...   +..-.++||+|.-+..|-.-+  +-+-||+|-+++...+
T Consensus         8 ~~~~~~~~~---~~~~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~~~~   53 (55)
T PF14447_consen    8 QPCVFCGFV---GTKGTVLPCGHLICDNCFPGE--RYNGCPFCGTPFEFDD   53 (55)
T ss_pred             eeEEEcccc---ccccccccccceeeccccChh--hccCCCCCCCcccCCC
Confidence            456666554   344557799999999996553  3468999999885543

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.21  E-value=0.36  Score=41.99  Aligned_cols=28  Identities=29%  Similarity=0.784  Sum_probs=22.8

Q ss_pred             CCCcccHHhHHHHHhc-------------CCCCCccCcCCC
Q 041711          176 CSHVHHRHCILKWLVT-------------GNNCPTCRFTLP  203 (210)
Q Consensus       176 C~H~Fh~~CI~~Wl~~-------------~~~CPlCR~~i~  203 (210)
                      |...+|..|+.+|+..             +-+||+||..+.
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fc  365 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFC  365 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceE
Confidence            7888999999999764             336999999774

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

Probab=92.15  E-value=0.14  Score=39.37  Aligned_cols=50  Identities=22%  Similarity=0.416  Sum_probs=35.6

Q ss_pred             ccccccccccccCCCeeEEe-C---CCCcccHHhHHHHHhc---CCCCCccCcCCCCCCC
Q 041711          155 QERCVICLEEFSEGDEVISL-Q---CSHVHHRHCILKWLVT---GNNCPTCRFTLPCTTT  207 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~L-p---C~H~Fh~~CI~~Wl~~---~~~CPlCR~~i~~~~~  207 (210)
                      -.+|.||.|.-.+   .+-| |   ||-..|..|-....+.   .+.||+|++++-....
T Consensus        80 lYeCnIC~etS~e---e~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~~  136 (140)
T PF05290_consen   80 LYECNICKETSAE---ERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSSS  136 (140)
T ss_pred             ceeccCcccccch---hhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccccc
Confidence            3689999988544   2345 3   8999999876554443   5799999999855433

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=92.05  E-value=0.1  Score=46.19  Aligned_cols=51  Identities=20%  Similarity=0.467  Sum_probs=34.2

Q ss_pred             CccccccccccccCCCee-EEeCCCCcccHHhHHHHHh-cCCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEV-ISLQCSHVHHRHCILKWLV-TGNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~-~~LpC~H~Fh~~CI~~Wl~-~~~~CPlCR~~i~~  204 (210)
                      +++-|+.|+|++...++- .-.|||-..|.-|-..--. .+..||-||+...+
T Consensus        13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~d   65 (480)
T COG5175          13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDD   65 (480)
T ss_pred             ccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccc
Confidence            445699999999865543 3347887767666433222 25789999987643

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

Probab=91.62  E-value=0.057  Score=51.31  Aligned_cols=42  Identities=36%  Similarity=0.672  Sum_probs=32.7

Q ss_pred             cccccccccccCCC-eeEEeCCCCcccHHhHHHHHhcCCCCCccCc
Q 041711          156 ERCVICLEEFSEGD-EVISLQCSHVHHRHCILKWLVTGNNCPTCRF  200 (210)
Q Consensus       156 ~~C~ICle~~~~~~-~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~  200 (210)
                      -.|.||+..|.... .++.|-|||+.|..|+..-  .+.+|| |++
T Consensus        12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~   54 (861)
T KOG3161|consen   12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKR   54 (861)
T ss_pred             hhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCc
Confidence            46999999887644 4667789999999999874  456788 654

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

Probab=91.49  E-value=0.11  Score=45.31  Aligned_cols=42  Identities=24%  Similarity=0.570  Sum_probs=32.8

Q ss_pred             cccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcC-CCCCccCc
Q 041711          156 ERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTG-NNCPTCRF  200 (210)
Q Consensus       156 ~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~-~~CPlCR~  200 (210)
                      -.|+.|-.-+.+   +..+ .|+|.||.+||...|... ..||.|.+
T Consensus       275 LkCplc~~Llrn---p~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRN---PMKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhC---cccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            469999877654   3345 589999999999988765 68999944

>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=90.89  E-value=0.12  Score=43.70  Aligned_cols=45  Identities=24%  Similarity=0.645  Sum_probs=34.8

Q ss_pred             ccccccccccccCCCeeEEe--C-CCCcccHHhHHHHHhcCC-CCC--ccC
Q 041711          155 QERCVICLEEFSEGDEVISL--Q-CSHVHHRHCILKWLVTGN-NCP--TCR  199 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~L--p-C~H~Fh~~CI~~Wl~~~~-~CP--lCR  199 (210)
                      +..|+||..+.--.-.+..|  | |-|.-|..|+++-++..+ .||  -|-
T Consensus        10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~   60 (314)
T COG5220          10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCG   60 (314)
T ss_pred             cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHH
Confidence            45799999876544444444  6 999999999999999875 799  663

>cd02127 PA_hPAP21_like PA_hPAP21_like: Protease-associated domain containing proteins like the human secreted glycoprotein hPAP21 (human protease-associated domain-containing protein, 21kDa)

Probab=90.79  E-value=0.061  Score=40.62  Aligned_cols=67  Identities=18%  Similarity=0.106  Sum_probs=43.6

Q ss_pred             CCceeeeEEeeccCCCCCcceeeecccccchhhhhhhhhhhcccCCCc-hhHHHH------HHHhhhhccCcChHHHHHH
Q 041711           29 SPGFYFIIQIFNTDELIHPQVRVRIPLNAQEHTFHLKLHEIFFEDSDQ-DSFLED------LRANLLSTQGLGECAQEIL  101 (210)
Q Consensus        29 ~~~fi~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~dd~~~-~~~~~~------l~~~ll~~~~l~~~~~e~l  101 (210)
                      -.++|.+++|..|+|..+       .+++|++|..+   -|++++... ......      .....++++++...+.+.|
T Consensus        33 ~~g~I~Lv~RG~C~F~~K-------~~~Aq~aGA~a---vII~n~~~~~~~~~~~m~~~~~~~~i~IP~v~Is~~dG~~L  102 (118)
T cd02127          33 INGNIALIERGGCSFLTK-------AINAQKAGALA---VIITDVNNDSDEYYVEMIQDDSSRRADIPAAFLLGKNGYMI  102 (118)
T ss_pred             cCCeEEEEECCCCCHHHH-------HHHHHHCCCcE---EEEEECCCCccccceEecCCCCCCCceEEEEEecHHHHHHH
Confidence            468999999999999544       56899999988   555544322 111100      1122467788888888877


Q ss_pred             HHHH
Q 041711          102 MKTI  105 (210)
Q Consensus       102 ~~~v  105 (210)
                      ...+
T Consensus       103 ~~~l  106 (118)
T cd02127         103 RKTL  106 (118)
T ss_pred             HHHH
Confidence            5544

This group contains various PA domain-containing proteins similar to hPAP21. Complex N-glycosylation may be required for the secretion of hPAP21. The significance of the PA domain to hPAP21 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.

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

Probab=90.63  E-value=0.17  Score=44.30  Aligned_cols=42  Identities=31%  Similarity=0.765  Sum_probs=32.4

Q ss_pred             ccccccccccccCCCeeEEeCC--CCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          155 QERCVICLEEFSEGDEVISLQC--SHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC--~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      --+|+||.+.+...    ++.|  ||.-|..|-.   .....||.||.++.
T Consensus        48 lleCPvC~~~l~~P----i~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   48 LLDCPVCFNPLSPP----IFQCDNGHLACSSCRT---KVSNKCPTCRLPIG   91 (299)
T ss_pred             hccCchhhccCccc----ceecCCCcEehhhhhh---hhcccCCccccccc
Confidence            35799999998752    4567  6888888854   45678999999886

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

Probab=90.11  E-value=0.19  Score=43.47  Aligned_cols=35  Identities=31%  Similarity=0.501  Sum_probs=29.7

Q ss_pred             CCeeEEeCCCCcccHHhHHHHHhcC-CCCCccCcCC
Q 041711          168 GDEVISLQCSHVHHRHCILKWLVTG-NNCPTCRFTL  202 (210)
Q Consensus       168 ~~~~~~LpC~H~Fh~~CI~~Wl~~~-~~CPlCR~~i  202 (210)
                      ...+++|.|||.||..|+.+-+... ..||.||...
T Consensus        19 ~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen   19 DHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             ccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            3457889999999999999988765 4899999985

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

Probab=89.00  E-value=0.13  Score=46.49  Aligned_cols=39  Identities=26%  Similarity=0.533  Sum_probs=28.8

Q ss_pred             Cccccccccccc-cCCCeeEEeCCCCcccHHhHHHHHhcC
Q 041711          154 GQERCVICLEEF-SEGDEVISLQCSHVHHRHCILKWLVTG  192 (210)
Q Consensus       154 ~~~~C~ICle~~-~~~~~~~~LpC~H~Fh~~CI~~Wl~~~  192 (210)
                      ...+|.||+.+. ...+...+..|+|.||..|+.+.+..+
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~  184 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK  184 (384)
T ss_pred             ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh
Confidence            456899999444 333444456899999999999888753

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

Probab=88.95  E-value=0.24  Score=48.04  Aligned_cols=39  Identities=36%  Similarity=0.952  Sum_probs=29.3

Q ss_pred             cccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCc
Q 041711          158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPT  197 (210)
Q Consensus       158 C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPl  197 (210)
                      |+||--.+. |.......|+|+-|..|...|+.....||.
T Consensus      1031 C~~C~l~V~-gss~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1031 CAICHLAVR-GSSNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             eeeEeeEee-ccchhhccccccccHHHHHHHHhcCCcCCC
Confidence            666544432 334445589999999999999999999985

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

Probab=88.10  E-value=0.24  Score=42.83  Aligned_cols=48  Identities=31%  Similarity=0.676  Sum_probs=35.7

Q ss_pred             ccccccccccccCCCe-eEEeCCC-----CcccHHhHHHHHhc--CCCCCccCcCC
Q 041711          155 QERCVICLEEFSEGDE-VISLQCS-----HVHHRHCILKWLVT--GNNCPTCRFTL  202 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~-~~~LpC~-----H~Fh~~CI~~Wl~~--~~~CPlCR~~i  202 (210)
                      +..|-||.++...... ....||.     +..|..|+..|+..  +..|.+|....
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~  133 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFF  133 (323)
T ss_pred             CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccc
Confidence            4679999998754322 3344774     67899999999995  46899998755

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

Probab=88.04  E-value=0.25  Score=46.62  Aligned_cols=46  Identities=30%  Similarity=0.730  Sum_probs=38.4

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCTT  206 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~~  206 (210)
                      ....|.||+++.    ..++.+|.   |..|..+|+..+.+||+|+..+..++
T Consensus       478 ~~~~~~~~~~~~----~~~~~~~~---~~~~l~~~~~~~~~~pl~~~~~~~~~  523 (543)
T KOG0802|consen  478 PNDVCAICYQEM----SARITPCS---HALCLRKWLYVQEVCPLCHTYMKEDD  523 (543)
T ss_pred             ccCcchHHHHHH----Hhcccccc---chhHHHhhhhhccccCCCchhhhccc
Confidence            567899999998    35567888   89999999999999999988775443

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

Probab=87.99  E-value=0.28  Score=40.73  Aligned_cols=41  Identities=29%  Similarity=0.536  Sum_probs=28.5

Q ss_pred             cccccccccCCCeeEEeCCCC-cccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          158 CVICLEEFSEGDEVISLQCSH-VHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       158 C~ICle~~~~~~~~~~LpC~H-~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      |-.|-+.   +..+..+||.| .+|..|-..    -+.||+|+......
T Consensus       161 Cr~C~~~---~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~s~  202 (207)
T KOG1100|consen  161 CRKCGER---EATVLLLPCRHLCLCGICDES----LRICPICRSPKTSS  202 (207)
T ss_pred             ceecCcC---CceEEeecccceEeccccccc----CccCCCCcChhhce
Confidence            8888765   34466669986 566667543    45699999876543

>cd02123 PA_C_RZF_like PA_C-RZF_ like: Protease-associated (PA) domain C_RZF-like

Probab=87.96  E-value=0.13  Score=40.63  Aligned_cols=73  Identities=22%  Similarity=0.217  Sum_probs=46.8

Q ss_pred             CCCCCCceeeeEEeeccCCCCCcceeeecccccchhhhhhhhhhhcccCCCchhH-H-HHH---HHhhhhccCcChHHHH
Q 041711           25 DRNLSPGFYFIIQIFNTDELIHPQVRVRIPLNAQEHTFHLKLHEIFFEDSDQDSF-L-EDL---RANLLSTQGLGECAQE   99 (210)
Q Consensus        25 ~~~~~~~fi~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~dd~~~~~~-~-~~l---~~~ll~~~~l~~~~~e   99 (210)
                      ......++|.+++|..|+|..+       .+++|++|..+   .++.++...... + ..-   ...-+++++++..+.+
T Consensus        62 ~~~~~~g~IvLV~RG~CtF~~K-------v~nAq~aGA~a---vII~n~~~~~~~~m~~~~~~~~~v~IP~v~Is~~dg~  131 (153)
T cd02123          62 NSNASGSFIVLIRRGNCSFETK-------VRNAQRAGYKA---AIVYNDESNDLISMSGNDQEIKGIDIPSVFVGKSTGE  131 (153)
T ss_pred             ccccCCCeEEEEECCCCCHHHH-------HHHHHHCCCCE---EEEEECCCCcceeccCCCCCCcCCEEEEEEeeHHHHH
Confidence            3467789999999999999544       55999999888   555554322111 0 000   1224577788888888


Q ss_pred             HHHHHHHH
Q 041711          100 ILMKTILD  107 (210)
Q Consensus       100 ~l~~~v~~  107 (210)
                      .|...+..
T Consensus       132 ~L~~~l~~  139 (153)
T cd02123         132 ILKKYASY  139 (153)
T ss_pred             HHHHHHhc
Confidence            77555443

This group includes various PA domain-containing proteins similar to C-RZF (chicken embryo RING zinc finger) protein. These proteins contain a C3H2C3 RING finger. C-RZF is expressed in embryo cells and is restricted mainly to brain and heart, it is localized to both the nucleus and endosomes. Additional C3H2C3 RING finger proteins belonging to this group, include Arabidopsis ReMembR-H2 protein and mouse sperizin. ReMembR-H2 is likely to be an integral membrane protein, and to traffic through the endosomal pathway. Sperizin is expressed in haploid germ cells and localized in the cytoplasm, it may participate in spermatogenesis. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and acce

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=87.78  E-value=0.6  Score=30.39  Aligned_cols=33  Identities=27%  Similarity=0.752  Sum_probs=27.2

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHH
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCIL  186 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~  186 (210)
                      ....|.+|-+.|..++.+++- .|+-.+|+.|-.
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~   37 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWE   37 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHh
Confidence            346799999999877777777 699999999943

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

Probab=87.53  E-value=0.42  Score=46.80  Aligned_cols=50  Identities=24%  Similarity=0.693  Sum_probs=37.1

Q ss_pred             CccccccccccccCCCeeEEeCCC-----CcccHHhHHHHHhcC--CCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCS-----HVHHRHCILKWLVTG--NNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~-----H~Fh~~CI~~Wl~~~--~~CPlCR~~i~~  204 (210)
                      +...|-||..+=..++ +-.-||+     ..-|.+|+.+|+...  ..|-+|+.++.-
T Consensus        11 d~~~CRICr~e~~~d~-pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~F   67 (1175)
T COG5183          11 DKRSCRICRTEDIRDD-PLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKF   67 (1175)
T ss_pred             cchhceeecCCCCCCC-cCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeee
Confidence            5578999998855444 3233776     468999999999864  579999987743

>cd02125 PA_VSR PA_VSR: Protease-associated (PA) domain-containing plant vacuolar sorting receptor (VSR)

Probab=87.47  E-value=0.22  Score=38.10  Aligned_cols=69  Identities=14%  Similarity=0.066  Sum_probs=43.4

Q ss_pred             CCCceeeeEEeeccCCCCCcceeeecccccchhhhhhhhhhhcccCCCchhH-H----H----HHH-HhhhhccCcChHH
Q 041711           28 LSPGFYFIIQIFNTDELIHPQVRVRIPLNAQEHTFHLKLHEIFFEDSDQDSF-L----E----DLR-ANLLSTQGLGECA   97 (210)
Q Consensus        28 ~~~~fi~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~dd~~~~~~-~----~----~l~-~~ll~~~~l~~~~   97 (210)
                      ...++|.+|+|..|+|..+       .+++|++|..+   -|+.++.+.... +    .    ... ...++++.+...+
T Consensus        40 ~~~~~IvLv~RG~C~F~~K-------~~~Aq~aGA~a---vII~n~~~~~~~~m~~~~~~~~~~~~~~i~IP~v~Is~~~  109 (127)
T cd02125          40 GRRPVILLLDRGGCFFTLK-------AWNAQQAGAAA---VLVADNVDEPLLTMDTPEESGSADYIEKITIPSALITKAF  109 (127)
T ss_pred             CCCceEEEEECCCcCHHHH-------HHHHHHCCCcE---EEEEECCCCccccccCcccccccccCCCceEeEEEECHHH
Confidence            4567999999999999544       56999999988   455444322110 0    0    000 1135677778878


Q ss_pred             HHHHHHHHH
Q 041711           98 QEILMKTIL  106 (210)
Q Consensus        98 ~e~l~~~v~  106 (210)
                      .+.|...+.
T Consensus       110 G~~L~~~l~  118 (127)
T cd02125         110 GEKLKKAIS  118 (127)
T ss_pred             HHHHHHHHh
Confidence            887755543

This group includes various PA domain-containing VSRs such as garden pea BP-80, pumpkin PV72, and various Arabidopsis VSRs including AtVSR1. In contrast to most eukaryotes, which only have one or two VSRs, plants have several. This may in part be a reflection of having a more complex vacuolar system with both lytic vacuoles and storage vacuoles. The lytic vacuole is thought to be equivalent to the mammalian lysosome and the yeast vacuole. Pea BP-80 is a type 1 transmembrane protein, involved in the targeting of proteins to the lytic vacuole; it has been suggested that this protein also mediates targeting to the storage vacuole. PV72 and AtVSR1 may mediate transport of seed storage proteins to protein storage vacuoles. The significance of the PA domain to VSRs has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may partic

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.10  E-value=0.3  Score=41.65  Aligned_cols=49  Identities=20%  Similarity=0.600  Sum_probs=34.7

Q ss_pred             CccccccccccccCCCee-EEeCC-----CCcccHHhHHHHHhcCC--------CCCccCcCC
Q 041711          154 GQERCVICLEEFSEGDEV-ISLQC-----SHVHHRHCILKWLVTGN--------NCPTCRFTL  202 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~-~~LpC-----~H~Fh~~CI~~Wl~~~~--------~CPlCR~~i  202 (210)
                      .+..|-||+..=+++... =+-||     .|--|..|+..|+..+.        +||-|++..
T Consensus        19 ~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY   81 (293)
T KOG3053|consen   19 LERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY   81 (293)
T ss_pred             cceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence            566799999875443221 22366     37889999999997642        499998864

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

Probab=86.18  E-value=0.67  Score=41.81  Aligned_cols=46  Identities=24%  Similarity=0.500  Sum_probs=38.2

Q ss_pred             ccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCC---CCCccCc
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN---NCPTCRF  200 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~---~CPlCR~  200 (210)
                      -..|+|=.+.-++...++.|.|||+...+-+.+..+...   .||-|-.
T Consensus       334 vF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~  382 (394)
T KOG2817|consen  334 VFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPV  382 (394)
T ss_pred             eeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence            357999888887778899999999999999999776643   6999944

>cd02122 PA_GRAIL_like PA _GRAIL_like: Protease-associated (PA) domain GRAIL-like

Probab=83.92  E-value=0.25  Score=38.36  Aligned_cols=68  Identities=7%  Similarity=-0.036  Sum_probs=43.6

Q ss_pred             CCCceeeeEEeeccCCCCCcceeeecccccchhhhhhhhhhhcccCCC-chhHHHHHH--HhhhhccCcChHHHHHHHHH
Q 041711           28 LSPGFYFIIQIFNTDELIHPQVRVRIPLNAQEHTFHLKLHEIFFEDSD-QDSFLEDLR--ANLLSTQGLGECAQEILMKT  104 (210)
Q Consensus        28 ~~~~fi~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~dd~~-~~~~~~~l~--~~ll~~~~l~~~~~e~l~~~  104 (210)
                      .-.++|.+|+|..|+|..+       .++++++|..+   -|++++.+ .......-.  ...++.+.+...+++.|...
T Consensus        58 ~~~g~IaLV~RG~C~F~~K-------~~nA~~aGA~a---VIIyn~~~~~~~~~~m~~~~~~~ip~v~Is~~~G~~l~~~  127 (138)
T cd02122          58 NGEPWIALIQRGNCTFEEK-------IKLAAERNASA---VVIYNNPGTGNETVKMSHPGTGDIVAIMITNPKGMEILEL  127 (138)
T ss_pred             cCCCeEEEEECCCCCHHHH-------HHHHHHCCCcE---EEEEECCCCCCceeeccCCCCCcceEEEEcHHHHHHHHHH
Confidence            3569999999999999543       45899999988   55555554 111110000  11245667778888888665


Q ss_pred             H
Q 041711          105 I  105 (210)
Q Consensus       105 v  105 (210)
                      +
T Consensus       128 l  128 (138)
T cd02122         128 L  128 (138)
T ss_pred             H
Confidence            4

This group includes PA domain containing E3 (ubiquitin ligases) similar to human GRAIL (gene related to anergy in lymphocytes) protein. Proteins in this group contain a C3H2C3 RING finger. E3 ubiquitin ligase is part of an enzymic cascade, the end result of which is the ubiquitination of proteins. In this cascade, E1 activates the ubiquitin, the activated ubiquitin is carried by E2, and E3 recognizes the acceptor protein as well as catalyzes the transfer of the activated ubiquitin from E2 to this acceptor. GRAIL, a transmembrane protein localized in the endosomes, controls the development of T cell clonal anergy, and may ubiquitinate membrane-associated targets for T cell activation. GRAIL1 is associated with, and regulated by, two isoforms of otubain 1 (the ubiquitin-specific protease). Additional E3s belonging to this group include human (h)Goliath and Xenopus GREUL1 (Goliath Related E3 Ubiquitin Ligase

>PF02757 YLP: YLP motif; InterPro: IPR004019 The YLP motif is found in one or several copies in various Drosophila proteins

Probab=82.66  E-value=0.77  Score=19.08  Aligned_cols=8  Identities=50%  Similarity=1.028  Sum_probs=6.5

Q ss_pred             cCCCCCCC
Q 041711           17 SNDYIPDQ   24 (210)
Q Consensus        17 ~~~~~~~~   24 (210)
                      ||+|+||.
T Consensus         1 s~eYLpP~    8 (9)
T PF02757_consen    1 SNEYLPPV    8 (9)
T ss_pred             CccccCCC
Confidence            58999985

Its function is unknown, however the presence of completely conserved tyrosine residues and its presence in the human Erbb-2 and ErbB-4 receptor protein-tyrosine kinases (2.7.10.1 from EC) may suggest it could be a substrate for tyrosine kinases. ErbBs (1-4) are single-pass transmembrane proteins that activate a wide variety of signalling pathways, including those involved in proliferation, migration, differentiation, survival, and apoptosis; they are frequently misregulated in cancer []. ErbB-2 is an essential component of a neuregulin-receptor complex, although neuregulins do not interact with it alone. ErbB-4 specifically binds and is activated by neuregulins, NRG-2, NRG-3, heparin-binding EGF-like growth factor, betacellulin and NTAK [].

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

Probab=82.03  E-value=0.36  Score=46.54  Aligned_cols=45  Identities=29%  Similarity=0.713  Sum_probs=36.3

Q ss_pred             cccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC---CCCCccCcCCC
Q 041711          156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG---NNCPTCRFTLP  203 (210)
Q Consensus       156 ~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~---~~CPlCR~~i~  203 (210)
                      .+|.||+..+...   ..+.|.|.|+..|+..-|...   ..||+|+..++
T Consensus        22 lEc~ic~~~~~~p---~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e   69 (684)
T KOG4362|consen   22 LECPICLEHVKEP---SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIE   69 (684)
T ss_pred             ccCCceeEEeecc---chhhhhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence            4799999998764   456999999999998777654   47999997663

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

Probab=81.65  E-value=0.75  Score=38.22  Aligned_cols=44  Identities=27%  Similarity=0.594  Sum_probs=35.0

Q ss_pred             ccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCc
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRF  200 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~  200 (210)
                      -..|.+|.+-.-.|  ++.=.|+-.+|..|+...+.....||.|-.
T Consensus       181 lk~Cn~Ch~LvIqg--~rCg~c~i~~h~~c~qty~q~~~~cphc~d  224 (235)
T KOG4718|consen  181 LKNCNLCHCLVIQG--IRCGSCNIQYHRGCIQTYLQRRDICPHCGD  224 (235)
T ss_pred             HHHHhHhHHHhhee--eccCcccchhhhHHHHHHhcccCcCCchhc
Confidence            35799998876543  233378899999999999999999999943

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

Probab=81.17  E-value=0.76  Score=41.66  Aligned_cols=44  Identities=18%  Similarity=0.460  Sum_probs=33.0

Q ss_pred             ccccccccccccCCCeeEEe--CCCCcccHHhHHHHHhcCCCCCcc
Q 041711          155 QERCVICLEEFSEGDEVISL--QCSHVHHRHCILKWLVTGNNCPTC  198 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~L--pC~H~Fh~~CI~~Wl~~~~~CPlC  198 (210)
                      ...|++|.-.++-.+....+  .|+|.||..|...|...+..|..|
T Consensus       306 wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~~~~~~  351 (384)
T KOG1812|consen  306 WRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNGECYEC  351 (384)
T ss_pred             cCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCccccCc
Confidence            45789888777544433222  699999999999999988877555

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

Probab=80.80  E-value=0.86  Score=42.00  Aligned_cols=37  Identities=35%  Similarity=0.734  Sum_probs=30.6

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG  192 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~  192 (210)
                      ....|.||.+.+..  ....+.|+|.||..|....+..+
T Consensus        69 ~~~~c~ic~~~~~~--~~~~~~c~H~~c~~cw~~yl~~k  105 (444)
T KOG1815|consen   69 GDVQCGICVESYDG--EIIGLGCGHPFCPPCWTGYLGTK  105 (444)
T ss_pred             ccccCCcccCCCcc--hhhhcCCCcHHHHHHHHHHhhhe
Confidence            45689999999865  45566999999999999999874

>cd02129 PA_hSPPL_like PA_hSPPL_like: Protease-associated domain containing human signal peptide peptidase-like (hSPPL)-like

Probab=80.72  E-value=0.3  Score=37.11  Aligned_cols=68  Identities=9%  Similarity=-0.181  Sum_probs=43.0

Q ss_pred             CCceeeeEEeeccCCCCCcceeeecccccchhhhhhhhhhhcccCCCchhHHH---HHHHhhhhccCcChHHHHHHHHHH
Q 041711           29 SPGFYFIIQIFNTDELIHPQVRVRIPLNAQEHTFHLKLHEIFFEDSDQDSFLE---DLRANLLSTQGLGECAQEILMKTI  105 (210)
Q Consensus        29 ~~~fi~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~dd~~~~~~~~---~l~~~ll~~~~l~~~~~e~l~~~v  105 (210)
                      -.|-|.+|+|..|+|..|       ..++|++|..+   -+++++........   ......++++++...+.+.++..+
T Consensus        43 l~gkIaLV~RG~CsF~~K-------~~~Aq~aGA~a---VII~nn~~~~~~~~~~~~~~~v~IP~v~Is~~dG~~i~~~l  112 (120)
T cd02129          43 LKGKAVVVMRGNCTFYEK-------ARLAQSLGAEG---LLIVSRERLVPPSGNRSEYEKIDIPVALLSYKDMLDIQQTF  112 (120)
T ss_pred             cCCeEEEEECCCcCHHHH-------HHHHHHCCCCE---EEEEECCCCCCCCCCCCCCcCCcccEEEEeHHHHHHHHHHh
Confidence            468899999999999544       45899999988   45444443111100   011234577777777777776555


Q ss_pred             H
Q 041711          106 L  106 (210)
Q Consensus       106 ~  106 (210)
                      .
T Consensus       113 ~  113 (120)
T cd02129         113 G  113 (120)
T ss_pred             c
Confidence            4

This group contains various PA domain-containing proteins similar to hSPPL2a and 2b. These SPPLs are GxGD aspartic proteases. SPPL2a is sorted to the late endosomes, SPPL2b to the plasma membrane. In activated dendritic cells, hSPPL2a and 2b catalyze the intramembrane proteolysis of tumor necrosis factor alpha triggering IL-12 production. hSPPL2a and 2b may have a broad substrate spectrum. The significance of the PA domain to these SPPLs has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.

>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=80.56  E-value=2.4  Score=26.92  Aligned_cols=42  Identities=21%  Similarity=0.558  Sum_probs=19.7

Q ss_pred             ccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC---C--CCCccCcC
Q 041711          157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG---N--NCPTCRFT  201 (210)
Q Consensus       157 ~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~---~--~CPlCR~~  201 (210)
                      .|+|....+..  .++...|.|.-|.+ +..||...   +  .||+|.++
T Consensus         4 ~CPls~~~i~~--P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    4 RCPLSFQRIRI--PVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             B-TTTSSB-SS--EEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eCCCCCCEEEe--CccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            58888877754  45666899984422 34555442   2  59999764

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	210
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		3e-06
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		6e-06
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		1e-05
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		1e-05
2ea6_A	69	Solution Structure Of The Ring Domain Of The Human		5e-04
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		7e-04
2xeu_A	64	Ring Domain Length = 64		7e-04

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 19/46 (41%), Positives = 28/46 (60%)
Query: 157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTL 202
           +C ICL    EG++V  L C H+ H+ C+ +WL+T   CP CR  +
Sbjct: 16  KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDI 61

>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 = 47.4 bits (111), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 153 LGQERCV-ICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP 203
           +GQE C  IC  E+ +GD    L C H  H+ C+  WL     CP CR   P
Sbjct: 37  VGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFP 88

>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 = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 33/55 (60%), Gaps = 5/55 (9%)
Query: 148 GSGLILGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTL 202
           GSGL      C +C E+++ G+ V  L C+H+ H  CI+ WL   ++CP CR +L
Sbjct: 13  GSGL-----ECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSL 62

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 25/47 (53%)
Query: 156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTL 202
           E C +CLE+F   DE+    C H  HR C++KWL     CP C   +
Sbjct: 16  ELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPV 62

>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring Finger Protein 4 Length = 69

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 4/50 (8%)
Query: 154 GQERCVICLEEFSE----GDEVISLQCSHVHHRHCILKWLVTGNNCPTCR 199
           G   C IC++ +SE    G  ++S +C HV    C+   L   N CPTCR
Sbjct: 14  GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 63

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 158 CVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTCRFTL 202
           C +CL E  +G+E   L +C H  H  C+  WL + + CP CR T+
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>pdb|2XEU|A Chain A, Ring Domain Length = 64

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 158 CVICLEEFSE----GDEVISLQCSHVHHRHCILKWLVTGNNCPTCR 199
           C IC++ +SE    G  ++S +C HV    C+   L   N CPTCR
Sbjct: 6   CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 51

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	210
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	5e-18
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	4e-17
2ect_A	78	Ring finger protein 126; metal binding protein, st	1e-16
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	5e-15
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	3e-14
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	6e-14
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	5e-13
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	9e-13
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	1e-12
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	5e-12
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	1e-11
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	5e-11
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	8e-11
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	2e-09
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	3e-09
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	1e-08
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	2e-08
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	5e-08
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	7e-08
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	2e-07
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	2e-07
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	1e-06
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-06
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	7e-04
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	2e-06
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	3e-06
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	5e-06
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	5e-06
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	2e-05
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	2e-05
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	4e-05
3nw0_A	238	Non-structural maintenance of chromosomes element	1e-04
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	2e-04
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	2e-04
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	2e-04
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	2e-04
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	4e-04
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	4e-04
1z6u_A	150	NP95-like ring finger protein isoform B; structura	5e-04
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	6e-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 = 74.7 bits (184), Expect = 5e-18
 Identities = 21/68 (30%), Positives = 30/68 (44%)

Query: 136 VIETWEIAILEEGSGLILGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNC 195
            I+     ++ E  G +  +  C IC  E+ +GD    L C H  H+ C+  WL     C
Sbjct: 21  SIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTC 80

Query: 196 PTCRFTLP 203
           P CR   P
Sbjct: 81  PVCRCMFP 88

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

 Score = 71.7 bits (176), Expect = 4e-17
 Identities = 20/56 (35%), Positives = 26/56 (46%)

Query: 155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCTTTGSD 210
            E C +CLE+F   DE+    C H  HR C++KWL     CP C   +      S 
Sbjct: 15  HELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLSG 70

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

 Score = 70.5 bits (173), Expect = 1e-16
 Identities = 19/53 (35%), Positives = 32/53 (60%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCTTTGSD 210
           C +C E+++ G+ V  L C+H+ H  CI+ WL   ++CP CR +L    T ++
Sbjct: 18  CPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATN 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 = 66.2 bits (162), Expect = 5e-15
 Identities = 20/49 (40%), Positives = 30/49 (61%)

Query: 155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP 203
           +E+C ICL    EG++V  L C H+ H+ C+ +WL+T   CP CR  + 
Sbjct: 14  EEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIE 62

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A Length = 55

 Score = 63.4 bits (155), Expect = 3e-14
 Identities = 18/50 (36%), Positives = 21/50 (42%), Gaps = 1/50 (2%)

Query: 154 GQERCVICLEEFSEGDEVIS-LQCSHVHHRHCILKWLVTGNNCPTCRFTL 202
           G   C ICLE+      V   L C H+ HR C  + L  G  CP C    
Sbjct: 4   GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPS 53

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

 Score = 63.5 bits (155), Expect = 6e-14
 Identities = 16/45 (35%), Positives = 22/45 (48%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTL 202
           CV+C+ +F     +  L C+H  H  C+ KWL     CP CR   
Sbjct: 26  CVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADS 70

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

 Score = 60.9 bits (148), Expect = 5e-13
 Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 2/45 (4%)

Query: 155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCR 199
            ERC ICLE+ S  +  ++L C H     CI +W+     CP C+
Sbjct: 5   AERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCK 47

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

 Score = 60.1 bits (146), Expect = 9e-13
 Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 4/56 (7%)

Query: 155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCTTTGSD 210
           +E C IC++        + L C+H   + CI KW     NCP CR  +      S 
Sbjct: 15  EEECCICMDGR----ADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANESSG 66

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

 Score = 59.1 bits (144), Expect = 1e-12
 Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 158 CVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTCRFTL 202
           C +CL E  +G+E   L +C H  H  C+  WL + + CP CR T+
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

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

 Score = 58.4 bits (141), Expect = 5e-12
 Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 4/53 (7%)

Query: 154 GQERCVICLEEFSE----GDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTL 202
           G   C IC++ +SE    G  ++S +C HV    C+   L   N CPTCR  +
Sbjct: 14  GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66

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

 Score = 57.6 bits (139), Expect = 1e-11
 Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 156 ERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTCR 199
           + C+ C  E  + D V+   +C+H  H  C+  W+   N CP C+
Sbjct: 27  DACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71

>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 = 55.6 bits (134), Expect = 5e-11
 Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 4/49 (8%)

Query: 158 CVICLEEFSE----GDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTL 202
           C IC++ +SE    G  ++S +C HV    C+   L   N CPTCR  +
Sbjct: 13  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61

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

 Score = 54.8 bits (132), Expect = 8e-11
 Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 4/49 (8%)

Query: 158 CVICLEEFSE----GDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTL 202
           C IC++ +SE    G  ++S +C HV    C+   L   N CPTCR  +
Sbjct: 6   CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54

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

 Score = 51.8 bits (124), Expect = 2e-09
 Identities = 15/50 (30%), Positives = 19/50 (38%), Gaps = 3/50 (6%)

Query: 154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP 203
               C ICL+        +SL C HV    C+      G  C  CR  +P
Sbjct: 14  TVPECAICLQTCVH---PVSLPCKHVFCYLCVKGASWLGKRCALCRQEIP 60

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

 Score = 50.9 bits (122), Expect = 3e-09
 Identities = 12/46 (26%), Positives = 17/46 (36%), Gaps = 2/46 (4%)

Query: 157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTL 202
            C IC       D     +C H   + CI++     N CP C   +
Sbjct: 17  LCSICKGYLI--DATTITECLHTFCKSCIVRHFYYSNRCPKCNIVV 60

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

 Score = 50.3 bits (120), Expect = 1e-08
 Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 3/48 (6%)

Query: 157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNN-CPTCRFTLP 203
           RC IC+E+    D  +   CS +    CI +WL      CP CR  L 
Sbjct: 24  RCFICMEKLR--DARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQ 69

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

 Score = 48.7 bits (116), Expect = 2e-08
 Identities = 11/43 (25%), Positives = 15/43 (34%), Gaps = 3/43 (6%)

Query: 157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCR 199
           RC IC + F      +  +C H     C L+       C  C 
Sbjct: 17  RCFICRQAFQNP---VVTKCRHYFCESCALEHFRATPRCYICD 56

>2ckl_A Polycomb group ring finger protein 4; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_B 2h0d_A Length = 108

 Score = 48.7 bits (116), Expect = 5e-08
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 2/49 (4%)

Query: 157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCT 205
            CV+C   F   D    ++C H   + CI+++L T   CP C   +  T
Sbjct: 17  MCVLCGGYFI--DATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT 63

>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 = 47.2 bits (112), Expect = 7e-08
 Identities = 12/52 (23%), Positives = 17/52 (32%), Gaps = 4/52 (7%)

Query: 154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNN--CPTCRFTLP 203
             + C IC     +G       C    H  C+ K+  +     CP C    P
Sbjct: 14  AVKICNICHSLLIQGQSC--ETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWP 63

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

 Score = 47.5 bits (112), Expect = 2e-07
 Identities = 16/64 (25%), Positives = 24/64 (37%), Gaps = 20/64 (31%)

Query: 156 ERCVICLEEFSEGDE---------------VISLQCSHVHHRHCILKWLVTGNN-----C 195
           E C+IC+E+ +                       +CSH  H  C+L     GN      C
Sbjct: 26  EDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQC 85

Query: 196 PTCR 199
           P+C+
Sbjct: 86  PSCK 89

>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 = 46.7 bits (110), Expect = 2e-07
 Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 1/46 (2%)

Query: 155 QERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTCR 199
              C       +  +  ++   C+H  H HCI +WL T   CP   
Sbjct: 51  CIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 96

>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 = 45.2 bits (106), Expect = 1e-06
 Identities = 15/45 (33%), Positives = 17/45 (37%)

Query: 155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCR 199
            E         SE   V    C+H  H HCI +WL T   CP   
Sbjct: 63  IECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

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

 Score = 45.2 bits (106), Expect = 1e-06
 Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 4/51 (7%)

Query: 158 CVICLEEFSE----GDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPC 204
           C IC++ +SE    G  ++S +C HV    C+   L   N CPTCR  +  
Sbjct: 10  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH 60

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

 Score = 37.5 bits (86), Expect = 7e-04
 Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 4/46 (8%)

Query: 158 CVICLEEFSE----GDEVISLQCSHVHHRHCILKWLVTGNNCPTCR 199
           C IC++ +SE    G  ++S +C HV    C+   L   N CPTCR
Sbjct: 75  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 120

>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 = 46.7 bits (110), Expect = 2e-06
 Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 4/46 (8%)

Query: 155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNN-CPTCR 199
            + C IC E   +   V    C H+    C+  W  +    CP CR
Sbjct: 332 FQLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCR 374

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

 Score = 46.0 bits (108), Expect = 3e-06
 Identities = 16/67 (23%), Positives = 24/67 (35%), Gaps = 16/67 (23%)

Query: 154 GQERCVICLEEFSEGDEVI-----SLQCSHVHHRHCILKWL-----------VTGNNCPT 197
            + RC IC     +G EV      + +C    H  C+ +W            V+   CP 
Sbjct: 307 EELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPF 366

Query: 198 CRFTLPC 204
           C+  L  
Sbjct: 367 CKAKLST 373

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

 Score = 43.9 bits (103), Expect = 5e-06
 Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 3/42 (7%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCR 199
           C+IC E F E    ++L C+H    +CI +W+     CP CR
Sbjct: 67  CIICSEYFIEA---VTLNCAHSFCSYCINEWMKRKIECPICR 105

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

 Score = 42.8 bits (101), Expect = 5e-06
 Identities = 20/46 (43%), Positives = 25/46 (54%), Gaps = 2/46 (4%)

Query: 157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTL 202
           RC IC E F+    +I  QCSH +   CI K+L     CPTC  T+
Sbjct: 24  RCGICFEYFN--IAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTV 67

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

 Score = 40.9 bits (95), Expect = 2e-05
 Identities = 12/47 (25%), Positives = 16/47 (34%), Gaps = 2/47 (4%)

Query: 155 QERCVICLEEFSEGDE-VISLQCSHVHHRHCILKWLVTGNN-CPTCR 199
              C +C+E     D       C +   R C  +     N  CP CR
Sbjct: 11  PVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACR 57

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

 Score = 41.4 bits (97), Expect = 2e-05
 Identities = 11/47 (23%), Positives = 16/47 (34%), Gaps = 4/47 (8%)

Query: 157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP 203
           RC  C       + V    C H+   +C+   +  G  CP C     
Sbjct: 24  RCSRCTNILR--EPVCLGGCEHIFCSNCVSDCI--GTGCPVCYTPAW 66

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

 Score = 40.1 bits (94), Expect = 4e-05
 Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 4/46 (8%)

Query: 158 CVICLEEFSEGDEV-ISLQCSHVHHRHCILKWLVTGNN---CPTCR 199
           C IC+E F+E       L C H   R C+ K L +  N   CP C 
Sbjct: 18  CPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCS 63

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

 Score = 40.5 bits (94), Expect = 1e-04
 Identities = 12/49 (24%), Positives = 16/49 (32%), Gaps = 4/49 (8%)

Query: 157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNN--CPTCRFTLP 203
            C IC     +G       C    H  C+ K+  +     CP C    P
Sbjct: 182 ICNICHSLLIQG--QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWP 228

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

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 4/47 (8%)

Query: 157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWL-VTGNNCPTCRFTL 202
            C IC    ++    +   C H+  R CIL+ L V G+ CP+CR+  
Sbjct: 25  SCQICEHILAD---PVETSCKHLFCRICILRCLKVMGSYCPSCRYPC 68

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

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 4/47 (8%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNN-CPTCRFTLP 203
           C+ C E        I+  C H   + C+ +        CP CR+ L 
Sbjct: 55  CICCQELVFR---PITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLG 98

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

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 4/46 (8%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWL-VTGNNCPTCRFTL 202
           C ICL    E    +   C H   + CI+K +   G+ CP     L
Sbjct: 21  CPICLMALRE---AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEIL 63

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

 Score = 38.4 bits (89), Expect = 2e-04
 Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 4/47 (8%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN-NCPTCRFTLP 203
           C IC+E   E    ++L C+H   + C    +   +  CP CR  + 
Sbjct: 18  CGICMEILVEP---VTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVS 61

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

 Score = 36.6 bits (85), Expect = 4e-04
 Identities = 6/42 (14%), Positives = 15/42 (35%), Gaps = 2/42 (4%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCR 199
           C I  +       V+S +   +  +  + +++    N P   
Sbjct: 6   CAISGKVPR--RPVLSPKSRTIFEKSLLEQYVKDTGNDPITN 45

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

 Score = 36.7 bits (85), Expect = 4e-04
 Identities = 8/46 (17%), Positives = 15/46 (32%), Gaps = 4/46 (8%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN-NCPTCRFTL 202
           C  C             +C H     C+   L + +  C  C+ ++
Sbjct: 18  CEKCHLVLCSP---KQTECGHRFCESCMAALLSSSSPKCTACQESI 60

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

 Score = 38.1 bits (88), Expect = 5e-04
 Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 4/47 (8%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN-NCPTCRFTLP 203
           CV C E      + ++ +C H   + C+ +       +CP CR  L 
Sbjct: 81  CVCCQELV---YQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLG 124

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

 Score = 38.0 bits (88), Expect = 6e-04
 Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 3/46 (6%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNN-CPTCRFTL 202
           C ICL+     + + + +C H     CI+  L +GN  CPTCR  L
Sbjct: 57  CPICLDMLK--NTMTTKECLHRFCADCIITALRSGNKECPTCRKKL 100

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	210
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.74
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.66
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.63
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.62
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.6
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.58
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.55
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.53
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.5
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.5
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.49
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.48
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.48
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.45
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.43
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.42
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.42
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.4
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.4
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.38
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.37
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.37
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.36
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.34
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.34
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.34
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.32
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.29
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.29
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.28
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.26
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.26
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.25
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.25
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.24
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.24
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.24
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.23
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.22
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.19
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.17
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.16
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.16
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.13
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.12
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.1
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.1
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.09
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.08
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.05
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.04
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.03
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.02
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.02
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.02
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.97
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.94
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.88
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.87
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.85
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.83
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.82
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.76
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.75
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.75
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.71
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.64
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.57
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.52
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.4
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.38
3nw0_A	238	Non-structural maintenance of chromosomes element	98.1
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	96.46
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	95.4
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	94.98
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	90.59
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	90.3
1we9_A	64	PHD finger family protein; structural genomics, PH	89.58
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	89.3
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	89.3
3icu_A	194	E3 ubiquitin-protein ligase RNF128; E3 ligase, ene	89.03
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	88.01
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	86.53
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	84.26
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	84.22
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	84.04
2yt5_A	66	Metal-response element-binding transcription facto	83.69
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	83.27
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	83.12
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	82.91
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	81.16
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	80.16

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

Probab=99.74  E-value=3.7e-18  Score=122.48  Aligned_cols=79  Identities=25%  Similarity=0.568  Sum_probs=66.3

Q ss_pred             cccccCCCHHHHhhcccceeeeecccCccccCccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCC
Q 041711          123 SLVAVGVQLEVVRVIETWEIAILEEGSGLILGQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTL  202 (210)
Q Consensus       123 ~~~~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i  202 (210)
                      .....|++++.++.|+.+......   ....+...|+||++.|..++.++.++|+|.||..||..|+..+.+||+||..+
T Consensus        11 ~~~~~~~s~~~i~~lp~~~~~~~~---~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~   87 (91)
T 2l0b_A           11 MVANPPASKESIDALPEILVTEDH---GAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMF   87 (91)
T ss_dssp             SSCCCCCCHHHHHTSCEEECCTTC---SSSSSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTCBCTTTCCBS
T ss_pred             CcCCCCCCHHHHHhCCCeeecccc---cccCCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCCcCcCcCccC
Confidence            346779999999999987654322   22235678999999999989899999999999999999999999999999998


Q ss_pred             CC
Q 041711          203 PC  204 (210)
Q Consensus       203 ~~  204 (210)
                      +.
T Consensus        88 ~~   89 (91)
T 2l0b_A           88 PP   89 (91)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

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

Probab=99.66  E-value=4.6e-17  Score=112.31  Aligned_cols=52  Identities=33%  Similarity=0.768  Sum_probs=47.7

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      +...|+||++.|..++.++.++|+|.||..||.+|+..+.+||+||+++...
T Consensus        22 ~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A           22 EQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             SCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             CCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            5678999999999988888999999999999999999999999999998643

>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=99.63  E-value=3.5e-16  Score=105.97  Aligned_cols=54  Identities=37%  Similarity=0.958  Sum_probs=48.7

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCTTT  207 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~~~  207 (210)
                      ....|+||++.|..++.++.++|+|.||..||.+|+..+.+||+||..+....+
T Consensus        13 ~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   66 (69)
T 2kiz_A           13 TEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQLP   66 (69)
T ss_dssp             CCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCSCCC
T ss_pred             CCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccCcCC
Confidence            557899999999888888889999999999999999999999999999976543

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

Probab=99.62  E-value=2.1e-16  Score=102.38  Aligned_cols=50  Identities=36%  Similarity=0.881  Sum_probs=45.9

Q ss_pred             CccccccccccccCCCeeEEeC-CCCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQ-CSHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~Lp-C~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      +..+|+||++.|..++.+..++ |+|.||..||.+|+..+.+||+||.++.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            4568999999999988888886 9999999999999999999999999874

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

Probab=99.60  E-value=1.1e-15  Score=104.92  Aligned_cols=52  Identities=37%  Similarity=0.850  Sum_probs=47.2

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      ....|+||++.|..+..++.++|+|.||..||.+|+..+.+||+||.++...
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (74)
T 2ep4_A           14 LHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQL   65 (74)
T ss_dssp             CSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCSBCTTTCCBCSSC
T ss_pred             CCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCCcCCCcCcccccc
Confidence            4578999999999888888889999999999999999999999999998543

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

Probab=99.58  E-value=1.3e-15  Score=105.64  Aligned_cols=52  Identities=35%  Similarity=0.892  Sum_probs=47.3

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      ....|+||++.|..+..++.++|+|.||..||.+|+..+.+||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (78)
T 2ect_A           14 SGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQ   65 (78)
T ss_dssp             SSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCCCS
T ss_pred             CCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccCCc
Confidence            5678999999999888888899999999999999999999999999998654

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

Probab=99.55  E-value=2.5e-15  Score=105.49  Aligned_cols=51  Identities=27%  Similarity=0.715  Sum_probs=41.8

Q ss_pred             CccccccccccccC-----------CCeeEEe-CCCCcccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSE-----------GDEVISL-QCSHVHHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~-----------~~~~~~L-pC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      ++..|+||++.|..           ++.++.+ +|+|.||..||.+||..+.+||+||+++..
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   76 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVV   76 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcch
Confidence            34568888888853           4456666 599999999999999999999999998854

>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=99.53  E-value=6.2e-15  Score=95.24  Aligned_cols=50  Identities=34%  Similarity=0.717  Sum_probs=43.7

Q ss_pred             CccccccccccccCCC-eeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGD-EVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~-~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      +...|+||++.|..++ .++.++|+|.||..||.+|+..+.+||+||.+++
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            4568999999996644 5667799999999999999999999999999875

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

Probab=99.50  E-value=8.9e-15  Score=99.26  Aligned_cols=52  Identities=37%  Similarity=0.837  Sum_probs=44.8

Q ss_pred             CccccccccccccC----CCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSE----GDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~----~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      +...|+||++.|..    ++.++.++|+|.||..||.+|+..+.+||+||.++...
T Consensus         9 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (71)
T 3ng2_A            9 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK   64 (71)
T ss_dssp             TCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCCC
T ss_pred             CCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccChh
Confidence            56789999999865    24457779999999999999999999999999998644

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

Probab=99.50  E-value=1.5e-14  Score=97.33  Aligned_cols=51  Identities=35%  Similarity=0.781  Sum_probs=44.0

Q ss_pred             CccccccccccccCC----CeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEG----DEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~----~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      +...|+||++.|...    +.++.++|+|.||..||..|+..+.+||+||.++..
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           14 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             CCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            567899999999753    345678999999999999999999999999998854

>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=99.49  E-value=1.8e-14  Score=106.22  Aligned_cols=50  Identities=30%  Similarity=0.590  Sum_probs=42.5

Q ss_pred             CccccccccccccCC-------------C--eeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEG-------------D--EVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~-------------~--~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      +.+.|+||++.|...             +  .++.++|+|.||..||.+||..+.+||+||+++.
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            457899999999754             1  2566799999999999999999999999999864

>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=99.48  E-value=2.4e-14  Score=106.08  Aligned_cols=51  Identities=27%  Similarity=0.643  Sum_probs=41.3

Q ss_pred             ccccccccccccCCC---------------eeEEeCCCCcccHHhHHHHHh-----cCCCCCccCcCCCCC
Q 041711          155 QERCVICLEEFSEGD---------------EVISLQCSHVHHRHCILKWLV-----TGNNCPTCRFTLPCT  205 (210)
Q Consensus       155 ~~~C~ICle~~~~~~---------------~~~~LpC~H~Fh~~CI~~Wl~-----~~~~CPlCR~~i~~~  205 (210)
                      +..|+||++.|..+.               .++.++|+|.||..||..|+.     .+.+||+||..+...
T Consensus        25 ~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            458999999996543               234669999999999999994     467999999988543

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

Probab=99.48  E-value=1.7e-14  Score=95.70  Aligned_cols=52  Identities=33%  Similarity=0.721  Sum_probs=44.4

Q ss_pred             CccccccccccccCC----CeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEG----DEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~----~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      +..+|+||++.+...    +.+..++|+|.||..||.+|+..+.+||+||.++...
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   57 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK   57 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTTT
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCcc
Confidence            346899999999752    4456779999999999999999999999999998654

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

Probab=99.45  E-value=4.7e-14  Score=98.91  Aligned_cols=51  Identities=24%  Similarity=0.668  Sum_probs=43.6

Q ss_pred             CccccccccccccCCCeeEEeCCC-----CcccHHhHHHHHhcC--CCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCS-----HVHHRHCILKWLVTG--NNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~-----H~Fh~~CI~~Wl~~~--~~CPlCR~~i~~~  205 (210)
                      +...|.||+++|..++.+ ++||+     |.||..||++||..+  .+||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~~~~l-~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~   71 (80)
T 2d8s_A           14 SQDICRICHCEGDDESPL-ITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIME   71 (80)
T ss_dssp             TSCCCSSSCCCCCSSSCE-ECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCC
T ss_pred             CCCCCeEcCccccCCCee-EeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecC
Confidence            567899999999876655 58996     999999999999876  4899999998654

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

Probab=99.43  E-value=3.4e-14  Score=96.35  Aligned_cols=49  Identities=33%  Similarity=0.859  Sum_probs=43.4

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCTT  206 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~~  206 (210)
                      +...|+||++.+..    +.++|+|.||..||.+|+..+.+||+||.++....
T Consensus        14 ~~~~C~IC~~~~~~----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (70)
T 2ecn_A           14 DEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGAN   62 (70)
T ss_dssp             CCCCCSSSCCSCCS----EEETTTEEECHHHHHHSSCCCSSCHHHHHCTTCCC
T ss_pred             CCCCCeeCCcCccC----cccCCCCcccHHHHHHHHHCcCcCCCcCCcccCCC
Confidence            45689999999875    67899999999999999999999999999996554

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

Probab=99.42  E-value=8.7e-14  Score=94.78  Aligned_cols=47  Identities=32%  Similarity=0.679  Sum_probs=41.9

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      +...|+||++.+..   .+.++|+|.||..||..|+..+.+||+||..+.
T Consensus        14 ~~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (71)
T 2d8t_A           14 TVPECAICLQTCVH---PVSLPCKHVFCYLCVKGASWLGKRCALCRQEIP   60 (71)
T ss_dssp             SCCBCSSSSSBCSS---EEEETTTEEEEHHHHHHCTTCSSBCSSSCCBCC
T ss_pred             CCCCCccCCcccCC---CEEccCCCHHHHHHHHHHHHCCCcCcCcCchhC
Confidence            45689999999854   567899999999999999999999999999884

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

Probab=99.42  E-value=1e-13  Score=93.37  Aligned_cols=49  Identities=35%  Similarity=0.810  Sum_probs=42.4

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      ....|+||++.+..  ..+.++|+|.||..||..|+..+.+||+||.++..
T Consensus         4 ~~~~C~IC~~~~~~--~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCeeCCccccC--CcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            45689999999864  34677999999999999999999999999998853

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

Probab=99.40  E-value=2.9e-13  Score=92.38  Aligned_cols=50  Identities=24%  Similarity=0.618  Sum_probs=43.0

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCCCCCccCcCCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTCRFTLPCTT  206 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~~  206 (210)
                      +...|+||++.+.+   ++.+ +|+|.||..||..|+..+..||+||..+...+
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~   64 (72)
T 2djb_A           14 PYILCSICKGYLID---ATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQ   64 (72)
T ss_dssp             GGGSCTTTSSCCSS---CEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSC
T ss_pred             CCCCCCCCChHHHC---cCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCccc
Confidence            45689999999875   4455 99999999999999999999999999986543

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

Probab=99.40  E-value=2.9e-13  Score=95.32  Aligned_cols=52  Identities=33%  Similarity=0.626  Sum_probs=44.8

Q ss_pred             CccccccccccccCCCe-eEEeCCCCcccHHhHHHHHhcC---CCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDE-VISLQCSHVHHRHCILKWLVTG---NNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~-~~~LpC~H~Fh~~CI~~Wl~~~---~~CPlCR~~i~~~  205 (210)
                      +...|+||++.|..++. ++.++|+|.||..||..|+..+   ..||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           14 EVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             SCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             CCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            45689999999987664 7778999999999999999986   7999999987543

>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=99.38  E-value=4.1e-14  Score=106.04  Aligned_cols=50  Identities=32%  Similarity=0.647  Sum_probs=1.0

Q ss_pred             CccccccccccccC-------------CCe--eEEeCCCCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSE-------------GDE--VISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~-------------~~~--~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      +.+.|+||++.|..             ++.  +..++|+|.||..||.+||..+.+||+||+++.
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~  111 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  111 (117)
T ss_dssp             CC---------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeee
Confidence            45689999999975             222  223499999999999999999999999999864

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

Probab=99.37  E-value=4.6e-13  Score=93.36  Aligned_cols=47  Identities=23%  Similarity=0.525  Sum_probs=41.8

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      ....|+||++.|..   +++++|+|.||..||..|+....+||+||.++.
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           14 IPFRCFICRQAFQN---PVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCSBCSSSCSBCCS---EEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCcCCCchhcC---eeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            45689999999865   557899999999999999999999999999985

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

Probab=99.37  E-value=2.7e-13  Score=104.01  Aligned_cols=47  Identities=34%  Similarity=0.856  Sum_probs=41.9

Q ss_pred             ccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      ...|+||++.|..   ++.++|||.||..||..|+..+.+||+||.++..
T Consensus        53 ~~~C~iC~~~~~~---~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           53 ELQCIICSEYFIE---AVTLNCAHSFCSYCINEWMKRKIECPICRKDIKS   99 (138)
T ss_dssp             HSBCTTTCSBCSS---EEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCC
T ss_pred             cCCCcccCcccCC---ceECCCCCCccHHHHHHHHHcCCcCCCCCCcCCC
Confidence            3479999999864   6678999999999999999999999999999854

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

Probab=99.36  E-value=8.1e-13  Score=90.01  Aligned_cols=50  Identities=22%  Similarity=0.520  Sum_probs=42.1

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHh---cCCCCCccCcCCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLV---TGNNCPTCRFTLPCTT  206 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~---~~~~CPlCR~~i~~~~  206 (210)
                      +...|+||++.+..   ++.++|+|.||..||..|+.   .+..||+||.++...+
T Consensus        19 ~~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           19 EEVICPICLDILQK---PVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCBCTTTCSBCSS---EEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             cCCEeccCCcccCC---eEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            45689999999874   66779999999999999997   3568999999986543

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

Probab=99.34  E-value=6.7e-13  Score=88.98  Aligned_cols=49  Identities=16%  Similarity=0.445  Sum_probs=41.3

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHh-cCCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLV-TGNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~-~~~~CPlCR~~i~~~  205 (210)
                      +...|+||++.+..   ++.++|+|.||..||..|+. .+..||+||.++..+
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           14 DKYKCEKCHLVLCS---PKQTECGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             CCEECTTTCCEESS---CCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             cCCCCCCCChHhcC---eeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            45789999999875   33579999999999999995 467999999998654

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

Probab=99.34  E-value=9.1e-13  Score=90.50  Aligned_cols=48  Identities=23%  Similarity=0.600  Sum_probs=41.0

Q ss_pred             CccccccccccccCCCeeEEeC-CCCcccHHhHHHHHhcC--CCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQ-CSHVHHRHCILKWLVTG--NNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~Lp-C~H~Fh~~CI~~Wl~~~--~~CPlCR~~i~~  204 (210)
                      +...|+||++.|..   ++.++ |+|.||..||..|+..+  ..||+||.++..
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A           14 DELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS   64 (74)
T ss_dssp             GGGSCSSSCCCCTT---CEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCC
T ss_pred             CCCCCcCCChHHhC---CeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCC
Confidence            45689999999875   55688 99999999999999876  689999998643

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

Probab=99.34  E-value=1.1e-12  Score=90.65  Aligned_cols=49  Identities=29%  Similarity=0.467  Sum_probs=42.5

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhc-CCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT-GNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~-~~~CPlCR~~i~~~  205 (210)
                      +...|+||++.|.+   ++.++|||.||..||..|+.. +.+||+||.++...
T Consensus         7 ~~~~C~IC~~~~~~---Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~   56 (78)
T 1t1h_A            7 EYFRCPISLELMKD---PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             SSSSCTTTSCCCSS---EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             ccCCCCCccccccC---CEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChh
Confidence            45689999999865   667899999999999999987 67999999998543

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

Probab=99.32  E-value=1.3e-12  Score=90.18  Aligned_cols=51  Identities=24%  Similarity=0.561  Sum_probs=43.0

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC--CCCCccCcCCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG--NNCPTCRFTLPCTT  206 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~--~~CPlCR~~i~~~~  206 (210)
                      ...+|+||++.|..++.  ...|+|.||..||.+||+.+  .+||+||++++...
T Consensus        14 ~i~~C~IC~~~i~~g~~--C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~   66 (74)
T 2ct0_A           14 AVKICNICHSLLIQGQS--CETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEI   66 (74)
T ss_dssp             SSCBCSSSCCBCSSSEE--CSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCC
T ss_pred             CCCcCcchhhHcccCCc--cCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCC
Confidence            45789999999987543  23899999999999999987  79999999986543

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

Probab=99.29  E-value=1.2e-12  Score=98.44  Aligned_cols=52  Identities=35%  Similarity=0.766  Sum_probs=44.6

Q ss_pred             CccccccccccccCC----CeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEG----DEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~----~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      +...|+||++.|...    +.++.++|||.||..||.+|+..+.+||+||..+...
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   61 (133)
T 4ap4_A            6 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK   61 (133)
T ss_dssp             CSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTT
T ss_pred             CCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCccc
Confidence            456899999999753    4457789999999999999999999999999988643

>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=99.29  E-value=1.7e-12  Score=94.33  Aligned_cols=48  Identities=33%  Similarity=0.770  Sum_probs=41.6

Q ss_pred             CccccccccccccCCCeeEE-eCCCCcccHHhHHHHHhcC-CCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVIS-LQCSHVHHRHCILKWLVTG-NNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~-LpC~H~Fh~~CI~~Wl~~~-~~CPlCR~~i~~  204 (210)
                      +...|+||++.|..   ++. ++|||.||..||..|+..+ .+||+||.++..
T Consensus        21 ~~~~C~IC~~~~~~---p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (100)
T 3lrq_A           21 EVFRCFICMEKLRD---ARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQL   70 (100)
T ss_dssp             HHTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCCCCccCCccccC---ccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCH
Confidence            44679999999864   556 7999999999999999988 699999999853

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

Probab=99.28  E-value=3.5e-12  Score=88.82  Aligned_cols=49  Identities=37%  Similarity=0.748  Sum_probs=42.0

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhc------CCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT------GNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~------~~~CPlCR~~i~~~  205 (210)
                      +...|+||++.|..   ++.++|+|.||..||..|+..      ...||+||..+...
T Consensus        18 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecw_A           18 EEVTCPICLELLKE---PVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG   72 (85)
T ss_dssp             TTTSCTTTCSCCSS---CEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTT
T ss_pred             cCCCCcCCChhhCc---ceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHH
Confidence            45689999999865   447899999999999999988      66899999998643

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

Probab=99.26  E-value=3.8e-12  Score=84.99  Aligned_cols=51  Identities=24%  Similarity=0.553  Sum_probs=41.0

Q ss_pred             ccccccccc-cccCCCee-EEeCCCCcccHHhHHHHHhcC-CCCCccCcCCCCC
Q 041711          155 QERCVICLE-EFSEGDEV-ISLQCSHVHHRHCILKWLVTG-NNCPTCRFTLPCT  205 (210)
Q Consensus       155 ~~~C~ICle-~~~~~~~~-~~LpC~H~Fh~~CI~~Wl~~~-~~CPlCR~~i~~~  205 (210)
                      +..|+||++ .+...... ..++|||.||..||..|+..+ ..||+||..+...
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   56 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccc
Confidence            457999999 77665433 456999999999999997754 6899999998543

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

Probab=99.26  E-value=3.7e-12  Score=92.04  Aligned_cols=48  Identities=40%  Similarity=0.723  Sum_probs=41.7

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      +...|+||++.|..   ++.+ +|||.||..||..|+..+.+||+||..+..
T Consensus        21 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           21 DLLRCGICFEYFNI---AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             HHTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCCCcccCChhhCC---cCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            34679999999865   5566 999999999999999999999999998853

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

Probab=99.25  E-value=9.9e-13  Score=90.83  Aligned_cols=48  Identities=33%  Similarity=0.683  Sum_probs=41.3

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhc-------CCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT-------GNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~-------~~~CPlCR~~i~~  204 (210)
                      +...|+||++.|..   ++.++|+|.||..||..|+..       ...||+||..+..
T Consensus        11 ~~~~C~IC~~~~~~---p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~   65 (79)
T 2egp_A           11 EEVTCPICLELLTE---PLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSF   65 (79)
T ss_dssp             CCCEETTTTEECSS---CCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCS
T ss_pred             cCCCCcCCCcccCC---eeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCH
Confidence            45789999999865   446799999999999999987       5689999998854

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

Probab=99.25  E-value=3.8e-12  Score=88.65  Aligned_cols=49  Identities=29%  Similarity=0.675  Sum_probs=42.0

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhc------CCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT------GNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~------~~~CPlCR~~i~~~  205 (210)
                      +...|+||++.+..   ++.++|+|.||..|+..|+..      ...||+||..+...
T Consensus        18 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecv_A           18 EEVTCPICLELLTQ---PLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPE   72 (85)
T ss_dssp             CCCCCTTTCSCCSS---CBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSS
T ss_pred             CCCCCCCCCcccCC---ceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHH
Confidence            45689999999865   446799999999999999987      67999999998643

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

Probab=99.24  E-value=6.9e-12  Score=83.13  Aligned_cols=42  Identities=29%  Similarity=0.638  Sum_probs=36.3

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhc---CCCCCcc
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT---GNNCPTC  198 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~---~~~CPlC  198 (210)
                      +...|+||++.|.+   ++.++|+|.||..||..|+..   +..||+|
T Consensus        19 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           19 EEVICPICLDILQK---PVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCBCTTTCSBCSS---CEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             cCCCCCcCCchhCC---eEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            45689999999875   567799999999999999983   5689998

>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=99.24  E-value=5.6e-12  Score=92.52  Aligned_cols=49  Identities=29%  Similarity=0.707  Sum_probs=42.6

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      +...|+||++.|..   ++.+ +|||.||..||..|+..+.+||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           14 PHLMCVLCGGYFID---ATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GGTBCTTTSSBCSS---EEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             CcCCCccCChHHhC---cCEeCCCCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            45689999999864   5566 9999999999999999999999999998643

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

Probab=99.24  E-value=8.3e-12  Score=88.81  Aligned_cols=46  Identities=24%  Similarity=0.638  Sum_probs=40.1

Q ss_pred             CccccccccccccCCCeeEEeC-CCCcccHHhHHHHHhcC--CCCCccCcCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQ-CSHVHHRHCILKWLVTG--NNCPTCRFTL  202 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~Lp-C~H~Fh~~CI~~Wl~~~--~~CPlCR~~i  202 (210)
                      +...|+||++.|..   ++.++ |||.||..||..|+..+  ..||+||..+
T Consensus        12 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~   60 (92)
T 3ztg_A           12 DELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQND   60 (92)
T ss_dssp             TTTEETTTTEECSS---CEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSS
T ss_pred             cCCCCCCCChhhcC---ceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcC
Confidence            56789999999874   56788 99999999999999754  5899999987

>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=99.23  E-value=5.3e-12  Score=94.87  Aligned_cols=48  Identities=25%  Similarity=0.584  Sum_probs=41.3

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCC-CCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN-NCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~-~CPlCR~~i~~  204 (210)
                      +...|+||++.|..   ++.++|||.||..||..|+..+. .||+||.++..
T Consensus        51 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           51 ETFQCICCQELVFR---PITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHTBCTTTSSBCSS---EEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             cCCCCCcCChHHcC---cEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            34579999999874   66789999999999999998654 99999999865

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

Probab=99.22  E-value=3.9e-12  Score=95.68  Aligned_cols=52  Identities=37%  Similarity=0.837  Sum_probs=44.4

Q ss_pred             CccccccccccccC----CCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSE----GDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~----~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      +...|+||++.|..    +...+.++|+|.||..||.+|+..+.+||+||.++..+
T Consensus        71 ~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  126 (133)
T 4ap4_A           71 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK  126 (133)
T ss_dssp             SSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChh
Confidence            45689999999975    23456779999999999999999999999999998643

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

Probab=99.19  E-value=9.8e-12  Score=80.72  Aligned_cols=42  Identities=31%  Similarity=0.865  Sum_probs=35.5

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHh---cCCCCCcc
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLV---TGNNCPTC  198 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~---~~~~CPlC  198 (210)
                      +...|+||++.+..   ++.++|+|.||..||..|+.   .+.+||+|
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           14 VEASCSVCLEYLKE---PVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCBCSSSCCBCSS---CCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cCCCCccCCcccCc---cEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            45689999999976   34679999999999999965   45789998

>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=99.17  E-value=1e-11  Score=91.22  Aligned_cols=48  Identities=33%  Similarity=0.749  Sum_probs=40.6

Q ss_pred             ccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCC---CCCccCcCCCCC
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN---NCPTCRFTLPCT  205 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~---~CPlCR~~i~~~  205 (210)
                      ...|+||++.|..   ++.++|||.||..||..|+..+.   .||+||.++...
T Consensus        21 ~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (112)
T 1jm7_A           21 ILECPICLELIKE---PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (112)
T ss_dssp             HTSCSSSCCCCSS---CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             CCCCcccChhhcC---eEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHh
Confidence            4579999999865   44579999999999999998754   899999988643

>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=99.16  E-value=1.9e-11  Score=95.21  Aligned_cols=48  Identities=25%  Similarity=0.566  Sum_probs=41.5

Q ss_pred             ccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCC-CCCccCcCCCCC
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN-NCPTCRFTLPCT  205 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~-~CPlCR~~i~~~  205 (210)
                      ...|+||++.|..   ++.++|+|.||..||..|+.... .||+||.++...
T Consensus        78 ~~~C~IC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           78 SFMCVCCQELVYQ---PVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HTBCTTTSSBCSS---EEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CCEeecCChhhcC---CEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            4579999999865   56789999999999999999765 899999998654

>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=99.16  E-value=2e-11  Score=96.12  Aligned_cols=47  Identities=32%  Similarity=0.737  Sum_probs=40.6

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhc-CCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVT-GNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~-~~~CPlCR~~i~  203 (210)
                      ....|+||++.|..   ++.+ +|+|.||..||..|+.. +..||+||.++.
T Consensus        53 ~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~  101 (165)
T 2ckl_B           53 SELMCPICLDMLKN---TMTTKECLHRFCADCIITALRSGNKECPTCRKKLV  101 (165)
T ss_dssp             HHHBCTTTSSBCSS---EEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCC
T ss_pred             CCCCCcccChHhhC---cCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCC
Confidence            44689999999875   4555 99999999999999997 678999999884

>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=99.13  E-value=2.8e-11  Score=90.27  Aligned_cols=48  Identities=27%  Similarity=0.567  Sum_probs=41.6

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCC-CCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN-NCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~-~CPlCR~~i~~  204 (210)
                      +...|+||++.+..   ++.++|+|.||..||..|+..+. +||+||.++..
T Consensus        17 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   65 (118)
T 3hct_A           17 SKYECPICLMALRE---AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLE   65 (118)
T ss_dssp             GGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCcCChhhcC---eEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCH
Confidence            45689999999865   56789999999999999998865 99999998854

>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=99.12  E-value=2.7e-11  Score=89.91  Aligned_cols=48  Identities=31%  Similarity=0.739  Sum_probs=41.5

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhc-CCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT-GNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~-~~~CPlCR~~i~~  204 (210)
                      +...|+||++.+..   ++.++|||.||..||..|+.. +.+||+||.++..
T Consensus        22 ~~~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (116)
T 1rmd_A           22 KSISCQICEHILAD---PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFP   70 (116)
T ss_dssp             HHTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCCCCCCCCcHhcC---cEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCH
Confidence            34679999999864   566899999999999999997 6799999999854

>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=99.10  E-value=1.2e-11  Score=91.69  Aligned_cols=47  Identities=28%  Similarity=0.646  Sum_probs=40.7

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhc-CCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT-GNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~-~~~CPlCR~~i~  203 (210)
                      +...|+||++.|..   ++.++|||.||..||..|+.. +..||+||..+.
T Consensus        14 ~~~~C~iC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~   61 (115)
T 3l11_A           14 SECQCGICMEILVE---PVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVS   61 (115)
T ss_dssp             HHHBCTTTCSBCSS---CEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCH
T ss_pred             CCCCCccCCcccCc---eeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccC
Confidence            45689999999864   667899999999999999987 568999999874

>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=99.10  E-value=4.7e-11  Score=79.85  Aligned_cols=47  Identities=26%  Similarity=0.490  Sum_probs=40.0

Q ss_pred             CccccccccccccCCCeeEEe--CCCCc-ccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISL--QCSHV-HHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L--pC~H~-Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      ++..|.||++...+   ...+  ||||. ||..|+..|...+..||+||+++.
T Consensus         7 ~~~~C~IC~~~~~~---~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            7 AIEPCVICQGRPKN---GCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             GGSCCTTTSSSCSC---EEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CcCCCCcCCCCCCC---EEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            45689999998654   4455  99999 899999999998899999999884

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

Probab=99.09  E-value=7.4e-11  Score=83.25  Aligned_cols=48  Identities=21%  Similarity=0.200  Sum_probs=43.1

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      +...|+||++.|.+   +++++|||.|+..||..|+..+.+||+||.++..
T Consensus        13 ~~~~CpI~~~~m~d---PV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   60 (85)
T 2kr4_A           13 DEFRDPLMDTLMTD---PVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTE   60 (85)
T ss_dssp             TTTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             hheECcccCchhcC---CeECCCCCEECHHHHHHHHhcCCCCCCCcCCCCh
Confidence            46789999999875   7788999999999999999988999999998854

>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=99.08  E-value=7.5e-11  Score=85.82  Aligned_cols=49  Identities=20%  Similarity=0.226  Sum_probs=43.7

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      +...|+||++.|.+   +++++|||.|+..||..|+..+.+||+||.++...
T Consensus        28 ~~~~CpI~~~~m~d---PV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~   76 (100)
T 2kre_A           28 DEFRDPLMDTLMTD---PVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTES   76 (100)
T ss_dssp             TTTBCTTTCSBCSS---EEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCTT
T ss_pred             HhhCCcCccCcccC---CeECCCCCEEchHHHHHHHHcCCCCCCCCCCCChh
Confidence            56789999999875   77889999999999999999888999999998643

>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=99.05  E-value=1.4e-10  Score=84.07  Aligned_cols=49  Identities=18%  Similarity=0.131  Sum_probs=43.5

Q ss_pred             CccccccccccccCCCeeEEeCCC-CcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCS-HVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~-H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      +...|+||++.|.+   +++++|| |.|+..||..|+..+.+||+||.++...
T Consensus        21 ~~~~CpI~~~~m~d---PV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~   70 (98)
T 1wgm_A           21 DEFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMD   70 (98)
T ss_dssp             TTTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTT
T ss_pred             HhcCCcCccccccC---CeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCChh
Confidence            45789999999875   7788999 9999999999999888999999998643

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

Probab=99.04  E-value=4.5e-11  Score=77.73  Aligned_cols=48  Identities=27%  Similarity=0.488  Sum_probs=39.8

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCTTT  207 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~~~  207 (210)
                      +...|+||++.|..   ++.|+|+|.||..||..|   ...||+||..+.....
T Consensus         5 ~~~~C~IC~~~~~~---p~~l~CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~~   52 (56)
T 1bor_A            5 QFLRCQQCQAEAKC---PKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLGAD   52 (56)
T ss_dssp             CCSSCSSSCSSCBC---CSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCCSS
T ss_pred             cCCCceEeCCccCC---eEEcCCCCcccHHHHccC---CCCCCcCCcEeecCCc
Confidence            45679999999875   457899999999999884   6789999999865544

>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=99.03  E-value=1.4e-10  Score=102.88  Aligned_cols=47  Identities=30%  Similarity=0.715  Sum_probs=41.0

Q ss_pred             ccccccccccccCCCeeEEeCCCCcccHHhHHHHHh-cCCCCCccCcCCCC
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLV-TGNNCPTCRFTLPC  204 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~-~~~~CPlCR~~i~~  204 (210)
                      ...|+||++.+..   ++.+||||.||..|+..|+. .+.+||+||.++..
T Consensus       332 ~~~C~ICle~~~~---pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~  379 (389)
T 2y1n_A          332 FQLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKG  379 (389)
T ss_dssp             SSBCTTTSSSBCC---EEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCE
T ss_pred             CCCCCccCcCCCC---eEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCC
Confidence            3589999999854   67789999999999999999 67899999998853

>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=99.02  E-value=9.9e-11  Score=90.24  Aligned_cols=47  Identities=23%  Similarity=0.500  Sum_probs=40.6

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCC-CCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN-NCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~-~CPlCR~~i~  203 (210)
                      +...|+||++.+..   ++.++|||.||..||..|+..+. +||+||.++.
T Consensus        30 ~~~~C~IC~~~~~~---pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~   77 (141)
T 3knv_A           30 AKYLCSACRNVLRR---PFQAQCGHRYCSFCLASILSSGPQNCAACVHEGI   77 (141)
T ss_dssp             GGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHGGGSCEECHHHHHTTC
T ss_pred             cCcCCCCCChhhcC---cEECCCCCccCHHHHHHHHhcCCCCCCCCCCccc
Confidence            45689999999865   46689999999999999998765 8999999864

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

Probab=99.02  E-value=1.7e-10  Score=80.23  Aligned_cols=51  Identities=24%  Similarity=0.543  Sum_probs=39.8

Q ss_pred             CccccccccccccCCCeeEEe--CCCCcccHHhHHHHHhc-CCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISL--QCSHVHHRHCILKWLVT-GNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L--pC~H~Fh~~CI~~Wl~~-~~~CPlCR~~i~~~  205 (210)
                      ++.+|+||++.+...+ +..+  +|||.||..|+..++.. ...||+||.++...
T Consensus        10 ~~~~CpICle~~~~~d-~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~   63 (78)
T 1e4u_A           10 DPVECPLCMEPLEIDD-INFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED   63 (78)
T ss_dssp             CCCBCTTTCCBCCTTT-TTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSC
T ss_pred             cCCcCCccCccCcccc-ccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCC
Confidence            5568999999986533 2234  49999999999998854 56899999988543

>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=99.02  E-value=1.5e-10  Score=77.10  Aligned_cols=47  Identities=19%  Similarity=0.485  Sum_probs=39.5

Q ss_pred             CccccccccccccCCCeeEEe--CCCCc-ccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISL--QCSHV-HHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L--pC~H~-Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      ....|.||++...+   ...+  ||||. ||..|+..|...+..||+||.++.
T Consensus         6 ~~~~C~IC~~~~~~---~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            6 LLKPCSLCEKRPRD---GNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GGSBCTTTSSSBSC---EEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             cCCCCcccCCcCCC---eEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            45689999998643   3344  99998 999999999988889999999884

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

Probab=98.97  E-value=1.5e-10  Score=79.45  Aligned_cols=44  Identities=20%  Similarity=0.676  Sum_probs=37.6

Q ss_pred             CccccccccccccCCCeeEEeCCCCc-ccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHV-HHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~-Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      +...|+||++.+.+   +..+||+|. ||..|+..|    ..||+||.++..
T Consensus        23 ~~~~C~iC~~~~~~---~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           23 EEKLCKICMDRNIA---IVFVPCGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HHTBCTTTSSSBCC---EEEETTCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             cCCCCCCCCCCCCC---EEEcCCCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            34679999998754   667899999 999999998    889999998853

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

Probab=98.94  E-value=1.2e-10  Score=86.74  Aligned_cols=46  Identities=24%  Similarity=0.564  Sum_probs=39.6

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      +...|+||++.|..   ++.+ +|||.||..||..|+.  ..||+||..+..
T Consensus        21 ~~~~C~IC~~~~~~---pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~   67 (117)
T 1jm7_B           21 KLLRCSRCTNILRE---PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWI   67 (117)
T ss_dssp             HTTSCSSSCSCCSS---CBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSC
T ss_pred             hCCCCCCCChHhhC---ccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCcc
Confidence            34679999999865   5577 9999999999999998  889999998853

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

Probab=98.88  E-value=1.9e-10  Score=99.91  Aligned_cols=53  Identities=26%  Similarity=0.592  Sum_probs=41.4

Q ss_pred             cCccccccccccccC-CCee----EEeCCCCcccHHhHHHHHhcC-----------CCCCccCcCCCCC
Q 041711          153 LGQERCVICLEEFSE-GDEV----ISLQCSHVHHRHCILKWLVTG-----------NNCPTCRFTLPCT  205 (210)
Q Consensus       153 ~~~~~C~ICle~~~~-~~~~----~~LpC~H~Fh~~CI~~Wl~~~-----------~~CPlCR~~i~~~  205 (210)
                      ++..+|+||++.+.. ++.+    ...+|+|.||..|+.+||...           .+||.||.+|...
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~s  374 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTS  374 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCcc
Confidence            356789999999987 3322    123799999999999999752           3699999998654

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.87  E-value=1.1e-09  Score=91.86  Aligned_cols=48  Identities=19%  Similarity=0.014  Sum_probs=41.6

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC-CCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG-NNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~-~~CPlCR~~i~~  204 (210)
                      ....|+||++.|.+   +++++|||+||..||..|+..+ .+||+||.++..
T Consensus       207 ~~~~c~i~~~~~~d---Pv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~  255 (281)
T 2c2l_A          207 DYLCGKISFELMRE---PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQ  255 (281)
T ss_dssp             STTBCTTTCSBCSS---EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             cccCCcCcCCHhcC---CeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCch
Confidence            56789999999865   7788999999999999999875 469999998853

>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=98.85  E-value=1.4e-09  Score=85.71  Aligned_cols=48  Identities=27%  Similarity=0.573  Sum_probs=41.4

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC-CCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG-NNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~-~~CPlCR~~i~~  204 (210)
                      +...|+||++.|..   ++.++|||.||..||..|+..+ .+||+||.++..
T Consensus        17 ~~~~C~IC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   65 (170)
T 3hcs_A           17 SKYECPICLMALRE---AVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLE   65 (170)
T ss_dssp             GGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCCCChhhcC---cEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcch
Confidence            45689999999865   5668999999999999999875 499999998854

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

Probab=98.83  E-value=2.5e-09  Score=70.63  Aligned_cols=48  Identities=31%  Similarity=0.688  Sum_probs=37.5

Q ss_pred             CccccccccccccCCCeeEEeCCC--C---cccHHhHHHHHhc--CCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCS--H---VHHRHCILKWLVT--GNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~--H---~Fh~~CI~~Wl~~--~~~CPlCR~~i~~  204 (210)
                      +...|.||+++.  ++.. ++||.  |   .||..|+.+|+..  +.+||+||..+..
T Consensus         5 ~~~~CrIC~~~~--~~~l-~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            5 DVPVCWICNEEL--GNER-FRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             SCCEETTTTEEC--SCCC-CCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCEeEEeecCC--CCce-ecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            456899999983  2333 57865  4   9999999999985  5689999998753

>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=98.82  E-value=1.6e-09  Score=77.72  Aligned_cols=45  Identities=24%  Similarity=0.547  Sum_probs=38.3

Q ss_pred             CccccccccccccCCCeeEEeC-CCCcccHHhHHHHHhcC------CCCCc--cCcC
Q 041711          154 GQERCVICLEEFSEGDEVISLQ-CSHVHHRHCILKWLVTG------NNCPT--CRFT  201 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~Lp-C~H~Fh~~CI~~Wl~~~------~~CPl--CR~~  201 (210)
                      ....|+||++.|.+   +++++ |||.|+..||..|+..+      .+||+  |+..
T Consensus         6 ~~~~CPI~~~~~~d---PV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            6 SGFTCPITKEEMKK---PVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             SCCBCTTTCSBCSS---EEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             cEeECcCcCchhcC---CEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            45689999999875   77785 99999999999999864      48999  9865

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

Probab=98.76  E-value=2.4e-09  Score=73.46  Aligned_cols=44  Identities=20%  Similarity=0.677  Sum_probs=36.1

Q ss_pred             ccccccccccccCCCeeEEeCCCCc-ccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHV-HHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~-Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      ...|+||++.+.+   +..+||+|. ||..|+..    ...||+||.++...
T Consensus        25 ~~~C~IC~~~~~~---~~~~pCgH~~~C~~C~~~----~~~CP~Cr~~i~~~   69 (75)
T 2ecg_A           25 EKLCKICMDRNIA---IVFVPCGHLVTCKQCAEA----VDKCPMCYTVITFK   69 (75)
T ss_dssp             HHSCSSSCSSCCC---BCCSSSCCCCBCHHHHHH----CSBCTTTCCBCCCC
T ss_pred             CCCCCcCCCCCCC---EEEecCCCHHHHHHHhhC----CCCCccCCceecCc
Confidence            4579999999754   556799999 99999964    47899999998543

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

Probab=98.75  E-value=5.6e-09  Score=70.54  Aligned_cols=44  Identities=25%  Similarity=0.583  Sum_probs=36.4

Q ss_pred             CccccccccccccCCCeeEEeCCCCc-ccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHV-HHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~-Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      +...|.||++...+   +..+||+|. ||..|+..    ...||+||.++..
T Consensus        14 ~~~~C~IC~~~~~~---~v~~pCgH~~~C~~C~~~----~~~CP~CR~~i~~   58 (68)
T 2ea5_A           14 NSKDCVVCQNGTVN---WVLLPCRHTCLCDGCVKY----FQQCPMCRQFVQE   58 (68)
T ss_dssp             CSSCCSSSSSSCCC---CEETTTTBCCSCTTHHHH----CSSCTTTCCCCCC
T ss_pred             CCCCCCCcCcCCCC---EEEECCCChhhhHHHHhc----CCCCCCCCcchhc
Confidence            45689999998643   667799999 99999984    5799999998843

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

Probab=98.75  E-value=5.4e-09  Score=83.57  Aligned_cols=48  Identities=19%  Similarity=0.005  Sum_probs=41.9

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC-CCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG-NNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~-~~CPlCR~~i~~  204 (210)
                      ....|+||++.|.+   +++++|||.|+..||..|+..+ .+||+||.++..
T Consensus       105 ~~f~CPI~~elm~D---PV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~  153 (179)
T 2f42_A          105 DYLCGKISFELMRE---PCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQ  153 (179)
T ss_dssp             GGGBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             HhhcccCccccCCC---CeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCCh
Confidence            56789999999875   7788999999999999999874 579999998854

>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=98.71  E-value=3.4e-09  Score=73.69  Aligned_cols=42  Identities=26%  Similarity=0.628  Sum_probs=35.6

Q ss_pred             ccccccccccccCCCeeEEeCCCCc-ccHHhHHHHHhcCCCCCccCcCCC
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHV-HHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~-Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      ...|.||++.+.+   +..+||||. ||..|+..|    ..||+||.++.
T Consensus        18 ~~~C~IC~~~~~~---~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~   60 (79)
T 2yho_A           18 AMLCMVCCEEEIN---STFCPCGHTVCCESCAAQL----QSCPVCRSRVE   60 (79)
T ss_dssp             HTBCTTTSSSBCC---EEEETTCBCCBCHHHHTTC----SBCTTTCCBCC
T ss_pred             CCEeEEeCcccCc---EEEECCCCHHHHHHHHHhc----CcCCCCCchhh
Confidence            4579999998654   667899999 999999887    49999999874

>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=98.64  E-value=1.2e-08  Score=72.72  Aligned_cols=48  Identities=23%  Similarity=0.585  Sum_probs=38.3

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC--------CCCCc--cCcC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG--------NNCPT--CRFT  201 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~--------~~CPl--CR~~  201 (210)
                      +..+|+||++++...+.....+|+|.||..|+..++..+        ..||.  |+..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            346799999998765544444899999999999998742        37999  9987

>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=98.57  E-value=2.3e-08  Score=66.16  Aligned_cols=46  Identities=11%  Similarity=0.127  Sum_probs=40.8

Q ss_pred             cccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          156 ERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       156 ~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      ..|+||++.+.+   ++++ +|||+|.+.||.+|+..+.+||+++.++..
T Consensus         4 ~~CpIs~~~m~d---PV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~   50 (61)
T 2bay_A            4 MLCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSI   50 (61)
T ss_dssp             CCCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCG
T ss_pred             EEecCCCCCCCC---CEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCCh
Confidence            469999999874   6677 899999999999999988899999998854

>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=98.52  E-value=2.1e-08  Score=87.80  Aligned_cols=43  Identities=23%  Similarity=0.714  Sum_probs=37.4

Q ss_pred             CccccccccccccCCCeeEEeCCCCc-ccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHV-HHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~-Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      +...|+||++.+..   +..+||||. ||..|+..|    ..||+||.++.
T Consensus       294 ~~~~C~IC~~~~~~---~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~  337 (345)
T 3t6p_A          294 EERTCKVCMDKEVS---VVFIPCGHLVVCQECAPSL----RKCPICRGIIK  337 (345)
T ss_dssp             TTCBCTTTSSSBCC---EEEETTCCEEECTTTGGGC----SBCTTTCCBCC
T ss_pred             CCCCCCccCCcCCc---eEEcCCCChhHhHHHHhcC----CcCCCCCCCcc
Confidence            45689999999864   667899999 999999988    78999999885

>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=98.40  E-value=1.3e-07  Score=79.49  Aligned_cols=48  Identities=27%  Similarity=0.564  Sum_probs=39.1

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC--CCCCc--cCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG--NNCPT--CRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~--~~CPl--CR~~i~  203 (210)
                      ....|+||++.|.+  .++.+.|||.||..||..|+..+  .+||+  ||..+.
T Consensus       180 ~el~CPIcl~~f~D--PVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~  231 (267)
T 3htk_C          180 IELTCPITCKPYEA--PLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVS  231 (267)
T ss_dssp             CCSBCTTTSSBCSS--EEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEEC
T ss_pred             eeeECcCccCcccC--CeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCc
Confidence            45679999999964  34335999999999999999864  47999  998774

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.38  E-value=2.6e-07  Score=66.43  Aligned_cols=45  Identities=20%  Similarity=0.362  Sum_probs=37.1

Q ss_pred             ccccccccccCCCeeEEeCCCCcccHHhHHHHHhc-CCCCCccCcCCC
Q 041711          157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT-GNNCPTCRFTLP  203 (210)
Q Consensus       157 ~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~-~~~CPlCR~~i~  203 (210)
                      -|.+|--.|..  ..+.+||+|+||.+|+..|.++ .++||+|+.++.
T Consensus         3 fC~~C~~Pi~i--ygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~   48 (101)
T 3vk6_A            3 FCDKCGLPIKV--YGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQ   48 (101)
T ss_dssp             BCTTTCSBCSE--EEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCS
T ss_pred             ecCccCCCeEE--EeeeccccccHHHHHHHHHHhccCCCCcCcCCeee
Confidence            37788777643  5677899999999999999866 579999999873

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

Probab=98.10  E-value=1.3e-06  Score=72.74  Aligned_cols=51  Identities=24%  Similarity=0.562  Sum_probs=41.3

Q ss_pred             ccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCC--CCCccCcCCCCCCC
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN--NCPTCRFTLPCTTT  207 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~--~CPlCR~~i~~~~~  207 (210)
                      -..|+||.+.+..|..  .-.|+|.||..|+..|++.+.  .||.|+...+...+
T Consensus       180 i~~C~iC~~iv~~g~~--C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~~~  232 (238)
T 3nw0_A          180 VKICNICHSLLIQGQS--CETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIP  232 (238)
T ss_dssp             CCBCTTTCSBCSSCEE--CSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSCCC
T ss_pred             CCcCcchhhHHhCCcc--cCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCC
Confidence            4679999999887542  225999999999999998754  89999998876543

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=95.40  E-value=0.0087  Score=39.67  Aligned_cols=45  Identities=22%  Similarity=0.527  Sum_probs=33.6

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCC----CCCccCcCC
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGN----NCPTCRFTL  202 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~----~CPlCR~~i  202 (210)
                      ....|.||.+.   ++ +..- .|...||..|+.+.|...+    .||.|+...
T Consensus        11 ~~~~C~vC~~~---~~-ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           11 PGARCGVCGDG---TD-VLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             TTCCCTTTSCC---TT-CEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCcCCCCCC---Ce-EEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            45679999753   44 3333 8999999999999887753    699997643

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=94.98  E-value=0.014  Score=41.16  Aligned_cols=35  Identities=11%  Similarity=0.295  Sum_probs=26.2

Q ss_pred             ccccccccccccCCCeeEEeCCCCcccHHhHHH-HH
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILK-WL  189 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~-Wl  189 (210)
                      +-.|.||++.+........+.|+|.||..|+.. |.
T Consensus         3 e~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~~h~   38 (101)
T 2jun_A            3 KVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKATHP   38 (101)
T ss_dssp             CCBCTTCCSSSCCBCCEEETTTTEEECHHHHHHHSC
T ss_pred             CCCCcCCCCCCCCCceEECCcCChHHhHHHCHHHhc
Confidence            457999998754333334479999999999998 53

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=90.59  E-value=0.13  Score=33.20  Aligned_cols=44  Identities=23%  Similarity=0.610  Sum_probs=31.2

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCC----CCCccCc
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN----NCPTCRF  200 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~----~CPlCR~  200 (210)
                      ....|.||...   ++.+..-.|...||..|+.+-+...+    .||.|+.
T Consensus        10 ~~~~C~vC~~~---g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A           10 HQDYCEVCQQG---GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             CCSSCTTTSCC---SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCCCCccCCCC---CcEEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            45679999863   33222227999999999998665432    6999965

>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=90.30  E-value=0.2  Score=34.68  Aligned_cols=31  Identities=23%  Similarity=0.658  Sum_probs=22.4

Q ss_pred             CccccccccccccCCCeeEEeC---CCCcccHHhHHHH
Q 041711          154 GQERCVICLEEFSEGDEVISLQ---CSHVHHRHCILKW  188 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~Lp---C~H~Fh~~CI~~W  188 (210)
                      .+..|.||- .+..++   .+|   |+-+||..|+.+-
T Consensus        14 ~D~~C~VC~-~~t~~~---l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           14 NDEMCDVCE-VWTAES---LFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CSCCCTTTC-CCCSSC---CSSCSSSSSCCCHHHHHHH
T ss_pred             CCcccCccc-cccccc---eeccccccccccHhhcccc
Confidence            567899994 343333   334   6899999999996

>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=89.58  E-value=0.064  Score=34.80  Aligned_cols=48  Identities=21%  Similarity=0.477  Sum_probs=33.8

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHh-----cCCCCCccCcC
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLV-----TGNNCPTCRFT  201 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~-----~~~~CPlCR~~  201 (210)
                      +...|+||...+..+...+.- .|..-||..|+.--..     .+-.||.|+..
T Consensus         5 e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            556799999988654434334 8999999999864322     23479999764

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=89.30  E-value=0.16  Score=31.33  Aligned_cols=43  Identities=26%  Similarity=0.654  Sum_probs=29.0

Q ss_pred             ccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCC----CCCccCc
Q 041711          157 RCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGN----NCPTCRF  200 (210)
Q Consensus       157 ~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~----~CPlCR~  200 (210)
                      .|.||...-..++ +..- .|...||..|+.+=+...+    .||.|+.
T Consensus         2 ~C~vC~~~~~~~~-ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDDK-LILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSC-CEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCC-EEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            4888886532222 3223 7999999999987555432    5999965

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=89.30  E-value=0.17  Score=35.35  Aligned_cols=48  Identities=27%  Similarity=0.529  Sum_probs=33.7

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCC----CCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN----NCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~----~CPlCR~~i~~  204 (210)
                      ....|.+|...   ++-+..-.|.-.||..|+.+=+...+    .||.|+..-+.
T Consensus        24 n~~~C~vC~~~---g~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~~~   75 (88)
T 1fp0_A           24 SATICRVCQKP---GDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDL   75 (88)
T ss_dssp             SSSCCSSSCSS---SCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCSS
T ss_pred             CCCcCcCcCCC---CCEEECCCCCCceecccCCCCCCCCcCCCcCCccccCCCcc
Confidence            45689999864   44222227899999999988776533    69999865433

>3icu_A E3 ubiquitin-protein ligase RNF128; E3 ligase, energy, PA domain, transmembrane,protein turnover conjugation pathway; HET: NAG; 2.10A {Homo sapiens}

Probab=89.03  E-value=0.026  Score=45.21  Aligned_cols=71  Identities=11%  Similarity=-0.000  Sum_probs=45.0

Q ss_pred             CCCCCceeeeEEeec-cCCCCCcceeeecccccchhhhhhhhhhhcccCCCchhHHHHH---HHhhhhccCcChHHHHHH
Q 041711           26 RNLSPGFYFIIQIFN-TDELIHPQVRVRIPLNAQEHTFHLKLHEIFFEDSDQDSFLEDL---RANLLSTQGLGECAQEIL  101 (210)
Q Consensus        26 ~~~~~~fi~~i~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~dd~~~~~~~~~l---~~~ll~~~~l~~~~~e~l  101 (210)
                      .+...++|.||+|.. |+|..|       .+++|++|..+   .|++++.+.......+   ...-++++++...+.+.|
T Consensus       100 ~~~~~gkIaLV~RG~~CsF~~K-------v~nAq~aGA~a---vIIyNn~~~g~~~~~m~~~~~~~IPsv~Is~~~G~~L  169 (194)
T 3icu_A          100 STVQVSWLALIQRGGGCTFADK-------IHLAYERGASG---AVIFNFPGTRNEVIPMSHPGAVDIVAIMIGNLKGTKI  169 (194)
T ss_dssp             SSCBCCEEEEEESCTTCCHHHH-------HHHHHHTTCSE---EEEECCTTCTTCCCCCCCTTCCSSEEEEECHHHHHHH
T ss_pred             cccCCCeEEEEECCCCcCHHHH-------HHHHHHCCCcE---EEEEeCCCCCCceeeecCCCCCceeEEEECHHHHHHH
Confidence            445678999999999 999533       55999999988   5555542111000000   012357777888888877


Q ss_pred             HHHHH
Q 041711          102 MKTIL  106 (210)
Q Consensus       102 ~~~v~  106 (210)
                      +..+.
T Consensus       170 ~~~L~  174 (194)
T 3icu_A          170 LQSIQ  174 (194)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            65543

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=88.01  E-value=0.044  Score=34.77  Aligned_cols=44  Identities=30%  Similarity=0.588  Sum_probs=30.7

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCC----CCCccCc
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN----NCPTCRF  200 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~----~CPlCR~  200 (210)
                      .+..|.||...   ++.+..-.|...||..|+.+-+...+    .||.|+.
T Consensus         8 ~~~~C~vC~~~---g~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            8 HEDFCSVCRKS---GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SCCSCSSSCCS---SCCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCccCCCC---CeEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            56779999874   33222227999999999997665432    5888854

>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=86.53  E-value=0.14  Score=33.05  Aligned_cols=46  Identities=26%  Similarity=0.515  Sum_probs=31.6

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCC----CCCccCcCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN----NCPTCRFTL  202 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~----~CPlCR~~i  202 (210)
                      ....|.||.+.   ++.+..-.|...||..|+.+-+...+    .||.|+...
T Consensus         8 ~~~~C~vC~~~---g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            8 HMEFCRVCKDG---GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SCSSCTTTCCC---SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCcCCCCCCC---CCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            45679999853   33222127899999999997665432    599997654

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=84.26  E-value=0.27  Score=34.10  Aligned_cols=49  Identities=22%  Similarity=0.443  Sum_probs=31.8

Q ss_pred             CccccccccccccCCCeeEEe--CCCCcccHHhHHHHHhc--CCCCCccCcCC
Q 041711          154 GQERCVICLEEFSEGDEVISL--QCSHVHHRHCILKWLVT--GNNCPTCRFTL  202 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L--pC~H~Fh~~CI~~Wl~~--~~~CPlCR~~i  202 (210)
                      +...|.||...-+..+...++  .|.-.||..|+.+-+.-  .=.||.|....
T Consensus        24 ~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~   76 (88)
T 2l43_A           24 EDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSR   76 (88)
T ss_dssp             CCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHT
T ss_pred             CCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCcc
Confidence            567899998753222222233  79999999999864321  12699997654

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=84.22  E-value=0.25  Score=32.98  Aligned_cols=49  Identities=20%  Similarity=0.351  Sum_probs=33.8

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhc----CCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVT----GNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~----~~~CPlCR~~i~  203 (210)
                      +...|.||..... ++..+.- .|.--||..|+..-...    .-.||.|+..+.
T Consensus        17 ~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~   70 (75)
T 2k16_A           17 QIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIK   70 (75)
T ss_dssp             EEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHC
T ss_pred             CCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchh
Confidence            4456999987753 3333333 89999999999865543    236999987653

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=84.04  E-value=0.052  Score=34.91  Aligned_cols=47  Identities=28%  Similarity=0.554  Sum_probs=32.5

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCC----CCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGN----NCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~----~CPlCR~~i~  203 (210)
                      .+..|.||...   ++-+..-.|...||..|+.+-+...+    .||.|+....
T Consensus         4 ~~~~C~vC~~~---g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~   54 (60)
T 2puy_A            4 HEDFCSVCRKS---GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQML   54 (60)
T ss_dssp             CCSSCTTTCCC---SSCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHHH
T ss_pred             CCCCCcCCCCC---CcEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccChhh
Confidence            35679999874   44222227999999999997665432    5999976543

>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=83.69  E-value=0.52  Score=30.48  Aligned_cols=50  Identities=26%  Similarity=0.573  Sum_probs=33.9

Q ss_pred             CccccccccccccCCCeeEEe--CCCCcccHHhHHHHHhc-------CCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISL--QCSHVHHRHCILKWLVT-------GNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L--pC~H~Fh~~CI~~Wl~~-------~~~CPlCR~~i~  203 (210)
                      +...|.||.......+...++  .|.-.||..|+.+-+..       .=.||.|+....
T Consensus         5 ~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~~   63 (66)
T 2yt5_A            5 SSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFATT   63 (66)
T ss_dssp             CCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTTS
T ss_pred             CCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCccc
Confidence            567899999875442323333  89999999999875432       226999976543

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A

Probab=83.27  E-value=0.89  Score=44.45  Aligned_cols=48  Identities=17%  Similarity=0.121  Sum_probs=41.7

Q ss_pred             CccccccccccccCCCeeEEeCCC-CcccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCS-HVHHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~-H~Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      +.-.|+|-++-+.+   ++++|-| +.|-+.+|.+||..+.+||+=|.++..
T Consensus       890 ~~F~cPIs~~lM~D---PVilpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~~  938 (968)
T 3m62_A          890 DEFLDPLMYTIMKD---PVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKL  938 (968)
T ss_dssp             GGGBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             HHhCCcchhhHHhC---CeEcCCCCEEECHHHHHHHHhcCCCCCCCCCCCCc
Confidence            56679999999865   7889987 699999999999999999999988853

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=83.12  E-value=0.13  Score=33.69  Aligned_cols=44  Identities=23%  Similarity=0.632  Sum_probs=31.4

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCC----CCCccCcC
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGN----NCPTCRFT  201 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~----~CPlCR~~  201 (210)
                      .+..|.||...   ++ +..- .|...||..|+.+-+...+    .||.|...
T Consensus         7 ~~~~C~vC~~~---g~-ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~   55 (66)
T 1xwh_A            7 NEDECAVCRDG---GE-LICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQA   55 (66)
T ss_dssp             CCCSBSSSSCC---SS-CEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHT
T ss_pred             CCCCCccCCCC---CC-EEEcCCCChhhcccccCCCcCcCCCCCeECccccCc
Confidence            45689999864   33 3333 7999999999987665432    59999654

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=82.91  E-value=0.32  Score=35.09  Aligned_cols=46  Identities=22%  Similarity=0.418  Sum_probs=30.8

Q ss_pred             ccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCC----CCCccCc
Q 041711          155 QERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGN----NCPTCRF  200 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~----~CPlCR~  200 (210)
                      -..|.||...-.+.+.+..- .|...||..|+.+-|...+    .||.|+.
T Consensus        61 C~~C~vC~~~~~~~~~ll~Cd~C~~~yH~~Cl~p~l~~~P~~~W~C~~C~~  111 (112)
T 3v43_A           61 CKTCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRP  111 (112)
T ss_dssp             TCCBTTTCCCCCTTCCCEECTTTCCEECGGGCSSCCSSCCSSCCCCTTTSC
T ss_pred             CCccccccCcCCCccceEEcCCCCCeeecccCCCCCCCCCCCCeECCCCCC
Confidence            34688888642222233333 7999999999987666532    6999975

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=81.16  E-value=0.55  Score=33.13  Aligned_cols=44  Identities=25%  Similarity=0.391  Sum_probs=28.9

Q ss_pred             cccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC---CCCCccCc
Q 041711          156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG---NNCPTCRF  200 (210)
Q Consensus       156 ~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~---~~CPlCR~  200 (210)
                      ..| ||-.....+..+..=.|.-.||..|+..=+..-   -.||.|+.
T Consensus        29 vrC-iC~~~~~~~~mi~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~   75 (98)
T 2lv9_A           29 TRC-ICGFTHDDGYMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQP   75 (98)
T ss_dssp             CCC-TTSCCSCSSCEEEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSS
T ss_pred             EEe-ECCCccCCCcEEEcCCCCCcCcCcCCCCCccCCCCCEECCCCcC
Confidence            457 887765544322222899999999997633322   37999974

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=80.16  E-value=1.9  Score=32.53  Aligned_cols=43  Identities=30%  Similarity=0.603  Sum_probs=31.5

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHh---------c--CCCCCccCc
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLV---------T--GNNCPTCRF  200 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~---------~--~~~CPlCR~  200 (210)
                      .++.|.+|-+.   |+ +... .|...||..||.+-+.         .  .=.||+|+.
T Consensus        62 ~~d~C~vC~~G---G~-LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~  116 (142)
T 2lbm_A           62 MDEQCRWCAEG---GN-LICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHP  116 (142)
T ss_dssp             CBCSCSSSCCC---SS-EEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCC
T ss_pred             CCCeecccCCC---Cc-EEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccC
Confidence            45679999864   44 4334 8999999999997663         1  226999975

---

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	210
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	1e-13
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	6e-12
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	7e-09
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-08
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	5e-08
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	1e-07
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	3e-07
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	5e-07
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	5e-06
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	6e-06
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	7e-06
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	2e-05
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	2e-04
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	2e-04

>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 = 61.0 bits (148), Expect = 1e-13
 Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 158 CVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTCRFTL 202
           C +CL E  +G+E   L +C H  H  C+  WL + + CP CR T+
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 56.9 bits (137), Expect = 6e-12
 Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 2/48 (4%)

Query: 156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP 203
           ERC ICLE+ S  +  ++L C H     CI +W+     CP C+  + 
Sbjct: 6   ERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE 51

>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 = 49.0 bits (116), Expect = 7e-09
 Identities = 15/62 (24%), Positives = 20/62 (32%), Gaps = 15/62 (24%)

Query: 153 LGQERCVICLEEFSE---------------GDEVISLQCSHVHHRHCILKWLVTGNNCPT 197
           +  + C IC     +                  V    C+H  H HCI +WL T   CP 
Sbjct: 19  IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 78

Query: 198 CR 199
             
Sbjct: 79  DN 80

>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 = 48.1 bits (114), Expect = 1e-08
 Identities = 13/48 (27%), Positives = 19/48 (39%), Gaps = 4/48 (8%)

Query: 156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNN-CPTCRFTL 202
           + C IC E      +V    C H+    C+  W  +    CP CR  +
Sbjct: 24  QLCKICAEND---KDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEI 68

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.6 bits (108), Expect = 5e-08
 Identities = 13/49 (26%), Positives = 15/49 (30%), Gaps = 6/49 (12%)

Query: 157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCT 205
           RC  C  E         L C H     C+      G  CP C+   P  
Sbjct: 8   RCQQCQAEA---KCPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLG 50

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.2 bits (106), Expect = 1e-07
 Identities = 11/51 (21%), Positives = 15/51 (29%), Gaps = 3/51 (5%)

Query: 155 QERCVICLEEFSEGDE--VISLQCSHVHHRHCILKWLVTGNN-CPTCRFTL 202
            + C  C           ++   C H     C+    V G   CP C   L
Sbjct: 3   DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 53

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 3e-07
 Identities = 12/44 (27%), Positives = 16/44 (36%), Gaps = 2/44 (4%)

Query: 158 CVICLEEFSEGDEVI-SLQCSHVHHRHCILKWLVTGN-NCPTCR 199
           C +C+E     D       C +   R C  +     N  CP CR
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACR 46

>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 = 44.1 bits (104), Expect = 5e-07
 Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 4/46 (8%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWL-VTGNNCPTCRFTL 202
           C IC        + +   C H+  R CIL+ L V G+ CP+CR+  
Sbjct: 26  CQICEHIL---ADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPC 68

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.9 bits (97), Expect = 5e-06
 Identities = 17/71 (23%), Positives = 24/71 (33%), Gaps = 20/71 (28%)

Query: 156 ERCVICLEEF---------------SEGDEVISLQCSHVHHRHCILKWLVTGNN-----C 195
           E C+IC+E+                         +CSH  H  C+L     GN      C
Sbjct: 26  EDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQC 85

Query: 196 PTCRFTLPCTT 206
           P+C+      T
Sbjct: 86  PSCKTIYGEKT 96

>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 = 41.2 bits (96), Expect = 6e-06
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 6/50 (12%)

Query: 157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNN---CPTCRFTLP 203
            C ICLE      E +S +C H+  + C+LK L        CP C+  + 
Sbjct: 23  ECPICLELI---KEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDIT 69

>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 = 40.8 bits (95), Expect = 7e-06
 Identities = 10/54 (18%), Positives = 17/54 (31%), Gaps = 8/54 (14%)

Query: 154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNN--------CPTCR 199
           G   C +CL E+         QC  +    C+ +++             CP   
Sbjct: 4   GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA 57

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

 Score = 38.7 bits (89), Expect = 2e-05
 Identities = 13/48 (27%), Positives = 14/48 (29%), Gaps = 4/48 (8%)

Query: 158 CVICLEEFSEGDEV--ISLQCSHVHHRHCILKWLVTGNN--CPTCRFT 201
           C IC EE                  HR C+  WL    N  C  C   
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 = 37.5 bits (86), Expect = 2e-04
 Identities = 11/43 (25%), Positives = 16/43 (37%), Gaps = 4/43 (9%)

Query: 157 RCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCR 199
           RC  C       + V    C H+   +C+   +  G  CP C 
Sbjct: 24  RCSRCTNILR--EPVCLGGCEHIFCSNCVSDCI--GTGCPVCY 62

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 36.3 bits (83), Expect = 2e-04
 Identities = 7/45 (15%), Positives = 16/45 (35%), Gaps = 2/45 (4%)

Query: 158 CVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTL 202
           C I  +       V+S +   +  +  + +++    N P     L
Sbjct: 3   CAISGKVPR--RPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPL 45

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	210
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.72
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.59
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.53
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.52
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.46
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.46
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.46
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.34
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.32
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.26
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.25
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.19
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.09
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.08
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.06
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.84
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.63
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	94.03
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	92.14
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	88.96
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	87.86
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	85.86
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	85.26
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	83.48
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	83.36

>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=99.72  E-value=1.3e-18  Score=112.29  Aligned_cols=50  Identities=36%  Similarity=0.893  Sum_probs=45.7

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      ++.+|+||+++|..++.++.+ +|+|.||..||.+||+.+.+||+||++|.
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            456799999999999988888 69999999999999999999999999873

>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=99.59  E-value=3.1e-16  Score=105.08  Aligned_cols=48  Identities=35%  Similarity=0.826  Sum_probs=42.3

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      ..+.|+||++.|.+  .++.++|+|.||..||.+|+..+++||+||+++.
T Consensus         4 ~~d~C~IC~~~~~~--~~~~~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~   51 (68)
T d1chca_           4 VAERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCCccCCcCccC--CcEEeCCCCcCcHHHHHHHHHhCCcCCCCCcchH
Confidence            45679999999864  4566799999999999999999999999999884

>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=99.53  E-value=8.2e-16  Score=97.74  Aligned_cols=48  Identities=25%  Similarity=0.551  Sum_probs=40.7

Q ss_pred             ccccccccccCCCee-EEeCCCCcccHHhHHHHHhcC-CCCCccCcCCCC
Q 041711          157 RCVICLEEFSEGDEV-ISLQCSHVHHRHCILKWLVTG-NNCPTCRFTLPC  204 (210)
Q Consensus       157 ~C~ICle~~~~~~~~-~~LpC~H~Fh~~CI~~Wl~~~-~~CPlCR~~i~~  204 (210)
                      +|+||+++|..++.. ..++|+|.||..|+.+|++.. .+||+||+++.+
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            699999999876543 445999999999999999864 579999999865

>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=99.52  E-value=3.4e-15  Score=104.81  Aligned_cols=50  Identities=30%  Similarity=0.551  Sum_probs=41.8

Q ss_pred             CccccccccccccCCC---------------eeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCC
Q 041711          154 GQERCVICLEEFSEGD---------------EVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLP  203 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~---------------~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~  203 (210)
                      ..+.|+||++.+....               .+..++|+|.||..||.+||..+.+||+||+++.
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            4457999999886422               2566799999999999999999999999999863

>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=99.46  E-value=1e-14  Score=96.77  Aligned_cols=52  Identities=21%  Similarity=0.481  Sum_probs=41.1

Q ss_pred             CccccccccccccCCC--eeEEeCCCCcccHHhHHHHHhc-CCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGD--EVISLQCSHVHHRHCILKWLVT-GNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~--~~~~LpC~H~Fh~~CI~~Wl~~-~~~CPlCR~~i~~~  205 (210)
                      ++..|+||++.+..+.  ...+++|+|.||..||.+|++. +.+||+||.++...
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~   56 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCcccc
Confidence            3568999999875433  3455699999999999999976 45899999998543

>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=99.46  E-value=2.5e-14  Score=98.35  Aligned_cols=48  Identities=31%  Similarity=0.729  Sum_probs=40.9

Q ss_pred             ccccccccccccCCCeeEEeCCCCcccHHhHHHHHhc-CCCCCccCcCCCCC
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT-GNNCPTCRFTLPCT  205 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~-~~~CPlCR~~i~~~  205 (210)
                      ...|+||++.+..   +++++|||.||..||..||.. +++||+||..|...
T Consensus        23 ~~~C~IC~~~~~~---~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~   71 (79)
T d1fbva4          23 FQLCKICAENDKD---VKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT   71 (79)
T ss_dssp             TTBCTTTSSSBCC---EECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCC
T ss_pred             CCCCccCCCcCCC---eEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCC
Confidence            3569999998754   778899999999999999975 57899999999644

>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=99.46  E-value=2.2e-14  Score=104.91  Aligned_cols=52  Identities=29%  Similarity=0.649  Sum_probs=40.8

Q ss_pred             CccccccccccccCC---------------CeeEEeCCCCcccHHhHHHHHhcC-----CCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEG---------------DEVISLQCSHVHHRHCILKWLVTG-----NNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~---------------~~~~~LpC~H~Fh~~CI~~Wl~~~-----~~CPlCR~~i~~~  205 (210)
                      .++.|+||+++|...               ..+..++|+|.||..||..||..+     .+||+||..+..+
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             ccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            345799999998542               234566999999999999999864     3799999987544

>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=99.34  E-value=1.4e-13  Score=88.54  Aligned_cols=46  Identities=11%  Similarity=0.141  Sum_probs=40.2

Q ss_pred             ccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          157 RCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       157 ~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      .|+||++.+.+   ++.+ .|||.||..||.+|+..+++||+||.++..+
T Consensus         2 ~C~Ic~~~~~~---Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~   48 (56)
T d2baya1           2 LCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   48 (56)
T ss_dssp             CCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             CCccCCchHHh---cCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHH
Confidence            59999999864   6566 6999999999999999999999999988543

>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=99.32  E-value=3.9e-13  Score=93.75  Aligned_cols=47  Identities=32%  Similarity=0.763  Sum_probs=40.3

Q ss_pred             ccccccccccccCCCeeEEeCCCCcccHHhHHHHHhc-CCCCCccCcCCCC
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT-GNNCPTCRFTLPC  204 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~-~~~CPlCR~~i~~  204 (210)
                      .-.|+||++.+.+   +++++|||.||..||.+|++. ++.||+||.++..
T Consensus        23 ~l~C~IC~~~~~~---pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~   70 (86)
T d1rmda2          23 SISCQICEHILAD---PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFP   70 (86)
T ss_dssp             HTBCTTTCSBCSS---EEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CcCCccCCcchhc---ceecCCCChhhHHHHHHHHhhCCCcCcccCCCCCh
Confidence            3579999999865   678899999999999999975 4689999998853

>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=99.26  E-value=1e-12  Score=94.30  Aligned_cols=47  Identities=34%  Similarity=0.779  Sum_probs=39.7

Q ss_pred             cccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC---CCCCccCcCCCCC
Q 041711          156 ERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG---NNCPTCRFTLPCT  205 (210)
Q Consensus       156 ~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~---~~CPlCR~~i~~~  205 (210)
                      -.|+||++.|..   ++.++|||.||..||..|+..+   ..||+||.++...
T Consensus        22 l~CpIC~~~~~~---pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (103)
T d1jm7a_          22 LECPICLELIKE---PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (103)
T ss_dssp             TSCSSSCCCCSS---CCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             cCCCccCchhCC---eEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChh
Confidence            469999999865   5568999999999999999775   3799999988543

>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=99.25  E-value=3.3e-13  Score=86.69  Aligned_cols=45  Identities=29%  Similarity=0.524  Sum_probs=37.9

Q ss_pred             ccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          155 QERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      .-+|+||++.|.+   ++.+||+|.||..||..|   +.+||+||++++..
T Consensus         6 ~l~C~IC~~~~~~---p~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T d1bora_           6 FLRCQQCQAEAKC---PKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CSSCSSSCSSCBC---CSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             CCCCcccCcccCC---CEEecCCCHHhHHHHHcC---CCcCcCCCCcccCC
Confidence            3479999999875   457899999999999765   67899999999654

>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=99.19  E-value=6.1e-12  Score=81.59  Aligned_cols=48  Identities=27%  Similarity=0.613  Sum_probs=37.7

Q ss_pred             CccccccccccccCCCeeEEeCC-----CCcccHHhHHHHHhc--CCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQC-----SHVHHRHCILKWLVT--GNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC-----~H~Fh~~CI~~Wl~~--~~~CPlCR~~i~~  204 (210)
                      +...|.||++++....   +.+|     +|.||..||.+|+..  +.+||+||+++..
T Consensus         5 d~~~C~IC~~~~~~~~---~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           5 DVPVCWICNEELGNER---FRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             SCCEETTTTEECSCCC---CCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCccCCccCCCce---eEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            5568999999986532   2344     599999999999964  4689999998753

>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=99.09  E-value=5.8e-11  Score=80.72  Aligned_cols=49  Identities=31%  Similarity=0.521  Sum_probs=42.2

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC-CCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG-NNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~-~~CPlCR~~i~~~  205 (210)
                      ++..|+||++.|.+   +++++|||.||..||..|+..+ ..||.|+.++...
T Consensus         7 ~~l~CpIc~~~m~d---PV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~   56 (78)
T d1t1ha_           7 EYFRCPISLELMKD---PVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             SSSSCTTTSCCCSS---EEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             ccCCCcCcCchhhC---ceEccCCCcchHHHHHHHHHHCCCCCCcccccCCcc
Confidence            45689999999865   6678999999999999999875 5799999988654

>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=99.08  E-value=3.9e-11  Score=82.05  Aligned_cols=48  Identities=21%  Similarity=0.083  Sum_probs=41.4

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhc-CCCCCccCcCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVT-GNNCPTCRFTLPC  204 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~-~~~CPlCR~~i~~  204 (210)
                      +...|+||++.|.+   ++.++|||.||..||..|+.. +.+||+||.++..
T Consensus         6 ~~l~CpIc~~l~~d---Pv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~   54 (80)
T d2c2la2           6 DYLCGKISFELMRE---PCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQ   54 (80)
T ss_dssp             STTBCTTTCSBCSS---EEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             ccccCcCcCchhhh---hcccCCcCeecHHHHHHHHhcCCccCCCccccccc
Confidence            45689999999865   667899999999999999986 4589999998853

>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=99.06  E-value=1.3e-11  Score=87.50  Aligned_cols=45  Identities=24%  Similarity=0.584  Sum_probs=36.9

Q ss_pred             ccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCCCCCccCcCCCC
Q 041711          155 QERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTCRFTLPC  204 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~~CPlCR~~i~~  204 (210)
                      .-.|+||++.|..   ++.+ +|||.||..||..|+.  ..||+||.++..
T Consensus        22 ~l~C~IC~~~~~~---pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~   67 (97)
T d1jm7b_          22 LLRCSRCTNILRE---PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWI   67 (97)
T ss_dssp             TTSCSSSCSCCSS---CBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSC
T ss_pred             cCCCccCCchhhc---CceeCCCCCchhHHHHHHHHh--ccccccCCcCch
Confidence            3579999999965   3344 8999999999999985  459999998754

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Ubiquitin conjugation factor E4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.84  E-value=1.6e-09  Score=76.74  Aligned_cols=49  Identities=18%  Similarity=0.131  Sum_probs=42.5

Q ss_pred             CccccccccccccCCCeeEEeCCC-CcccHHhHHHHHhcCCCCCccCcCCCCC
Q 041711          154 GQERCVICLEEFSEGDEVISLQCS-HVHHRHCILKWLVTGNNCPTCRFTLPCT  205 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~-H~Fh~~CI~~Wl~~~~~CPlCR~~i~~~  205 (210)
                      +...|+||++.|.+   +++++|+ |.|+..||..||..+.+||+||.++...
T Consensus        21 ~~f~CPI~~~lm~d---PV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~   70 (98)
T d1wgma_          21 DEFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMD   70 (98)
T ss_dssp             TTTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTT
T ss_pred             HHhCCcCchhHHHH---HHhcccccchhhHHHHHHHHHhcCCcccccccccch
Confidence            46789999999876   7788766 5899999999999999999999998643

>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=98.63  E-value=5.6e-09  Score=72.88  Aligned_cols=47  Identities=21%  Similarity=0.538  Sum_probs=37.5

Q ss_pred             CccccccccccccCCCeeEEeCCCCcccHHhHHHHHhcC----C----CCCccCc
Q 041711          154 GQERCVICLEEFSEGDEVISLQCSHVHHRHCILKWLVTG----N----NCPTCRF  200 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~LpC~H~Fh~~CI~~Wl~~~----~----~CPlCR~  200 (210)
                      +...|+||++++...+.+..++|+|.||..|+..|+..+    .    .||.|+-
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            456899999999776656666999999999999999742    1    5998643

>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=94.03  E-value=0.0093  Score=35.61  Aligned_cols=43  Identities=26%  Similarity=0.659  Sum_probs=30.3

Q ss_pred             ccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCC----CCCccCc
Q 041711          157 RCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGN----NCPTCRF  200 (210)
Q Consensus       157 ~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~----~CPlCR~  200 (210)
                      .|.||-..-..+ ....- .|...||..|+.+-+...+    .||.||.
T Consensus         2 ~C~vC~~~~~~~-~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCC-CEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            488887654332 23323 7999999999998776533    5999975

>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=92.14  E-value=0.024  Score=36.09  Aligned_cols=46  Identities=26%  Similarity=0.562  Sum_probs=31.9

Q ss_pred             ccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCC----CCCccCcCCCC
Q 041711          155 QERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGN----NCPTCRFTLPC  204 (210)
Q Consensus       155 ~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~----~CPlCR~~i~~  204 (210)
                      ...|.||...   ++ +..- .|...||..|+.+.+...+    .||.|+..-..
T Consensus         7 c~~C~~C~~~---~~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~~   57 (70)
T d1fp0a1           7 ATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDL   57 (70)
T ss_dssp             SSCCSSSCSS---SC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCSS
T ss_pred             CCCCCCCCCc---CE-EEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCcc
Confidence            4567777643   44 3333 8999999999998876543    59999765433

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.96  E-value=0.028  Score=34.75  Aligned_cols=45  Identities=27%  Similarity=0.575  Sum_probs=31.0

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcC----CCCCccCcCC
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTG----NNCPTCRFTL  202 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~----~~CPlCR~~i  202 (210)
                      ..+.|.+|.+.   ++ ++.- .|.-.||..|+...+...    -.||.|+...
T Consensus         8 ~~~~C~~C~~~---g~-lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           8 HMEFCRVCKDG---GE-LLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SCSSCTTTCCC---SS-CBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CcCCCcCCCCC---Ce-EEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            34579999753   44 2222 799999999998766542    2699997643

>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=87.86  E-value=0.13  Score=31.66  Aligned_cols=48  Identities=21%  Similarity=0.475  Sum_probs=34.1

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhc-----CCCCCccCcC
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVT-----GNNCPTCRFT  201 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~-----~~~CPlCR~~  201 (210)
                      ....|.||......++..+.- .|+.-||..|+..=...     +-.||.|+..
T Consensus         5 ~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            456899999887766554444 89999999999642221     2379999764

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.86  E-value=0.21  Score=32.73  Aligned_cols=31  Identities=26%  Similarity=0.727  Sum_probs=24.0

Q ss_pred             CccccccccccccCCCeeEEeC---CCCcccHHhHHHH
Q 041711          154 GQERCVICLEEFSEGDEVISLQ---CSHVHHRHCILKW  188 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~Lp---C~H~Fh~~CI~~W  188 (210)
                      .+..|.|| +.+...+   .+|   |+-+||..|+.+-
T Consensus        14 ~D~mC~vC-~v~t~~~---l~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          14 NDEMCDVC-EVWTAES---LFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CSCCCTTT-CCCCSSC---CSSCSSSSSCCCHHHHHHH
T ss_pred             cCcccccc-Ccccccc---eecceeecchhhHHHHHHh
Confidence            56789999 6776544   335   6899999999986

>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=85.26  E-value=0.033  Score=36.85  Aligned_cols=48  Identities=17%  Similarity=0.465  Sum_probs=31.2

Q ss_pred             ccccccccccccCCC-eeEEe-CCCCcccHHhHHHHHh-----c---CCCCCccCcCC
Q 041711          155 QERCVICLEEFSEGD-EVISL-QCSHVHHRHCILKWLV-----T---GNNCPTCRFTL  202 (210)
Q Consensus       155 ~~~C~ICle~~~~~~-~~~~L-pC~H~Fh~~CI~~Wl~-----~---~~~CPlCR~~i  202 (210)
                      ...|.||........ .++.- .|...||..|+.+.+.     .   .-.||.|....
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~   73 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQM   73 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHH
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchH
Confidence            456999987544322 23333 7999999999875432     1   23699997543

>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=83.48  E-value=1.6  Score=27.67  Aligned_cols=46  Identities=17%  Similarity=0.404  Sum_probs=30.5

Q ss_pred             ccccccccccCCCeeEEe-CCCCcccHHhHHH--HHhc---CCCCCccCcCC
Q 041711          157 RCVICLEEFSEGDEVISL-QCSHVHHRHCILK--WLVT---GNNCPTCRFTL  202 (210)
Q Consensus       157 ~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~--Wl~~---~~~CPlCR~~i  202 (210)
                      .+-||...+..++..+.- .|.--||..|+..  .-..   +-.||.|+...
T Consensus        13 v~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~   64 (79)
T d1wepa_          13 VYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             eEeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCc
Confidence            344998876654434334 8999999999952  2111   24799998754

>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=83.36  E-value=0.24  Score=30.29  Aligned_cols=44  Identities=25%  Similarity=0.514  Sum_probs=30.0

Q ss_pred             CccccccccccccCCCeeEEe-CCCCcccHHhHHHHHhcCCCCCcc
Q 041711          154 GQERCVICLEEFSEGDEVISL-QCSHVHHRHCILKWLVTGNNCPTC  198 (210)
Q Consensus       154 ~~~~C~ICle~~~~~~~~~~L-pC~H~Fh~~CI~~Wl~~~~~CPlC  198 (210)
                      ....|.-|+..+.+. ....- .|++.||.+|=.---..-..||-|
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            346799999988643 33333 799999999954322233579987