Citrus Sinensis ID: 028116

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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
MDDLEFEDPNLFQSIPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVELLEASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSYDVNDTDCRALSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHcHHHHHHHHHHHccccccccccccccccccccccccHHHHHcccEEEEEcccccccccccHHHHccccccccccccccccccccccHHHHHHccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEcHHHHHHHHHHHEHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHccccccccccccccccccccccHHHHHHccEEEEEcccccccccccEEEHHccccccEEEEcccccccccHHHHHHHHHHccccccccccc
Coil and Loop (DISEMBL)
mddlefedpnlfqsIPKFIAGAISGTLTGLFALAGAFTGAITGALagrasdcgvlrgAGLGAIAGAVLSVELLEASRAYWCLertgsrgsssmADFVEDLLRGrfieeqftpaILGAYHWQVRIASmsydvndtdcralsrgltgeslkklpchvildeikptqssccsiclqdIIVGElarslphchhtfHLACVDKWlirhgscpvcrrdv
Flexible Loop (DISEMBL)
MDDLEFEDPNLFQSIPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVELLEASRAYWCLErtgsrgsssmADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSYDVNDTDCRALsrgltgeslkklPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV
Low Complexity Region (SEG)
MDDLEFEDPNLFQSIPKFIAGAISgtltglfalagaftgaitgalagRASDCgvlrgaglgaiagavlsvELLEASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSYDVNDTDCRALSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV
Disordered region (IsUnstruct)
**********LFQSIPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVELLEASRAYWCLERTG******MADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSYDVNDTDCRALSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVC****
Disordered Region (DISOPRED)
*********NLFQSIPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVELLEASRAY***********SSMADFVEDLLRGRFIEEQFTPAILGAYHWQ************************ESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD*
Disordered Region (DISEMBL)
MDDLEFEDPNLFQSIPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVELLEASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSYDVNDTDCRALSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV
Disordered Region (DISPRO)
*****FEDPNLFQSIPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVELLEASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSYDVNDTDCRALSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVC****
Transmembrane Helix (TMHMM)
ooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDDLEFEDPNLFQSIPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVELLEASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSYDVNDTDCRALSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV
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	213	2.2.26 [Sep-21-2011]
Q8LBA0	223	NEP1-interacting protein-	yes	no	0.938	0.896	0.611	2e-64
Q9FKX5	221	NEP1-interacting protein-	no	no	0.929	0.895	0.442	7e-42
Q8GT74	241	NEP1-interacting protein	no	no	0.877	0.775	0.437	1e-40
Q8GT75	236	NEP1-interacting protein	no	no	0.882	0.796	0.419	1e-37
Q9FLC6	176	RING-H2 finger protein AT	no	no	0.347	0.420	0.4	8e-12
Q9LS99	220	RING-H2 finger protein AT	no	no	0.342	0.331	0.445	9e-12
Q94BY6	226	RING-H2 finger protein AT	no	no	0.366	0.345	0.405	1e-11
Q8RX29	217	RING-H2 finger protein AT	no	no	0.319	0.313	0.457	5e-11
Q9Y252	685	E3 ubiquitin-protein liga	yes	no	0.384	0.119	0.369	6e-11
Q8L9T5	304	RING-H2 finger protein AT	no	no	0.319	0.223	0.410	6e-11

>sp|Q8LBA0|NIPL2_ARATH NEP1-interacting protein-like 2 OS=Arabidopsis thaliana GN=ATL24 PE=1 SV=2

 Score =  245 bits (625), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 123/201 (61%), Positives = 158/201 (78%), Gaps = 1/201 (0%)

Query: 14  SIPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVELL 73
           ++ + IAG  SG LTG+FA+AGAFTGA+TGA+AGRA+  GVLRGA LGA+AGA+LSVE+L
Sbjct: 21  TVSRLIAGVFSGALTGIFAMAGAFTGAVTGAVAGRAAQYGVLRGAALGAVAGAILSVEVL 80

Query: 74  EASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSYDV-N 132
           EASRAYW LE +GSRG SSMADFVE L RGR ++EQ    ++ ++HWQ+RI+ +SY+   
Sbjct: 81  EASRAYWYLELSGSRGPSSMADFVEQLFRGRLVDEQLMSTMINSHHWQLRISDVSYEERE 140

Query: 133 DTDCRALSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFH 192
           D      +RGL+G+SL+KLPC+++  E+   Q + C+ICLQDI  GE+ RSLP C HTFH
Sbjct: 141 DVYGELEARGLSGDSLRKLPCYIMSSEMVRRQVTHCTICLQDIKTGEITRSLPKCDHTFH 200

Query: 193 LACVDKWLIRHGSCPVCRRDV 213
           L CVDKWLIRHGSCP+CR+ V
Sbjct: 201 LVCVDKWLIRHGSCPICRQAV 221

May be involved in the early steps of the plant defense signaling pathway. Does not display E3 catalytic activity.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9FKX5|NIPL1_ARATH NEP1-interacting protein-like 1 OS=Arabidopsis thaliana GN=ATL27 PE=2 SV=1

 Score =  170 bits (430), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 89/201 (44%), Positives = 122/201 (60%), Gaps = 3/201 (1%)

Query: 14  SIPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVELL 73
           ++   +A   S   T  FAL G   GA+TGAL G+ ++ G +RGA +GAI+GAV S+E+ 
Sbjct: 23  AVSALLANLFSALFTFFFALVGTLLGALTGALIGQETESGFIRGAAVGAISGAVFSIEVF 82

Query: 74  EASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQV-RIASMSYDVN 132
           E+S   W  + +G      + D +  LL GR + E+  PA+L A   Q+  + S   D  
Sbjct: 83  ESSLLLWQSDESGIGCLLYLIDVIASLLSGRLVRERIGPAMLSAVQSQMGAVESQFQDHT 142

Query: 133 DTDCRALSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFH 192
           D    A+S+GLTG+SL ++P  V + +  P   SC S+CLQD  VGE  RSLPHCHH FH
Sbjct: 143 DIFDTAISKGLTGDSLNRIP-KVRITDTSPEIVSC-SVCLQDFQVGETVRSLPHCHHMFH 200

Query: 193 LACVDKWLIRHGSCPVCRRDV 213
           L C+DKWL RH SCP+CRR +
Sbjct: 201 LPCIDKWLRRHASCPLCRRHL 221

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  166 bits (420), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 87/199 (43%), Positives = 119/199 (59%), Gaps = 12/199 (6%)

Query: 23  ISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVELLEASRAYWCL 82
           IS  LT  FAL G   GA+TGAL G+ ++ G +RGA +GAI+GAV S+E+ E+S   W  
Sbjct: 47  ISAILTFFFALVGTLLGALTGALIGQETESGFIRGAAIGAISGAVFSIEVFESSLDLWKS 106

Query: 83  ERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSYDVNDTDCRAL--- 139
           + +G      + D +  LL GR + E+  PA+L A   Q+     ++D    D  +L   
Sbjct: 107 DESGFGCFLYLIDVIVSLLSGRLVRERIGPAMLSAVQSQMGAVDTAFD----DHTSLFDT 162

Query: 140 --SRGLTGESLKKLPCHVILDEIKPTQSS---CCSICLQDIIVGELARSLPHCHHTFHLA 194
             S+GLTG+ ++K+P   I        S     CS+CLQD  +GE  RSLPHCHH FHL 
Sbjct: 163 GGSKGLTGDLVEKIPKMTITGNNNTDASENTDSCSVCLQDFQLGETVRSLPHCHHMFHLP 222

Query: 195 CVDKWLIRHGSCPVCRRDV 213
           C+D WL+RHGSCP+CRRD+
Sbjct: 223 CIDNWLLRHGSCPMCRRDI 241

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q8GT75|NIP1_ARATH NEP1-interacting protein 1 OS=Arabidopsis thaliana GN=NIP1 PE=1 SV=2

 Score =  155 bits (393), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 83/198 (41%), Positives = 116/198 (58%), Gaps = 10/198 (5%)

Query: 23  ISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVELLEASRAYWCL 82
           +S  LT  FAL G   GA+TGAL G+ ++ G +RGA +GAI+GAV S+E+ E+S   W  
Sbjct: 42  LSAVLTFFFALVGTLLGALTGALIGQETESGFIRGAAVGAISGAVFSIEVFESSLVLWKS 101

Query: 83  ERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSYD----VNDTDCRA 138
             +       + D +  L+ GR + E+  PA+L A   Q+     +++    + DT    
Sbjct: 102 NESRFGCLLYLIDVIVSLISGRLVRERIGPAMLSAVQSQMGAVDSTFEELSSIFDT---G 158

Query: 139 LSRGLTGESLKKLPCHVILDEIKPTQS---SCCSICLQDIIVGELARSLPHCHHTFHLAC 195
            S+GLTG+ + K+P   I  +     S     CS+CLQD  +GE  RSLPHCHH FHL C
Sbjct: 159 GSKGLTGDLVDKIPKIKITGKNNLDASGNKDSCSVCLQDFQLGETVRSLPHCHHMFHLPC 218

Query: 196 VDKWLIRHGSCPVCRRDV 213
           +D WL RHGSCP+CRRD+
Sbjct: 219 IDNWLFRHGSCPMCRRDL 236

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 70.5 bits (171), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 47/75 (62%), Gaps = 1/75 (1%)

Query: 139 LSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDK 198
           +++G+   +LK +P      E+K  +++ C ICL D + GE  R LP C+H FH+ C+D 
Sbjct: 85  VAKGIKKRALKVIPVDSYSPELK-MKATECLICLGDFVEGETVRVLPKCNHGFHVKCIDT 143

Query: 199 WLIRHGSCPVCRRDV 213
           WL+ H SCP CR+ +
Sbjct: 144 WLLSHSSCPTCRQSL 158

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LS99|ATL77_ARATH RING-H2 finger protein ATL77 OS=Arabidopsis thaliana GN=ATL77 PE=2 SV=1

 Score = 70.5 bits (171), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 33/74 (44%), Positives = 45/74 (60%), Gaps = 1/74 (1%)

Query: 138 ALSRGLTGESLKKLPCHVILDEIK-PTQSSCCSICLQDIIVGELARSLPHCHHTFHLACV 196
           ++++G+  ++LK LP      EI  P     C ICL D + GE  R LP C+H FHL C+
Sbjct: 99  SVNKGIKKKALKMLPVVNYSPEINLPGVGEECVICLSDFVAGEQLRVLPKCNHGFHLRCI 158

Query: 197 DKWLIRHGSCPVCR 210
           DKWL +H +CP CR
Sbjct: 159 DKWLTQHMTCPKCR 172

Arabidopsis thaliana (taxid: 3702)

>sp|Q94BY6|ATL75_ARATH RING-H2 finger protein ATL75 OS=Arabidopsis thaliana GN=ATL75 PE=2 SV=1

 Score = 69.7 bits (169), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 32/79 (40%), Positives = 45/79 (56%), Gaps = 1/79 (1%)

Query: 133 DTDCRALSRGLTGESLKKLPCHVILDEIK-PTQSSCCSICLQDIIVGELARSLPHCHHTF 191
            T C + ++G+  ++L+  P      E+  P     C ICL D + GE  R LP CHH F
Sbjct: 100 STPCGSSNKGINKKALRMFPVVSYSPEMNLPGLGEECVICLSDFVSGEQIRMLPKCHHGF 159

Query: 192 HLACVDKWLIRHGSCPVCR 210
           H+ C+DKWL +H +CP CR
Sbjct: 160 HVRCIDKWLQQHLTCPKCR 178

Arabidopsis thaliana (taxid: 3702)

>sp|Q8RX29|ATL70_ARATH RING-H2 finger protein ATL70 OS=Arabidopsis thaliana GN=ATL70 PE=2 SV=1

 Score = 67.8 bits (164), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 32/70 (45%), Positives = 44/70 (62%), Gaps = 2/70 (2%)

Query: 142 GLTGESLKKLPCHVILDEIK-PTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWL 200
           GL  ++++  P  ++  E K PT +SCC+ICL D     L R LP C+H FHL C+D WL
Sbjct: 121 GLDEDTIQSYP-KILYSEAKGPTTASCCAICLGDYKGKHLLRQLPDCNHLFHLKCIDTWL 179

Query: 201 IRHGSCPVCR 210
             + +CPVCR
Sbjct: 180 RLNPTCPVCR 189

Arabidopsis thaliana (taxid: 3702)

>sp|Q9Y252|RNF6_HUMAN E3 ubiquitin-protein ligase RNF6 OS=Homo sapiens GN=RNF6 PE=1 SV=1

 Score = 67.4 bits (163), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 31/84 (36%), Positives = 46/84 (54%), Gaps = 2/84 (2%)

Query: 131 VNDTDCRALSRGLTGESLKKLPC-HVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHH 189
           +N++D     RGLT E +  L   H   + I       CS+C+ D + G   R LP C H
Sbjct: 594 LNESDDDDRIRGLTKEQIDNLSTRHYEHNSIDSELGKICSVCISDYVTGNKLRQLP-CMH 652

Query: 190 TFHLACVDKWLIRHGSCPVCRRDV 213
            FH+ C+D+WL  + +CP+CR+ V
Sbjct: 653 EFHIHCIDRWLSENCTCPICRQPV 676

E3 ubiquitin-protein ligase mediating 'Lys-48'-linked polyubiquitination of LIMK1 and its subsequent targeting to the proteasome for degradation. Negatively regulates axonal outgrowth through regulation of the LIMK1 turnover. Mediates 'Lys-6' and 'Lys-27'-linked polyubiquitination of AR/androgen receptor thereby modulating its transcriptional activity. May also bind DNA and function as a transcriptional regulator.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q8L9T5|ATL2_ARATH RING-H2 finger protein ATL2 OS=Arabidopsis thaliana GN=ATL2 PE=2 SV=2

 Score = 67.4 bits (163), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 40/73 (54%), Gaps = 5/73 (6%)

Query: 140 SRGLTGESLKKLPCHVILDEI--KPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVD 197
           SRGL    +K LP     DE    P +   C++CL +    E  R LP+C HTFH+ C+D
Sbjct: 92  SRGLDPNVIKSLPVFTFSDETHKDPIE---CAVCLSEFEESETGRVLPNCQHTFHVDCID 148

Query: 198 KWLIRHGSCPVCR 210
            W   H +CP+CR
Sbjct: 149 MWFHSHSTCPLCR 161

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

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	213
255547343	214	RING-H2 finger protein ATL1Q, putative [	0.981	0.976	0.725	5e-78
225457359	217	PREDICTED: NEP1-interacting protein-like	0.953	0.935	0.735	6e-77
297839315	665	hypothetical protein ARALYDRAFT_339633 [	0.938	0.300	0.626	3e-65
116788582	261	unknown [Picea sitchensis]	0.934	0.762	0.660	2e-64
21592935	223	putative RING zinc finger protein [Arabi	0.938	0.896	0.616	5e-63
18410608	223	NEP1-interacting protein-like 2 [Arabido	0.938	0.896	0.611	9e-63
356512042	223	PREDICTED: NEP1-interacting protein-like	0.995	0.950	0.589	4e-61
351726878	213	uncharacterized protein LOC100306666 [Gl	0.981	0.981	0.580	3e-59
357118274	229	PREDICTED: NEP1-interacting protein-like	0.934	0.868	0.599	1e-58
115448635	220	Os02g0743700 [Oryza sativa Japonica Grou	0.967	0.936	0.588	3e-58

>gi|255547343|ref|XP_002514729.1| RING-H2 finger protein ATL1Q, putative [Ricinus communis] gi|223546333|gb|EEF47835.1| RING-H2 finger protein ATL1Q, putative [Ricinus communis]

 Score =  296 bits (757), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 153/211 (72%), Positives = 179/211 (84%), Gaps = 2/211 (0%)

Query: 4   LEFEDPNLFQSIPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAI 63
           ++FE       +PK +AGAISG LTG FALAGAFTGAI GALAGRAS+CGV RGAGLGAI
Sbjct: 5   VQFEGSRFLDYVPKLVAGAISGALTGFFALAGAFTGAIAGALAGRASNCGVFRGAGLGAI 64

Query: 64  AGAVLSVELLEASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVR 123
           AGAVLSVE+LEASRAYWCLE++GSRG SSMADF+E+LLRGRF +EQF+PA+L  YHWQV 
Sbjct: 65  AGAVLSVEVLEASRAYWCLEQSGSRGPSSMADFMEELLRGRFADEQFSPAVLTTYHWQVS 124

Query: 124 IASMSYD-VNDTDCRALSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELAR 182
           IA++SYD ++D +  A S+GL+G+ LKKLP H  LDEIK  Q+ CC+ICLQDI+ GE+AR
Sbjct: 125 IANLSYDEIHDVNGEAASKGLSGDLLKKLPSHT-LDEIKAKQTICCTICLQDIVKGEIAR 183

Query: 183 SLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           SLP C HTFHLACVDKWLIRHGSCPVCR+DV
Sbjct: 184 SLPRCCHTFHLACVDKWLIRHGSCPVCRQDV 214

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225457359|ref|XP_002284762.1| PREDICTED: NEP1-interacting protein-like 2 [Vitis vinifera] gi|297733952|emb|CBI15199.3| unnamed protein product [Vitis vinifera]

 Score =  292 bits (748), Expect = 6e-77,   Method: Compositional matrix adjust.
 Identities = 150/204 (73%), Positives = 175/204 (85%), Gaps = 1/204 (0%)

Query: 11  LFQSIPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSV 70
           ++  IP+ IAGA+SG LTG+FALAGAFTGAITGA+AGRASD GVLRGAGLGAIAGAVLSV
Sbjct: 14  VYHYIPRLIAGALSGALTGVFALAGAFTGAITGAIAGRASDSGVLRGAGLGAIAGAVLSV 73

Query: 71  ELLEASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSYD 130
           E+LEASRAYWC +R+ S+ S S+ DF+E+LLRGR +EE FTPA+L  Y WQV I ++SYD
Sbjct: 74  EVLEASRAYWCSDRSNSQNSLSITDFIEELLRGRIVEESFTPAVLTTYRWQVSIGNLSYD 133

Query: 131 -VNDTDCRALSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHH 189
            + D      SRGL+G+SLKKLPCHVILDEIK  QS+CC+ICLQDI VGE+ARSLP CHH
Sbjct: 134 EMYDVYGEVASRGLSGDSLKKLPCHVILDEIKAAQSNCCTICLQDIEVGEIARSLPWCHH 193

Query: 190 TFHLACVDKWLIRHGSCPVCRRDV 213
           TFHLACVDKWLIRHG+CPVCRR+V
Sbjct: 194 TFHLACVDKWLIRHGTCPVCRRNV 217

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297839315|ref|XP_002887539.1| hypothetical protein ARALYDRAFT_339633 [Arabidopsis lyrata subsp. lyrata] gi|297333380|gb|EFH63798.1| hypothetical protein ARALYDRAFT_339633 [Arabidopsis lyrata subsp. lyrata]

 Score =  253 bits (647), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 126/201 (62%), Positives = 159/201 (79%), Gaps = 1/201 (0%)

Query: 14  SIPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVELL 73
           ++ + IAGA SG LTG+FA+AGAFTGA+TGA+AGRA+  GVLRGA LGA+AGA+LSVE+L
Sbjct: 463 TVSRLIAGAFSGALTGIFAMAGAFTGAVTGAVAGRAAQYGVLRGAALGAVAGAILSVEVL 522

Query: 74  EASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSYDVND 133
           EASRAYW LE +GSRG SSMADFVE L RGR ++EQ    ++ +YHWQ+RI+ +SY+  D
Sbjct: 523 EASRAYWYLELSGSRGPSSMADFVEQLFRGRLVDEQLMSTMINSYHWQLRISDVSYEERD 582

Query: 134 TDCRAL-SRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFH 192
                L +RGL+G+SL+KLPC ++  E+   Q + C+ICLQDI  GE+ RSLP C HTFH
Sbjct: 583 DVYGELEARGLSGDSLRKLPCFIMSSELVKRQVTHCTICLQDIKTGEITRSLPRCDHTFH 642

Query: 193 LACVDKWLIRHGSCPVCRRDV 213
           L CVDKWLIRHGSCP+CR+ V
Sbjct: 643 LVCVDKWLIRHGSCPICRQAV 663

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116788582|gb|ABK24929.1| unknown [Picea sitchensis]

 Score =  250 bits (639), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 134/203 (66%), Positives = 164/203 (80%), Gaps = 4/203 (1%)

Query: 15  IPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVELLE 74
           +P  ++GA+SG LTG+FALAGAFTGA+TGA+AGRASD G+LRGAGLGA+AGAVLSVE+LE
Sbjct: 59  VPGLLSGALSGALTGMFALAGAFTGAVTGAIAGRASDSGLLRGAGLGAVAGAVLSVEVLE 118

Query: 75  ASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSY-DVND 133
           ASRAYW  ER+GSR SSSMADF+E+LL GRF++EQ  PA+L AY WQV IA MS+ ++ D
Sbjct: 119 ASRAYWYSERSGSRNSSSMADFIEELLNGRFVQEQVGPAMLTAYRWQVNIAEMSHEEIFD 178

Query: 134 TDCRALSRGLTGESLKKLPCHVILDEIKPTQSS---CCSICLQDIIVGELARSLPHCHHT 190
                 ++GL+G SL KLP H+I  E K   S    CC+ICLQD+  GE+ARSLP CHH 
Sbjct: 179 IFGEVGTQGLSGASLAKLPSHLITKENKKDASGENICCTICLQDLQQGEIARSLPLCHHM 238

Query: 191 FHLACVDKWLIRHGSCPVCRRDV 213
           FH++CVDKWLIRHGSCPVCR+D+
Sbjct: 239 FHMSCVDKWLIRHGSCPVCRQDI 261

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21592935|gb|AAM64885.1| putative RING zinc finger protein [Arabidopsis thaliana]

 Score =  246 bits (627), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 124/201 (61%), Positives = 158/201 (78%), Gaps = 1/201 (0%)

Query: 14  SIPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVELL 73
           ++ + IAG  SG LTG+FA+AGAFTGA+TGA+AGRA+  GVLRGA LGA+AGA+LSVE+L
Sbjct: 21  TVSRLIAGVFSGALTGIFAMAGAFTGAVTGAVAGRAAQYGVLRGAALGAVAGAILSVEVL 80

Query: 74  EASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSYDV-N 132
           EASRAYW LE +GSRG SSMADFVE L RGR ++EQ    I+ ++HWQ+RI+ +SY+   
Sbjct: 81  EASRAYWYLELSGSRGPSSMADFVEQLFRGRLVDEQLMSTIINSHHWQLRISDVSYEERE 140

Query: 133 DTDCRALSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFH 192
           D      +RGL+G+SL+KLPC+++  E+   Q + C+ICLQDI  GE+ RSLP C HTFH
Sbjct: 141 DVYGELEARGLSGDSLRKLPCYIMSSEMVRRQVTHCTICLQDIKTGEITRSLPKCDHTFH 200

Query: 193 LACVDKWLIRHGSCPVCRRDV 213
           L CVDKWLIRHGSCP+CR+ V
Sbjct: 201 LVCVDKWLIRHGSCPICRQAV 221

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18410608|ref|NP_565085.1| NEP1-interacting protein-like 2 [Arabidopsis thaliana] gi|68565204|sp|Q8LBA0.2|NIPL2_ARATH RecName: Full=NEP1-interacting protein-like 2; AltName: Full=RING-H2 finger protein ATL24 gi|15215808|gb|AAK91449.1| At1g74410/F1M20_9 [Arabidopsis thaliana] gi|20147407|gb|AAM10413.1| At1g74410/F1M20_9 [Arabidopsis thaliana] gi|66865914|gb|AAY57591.1| RING finger family protein [Arabidopsis thaliana] gi|332197467|gb|AEE35588.1| NEP1-interacting protein-like 2 [Arabidopsis thaliana]

 Score =  245 bits (625), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 123/201 (61%), Positives = 158/201 (78%), Gaps = 1/201 (0%)

Query: 14  SIPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVELL 73
           ++ + IAG  SG LTG+FA+AGAFTGA+TGA+AGRA+  GVLRGA LGA+AGA+LSVE+L
Sbjct: 21  TVSRLIAGVFSGALTGIFAMAGAFTGAVTGAVAGRAAQYGVLRGAALGAVAGAILSVEVL 80

Query: 74  EASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSYDV-N 132
           EASRAYW LE +GSRG SSMADFVE L RGR ++EQ    ++ ++HWQ+RI+ +SY+   
Sbjct: 81  EASRAYWYLELSGSRGPSSMADFVEQLFRGRLVDEQLMSTMINSHHWQLRISDVSYEERE 140

Query: 133 DTDCRALSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFH 192
           D      +RGL+G+SL+KLPC+++  E+   Q + C+ICLQDI  GE+ RSLP C HTFH
Sbjct: 141 DVYGELEARGLSGDSLRKLPCYIMSSEMVRRQVTHCTICLQDIKTGEITRSLPKCDHTFH 200

Query: 193 LACVDKWLIRHGSCPVCRRDV 213
           L CVDKWLIRHGSCP+CR+ V
Sbjct: 201 LVCVDKWLIRHGSCPICRQAV 221

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356512042|ref|XP_003524730.1| PREDICTED: NEP1-interacting protein-like 2-like [Glycine max]

 Score =  239 bits (611), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 128/217 (58%), Positives = 166/217 (76%), Gaps = 5/217 (2%)

Query: 1   MDDLEFEDPNLFQSIPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGL 60
           M+    + P  F+S+ K +   ISG LT  FA+AGA TGAI GALA +A+  G+LRG  L
Sbjct: 1   METGRIQGPWGFRSLSKVVLCTISGALTVCFAIAGALTGAIAGALAAKATKSGLLRGVSL 60

Query: 61  GAIAGAVLSVELLEASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHW 120
           GAIAG++LSVE+LEASRAYWC+E+TGSRG+SSMADF+E+L+RGR +EE  TPAIL AY+ 
Sbjct: 61  GAIAGSILSVEVLEASRAYWCMEQTGSRGASSMADFIEELVRGRLVEESLTPAILTAYNL 120

Query: 121 ---QVRIASMSYD-VNDTDCRALSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDII 176
              QV IA+  YD ++D       RGL+G+SLK+LP H+I  ++K   ++CC+ICLQDI 
Sbjct: 121 QFEQVGIANTGYDEIHDVHGLVAPRGLSGDSLKRLPHHMISKDMK-ADNTCCAICLQDIE 179

Query: 177 VGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           VGE+ARSLP CHHTFHL CVDKWL+++ SCPVCR++V
Sbjct: 180 VGEIARSLPRCHHTFHLICVDKWLVKNDSCPVCRQNV 216

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351726878|ref|NP_001238421.1| uncharacterized protein LOC100306666 [Glycine max] gi|255629221|gb|ACU14955.1| unknown [Glycine max]

 Score =  233 bits (595), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 126/217 (58%), Positives = 162/217 (74%), Gaps = 8/217 (3%)

Query: 1   MDDLEFEDPNLFQSIPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGL 60
           M+    + P  F+S+ KF+   ISG LT  FALAGA TGAI GALA +A+  G+LRG  L
Sbjct: 1   METGIIQGPWGFRSLSKFVLCTISGALTVCFALAGALTGAIAGALAAKATKSGLLRGVSL 60

Query: 61  GAIAGAVLSVELLEASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHW 120
           GAIAG++LSVE+LEASRAYWC+E+TGSR +SSMADF+E+L+RGR +EE  TPAIL AY+ 
Sbjct: 61  GAIAGSILSVEVLEASRAYWCMEQTGSRSASSMADFIEELVRGRLVEESLTPAILTAYNL 120

Query: 121 ---QVRIASMSY-DVNDTDCRALSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDII 176
              QV IA+  Y + +D       RGL+G+SLK+LP H+        +++CC+ICLQDI 
Sbjct: 121 QFEQVGIANTGYVETHDVHGLVAPRGLSGDSLKRLPHHM----FSKAENTCCAICLQDIE 176

Query: 177 VGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           VGE+ARSLP CHHTFHL CVDKWL+++ SCPVCR++V
Sbjct: 177 VGEIARSLPRCHHTFHLICVDKWLVKNDSCPVCRQNV 213

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357118274|ref|XP_003560881.1| PREDICTED: NEP1-interacting protein-like 2-like [Brachypodium distachyon]

 Score =  231 bits (589), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 121/202 (59%), Positives = 153/202 (75%), Gaps = 3/202 (1%)

Query: 15  IPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVELLE 74
           +P+ +AG +SG LTGLFA+AG  TGAITGALAGRASD GVLRGAGLGA AGAVLS+E+LE
Sbjct: 28  LPRLVAGVLSGVLTGLFAVAGGLTGAITGALAGRASDSGVLRGAGLGAFAGAVLSIEVLE 87

Query: 75  ASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASM-SYDVND 133
           ASRAYWC +R+  + +SSM DFV+ L+  RF++EQ+ P++  AY WQV +A   + D++ 
Sbjct: 88  ASRAYWCADRSSPQSTSSMGDFVDQLIHARFVQEQYEPSVYMAYRWQVGVAEFGNDDLHG 147

Query: 134 TDCRALSRGLTGESLKKLPCHVILDEIKPT--QSSCCSICLQDIIVGELARSLPHCHHTF 191
               A S GL+ +SLKKLPCHV+ D+ +    ++  C ICLQDI+ GE AR LP C H+F
Sbjct: 148 ILGEASSYGLSQDSLKKLPCHVVTDQKQEPVDENLSCPICLQDIVTGETARRLPKCSHSF 207

Query: 192 HLACVDKWLIRHGSCPVCRRDV 213
           H  CVDKWLI HGSCPVCR+DV
Sbjct: 208 HQPCVDKWLIGHGSCPVCRQDV 229

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115448635|ref|NP_001048097.1| Os02g0743700 [Oryza sativa Japonica Group] gi|46390629|dbj|BAD16112.1| putative NEP1-interacting protein [Oryza sativa Japonica Group] gi|113537628|dbj|BAF10011.1| Os02g0743700 [Oryza sativa Japonica Group] gi|215687293|dbj|BAG91880.1| unnamed protein product [Oryza sativa Japonica Group] gi|215765618|dbj|BAG87315.1| unnamed protein product [Oryza sativa Japonica Group] gi|218191566|gb|EEC73993.1| hypothetical protein OsI_08908 [Oryza sativa Indica Group]

 Score =  230 bits (587), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 123/209 (58%), Positives = 155/209 (74%), Gaps = 3/209 (1%)

Query: 6   FEDPNLFQSIPKFIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAG 65
            E+  +   +P+ +AG ISG LTGLFALAGA TGA+TGALAGRASD GVLRGAGLGA AG
Sbjct: 10  LEESGVAVYLPRLLAGVISGALTGLFALAGALTGAVTGALAGRASDSGVLRGAGLGAFAG 69

Query: 66  AVLSVELLEASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIA 125
           AVLS+E+LEASRAYWC +R GS G+SSMADF+E LL+ RF++EQ  P+    + WQV I+
Sbjct: 70  AVLSIEVLEASRAYWCSDRLGSHGTSSMADFIEQLLQARFVQEQIVPSGYATHRWQVSIS 129

Query: 126 SMSY-DVNDTDCRALSRGLTGESLKKLPCHVILDEIKPT--QSSCCSICLQDIIVGELAR 182
              + D+ D      S+GL+ ESL KLP +V+ D+ + +  +   C+ICLQDI+ GE AR
Sbjct: 130 DFGHDDLYDIFGDCSSKGLSRESLNKLPHYVVTDQTRNSFGEDLSCTICLQDIVTGETAR 189

Query: 183 SLPHCHHTFHLACVDKWLIRHGSCPVCRR 211
            LP+C HTFH  CVDKWL+ HGSCPVCR+
Sbjct: 190 RLPNCSHTFHQPCVDKWLVGHGSCPVCRQ 218

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	213
TAIR|locus:2019110	223	AT1G74410 [Arabidopsis thalian	0.938	0.896	0.447	7.1e-45
TAIR|locus:2156867	245	AT5G66070 [Arabidopsis thalian	0.361	0.314	0.585	5.9e-29
TAIR|locus:2125364	236	AT4G35840 [Arabidopsis thalian	0.671	0.605	0.380	6.8e-24
TAIR|locus:4010713762	223	AT3G20395 [Arabidopsis thalian	0.511	0.488	0.398	2e-17
TAIR|locus:2153554	176	DAF "DEFECTIVE IN ANTHER DEHIS	0.384	0.465	0.392	3.8e-14
TAIR|locus:2028411	226	AT1G49200 [Arabidopsis thalian	0.361	0.340	0.410	1e-13
TAIR|locus:2830088	220	AT3G18773 [Arabidopsis thalian	0.342	0.331	0.445	1e-13
TAIR|locus:2039170	217	AT2G35910 [Arabidopsis thalian	0.319	0.313	0.457	3.4e-13
TAIR|locus:2193992	324	ATL3 [Arabidopsis thaliana (ta	0.352	0.231	0.428	1.5e-12
TAIR|locus:2181032	159	DAFL2 "DAF-Like gene 2" [Arabi	0.333	0.446	0.424	1.9e-12

TAIR|locus:2019110 AT1G74410 [Arabidopsis thaliana (taxid:3702)]

 Score = 472 (171.2 bits), Expect = 7.1e-45, P = 7.1e-45
 Identities = 90/201 (44%), Positives = 120/201 (59%)

Query:    14 SIPKFIAGAISXXXXXXXXXXXXXXXXXXXXXXXRASDCXXXXXXXXXXXXXXXXXXELL 73
             ++ + IAG  S                       RA+                    E+L
Sbjct:    21 TVSRLIAGVFSGALTGIFAMAGAFTGAVTGAVAGRAAQYGVLRGAALGAVAGAILSVEVL 80

Query:    74 EASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSYDVND 133
             EASRAYW LE +GSRG SSMADFVE L RGR ++EQ    ++ ++HWQ+RI+ +SY+  +
Sbjct:    81 EASRAYWYLELSGSRGPSSMADFVEQLFRGRLVDEQLMSTMINSHHWQLRISDVSYEERE 140

Query:   134 TDCRAL-SRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFH 192
                  L +RGL+G+SL+KLPC+++  E+   Q + C+ICLQDI  GE+ RSLP C HTFH
Sbjct:   141 DVYGELEARGLSGDSLRKLPCYIMSSEMVRRQVTHCTICLQDIKTGEITRSLPKCDHTFH 200

Query:   193 LACVDKWLIRHGSCPVCRRDV 213
             L CVDKWLIRHGSCP+CR+ V
Sbjct:   201 LVCVDKWLIRHGSCPICRQAV 221

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

GO:0010200 "response to chitin" evidence=IEP

TAIR|locus:2156867 AT5G66070 [Arabidopsis thaliana (taxid:3702)]

 Score = 255 (94.8 bits), Expect = 5.9e-29, Sum P(2) = 5.9e-29
 Identities = 48/82 (58%), Positives = 59/82 (71%)

Query:   130 DVNDTDCRALSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHH 189
             D+ DT   A+S+GLTG+SL ++P  V + +  P   SC S+CLQD  VGE  RSLPHCHH
Sbjct:   167 DIFDT---AISKGLTGDSLNRIP-KVRITDTSPEIVSC-SVCLQDFQVGETVRSLPHCHH 221

Query:   190 TFHLACVDKWLIRHGSCPVCRR 211
              FHL C+DKWL RH SCP+CRR
Sbjct:   222 MFHLPCIDKWLRRHASCPLCRR 243

GO:0005739 "mitochondrion" evidence=ISM

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

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

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

GO:0035556 "intracellular signal transduction" evidence=RCA

TAIR|locus:2125364 AT4G35840 [Arabidopsis thaliana (taxid:3702)]

 Score = 274 (101.5 bits), Expect = 6.8e-24, P = 6.8e-24
 Identities = 56/147 (38%), Positives = 81/147 (55%)

Query:    71 ELLEASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSYD 130
             E+ E+S   W    +       + D +  L+ GR + E+  PA+L A   Q+     +++
Sbjct:    90 EVFESSLVLWKSNESRFGCLLYLIDVIVSLISGRLVRERIGPAMLSAVQSQMGAVDSTFE 149

Query:   131 -VNDTDCRALSRGLTGESLKKLPCHVILDEIKPTQSS---CCSICLQDIIVGELARSLPH 186
              ++       S+GLTG+ + K+P   I  +     S     CS+CLQD  +GE  RSLPH
Sbjct:   150 ELSSIFDTGGSKGLTGDLVDKIPKIKITGKNNLDASGNKDSCSVCLQDFQLGETVRSLPH 209

Query:   187 CHHTFHLACVDKWLIRHGSCPVCRRDV 213
             CHH FHL C+D WL RHGSCP+CRRD+
Sbjct:   210 CHHMFHLPCIDNWLFRHGSCPMCRRDL 236

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:4010713762 AT3G20395 [Arabidopsis thaliana (taxid:3702)]

 Score = 213 (80.0 bits), Expect = 2.0e-17, P = 2.0e-17
 Identities = 45/113 (39%), Positives = 64/113 (56%)

Query:   100 LLRGRFIEEQFTPAILGAYHWQVRIASMSY--DVNDTDCRALSRGLTGESLKKLPCHVIL 157
             ++ G+ I     P +L AY WQ+     SY    N  D     +GL+  S++ +P     
Sbjct:   103 VVNGKAIMGLVRPFVLKAYQWQIIALDTSYMESSNLYDFNHEKKGLSKSSIQNIPMFYNR 162

Query:   158 DEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCR 210
              E + T+SSC SICLQD   GE+ R L  C HTFH+ C+D+WL+R  +CP+CR
Sbjct:   163 SEHQ-TKSSC-SICLQDWEEGEVGRKLARCGHTFHMNCIDEWLLRQETCPICR 213

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 182 (69.1 bits), Expect = 3.8e-14, P = 3.8e-14
 Identities = 33/84 (39%), Positives = 49/84 (58%)

Query:   130 DVNDTDCRALSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHH 189
             D  DT+   +++G+   +LK +P      E+K   + C  ICL D + GE  R LP C+H
Sbjct:    77 DPVDTNAN-VAKGIKKRALKVIPVDSYSPELKMKATECL-ICLGDFVEGETVRVLPKCNH 134

Query:   190 TFHLACVDKWLIRHGSCPVCRRDV 213
              FH+ C+D WL+ H SCP CR+ +
Sbjct:   135 GFHVKCIDTWLLSHSSCPTCRQSL 158

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

TAIR|locus:2028411 AT1G49200 [Arabidopsis thaliana (taxid:3702)]

 Score = 178 (67.7 bits), Expect = 1.0e-13, P = 1.0e-13
 Identities = 32/78 (41%), Positives = 45/78 (57%)

Query:   134 TDCRALSRGLTGESLKKLPCHVILDEIK-PTQSSCCSICLQDIIVGELARSLPHCHHTFH 192
             T C + ++G+  ++L+  P      E+  P     C ICL D + GE  R LP CHH FH
Sbjct:   101 TPCGSSNKGINKKALRMFPVVSYSPEMNLPGLGEECVICLSDFVSGEQIRMLPKCHHGFH 160

Query:   193 LACVDKWLIRHGSCPVCR 210
             + C+DKWL +H +CP CR
Sbjct:   161 VRCIDKWLQQHLTCPKCR 178

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

TAIR|locus:2830088 AT3G18773 [Arabidopsis thaliana (taxid:3702)]

 Score = 178 (67.7 bits), Expect = 1.0e-13, P = 1.0e-13
 Identities = 33/74 (44%), Positives = 45/74 (60%)

Query:   138 ALSRGLTGESLKKLPCHVILDEIK-PTQSSCCSICLQDIIVGELARSLPHCHHTFHLACV 196
             ++++G+  ++LK LP      EI  P     C ICL D + GE  R LP C+H FHL C+
Sbjct:    99 SVNKGIKKKALKMLPVVNYSPEINLPGVGEECVICLSDFVAGEQLRVLPKCNHGFHLRCI 158

Query:   197 DKWLIRHGSCPVCR 210
             DKWL +H +CP CR
Sbjct:   159 DKWLTQHMTCPKCR 172

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

TAIR|locus:2039170 AT2G35910 [Arabidopsis thaliana (taxid:3702)]

 Score = 173 (66.0 bits), Expect = 3.4e-13, P = 3.4e-13
 Identities = 32/70 (45%), Positives = 44/70 (62%)

Query:   142 GLTGESLKKLPCHVILDEIK-PTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWL 200
             GL  ++++  P  ++  E K PT +SCC+ICL D     L R LP C+H FHL C+D WL
Sbjct:   121 GLDEDTIQSYP-KILYSEAKGPTTASCCAICLGDYKGKHLLRQLPDCNHLFHLKCIDTWL 179

Query:   201 IRHGSCPVCR 210
               + +CPVCR
Sbjct:   180 RLNPTCPVCR 189

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2193992 ATL3 [Arabidopsis thaliana (taxid:3702)]

 Score = 171 (65.3 bits), Expect = 1.5e-12, P = 1.5e-12
 Identities = 33/77 (42%), Positives = 44/77 (57%)

Query:   138 ALSR-GLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACV 196
             ALS  GLT   L  LP  V   +        CSICL +++ G+ AR LP C+H+FH+ C+
Sbjct:    97 ALSNTGLTSFELSSLPI-VFFRQDSCKDGLECSICLSELVKGDKARLLPKCNHSFHVECI 155

Query:   197 DKWLIRHGSCPVCRRDV 213
             D W   H +CP+CR  V
Sbjct:   156 DMWFQSHSTCPICRNTV 172

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2181032 DAFL2 "DAF-Like gene 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 166 (63.5 bits), Expect = 1.9e-12, P = 1.9e-12
 Identities = 31/73 (42%), Positives = 42/73 (57%)

Query:   142 GLTGESLKKLP-CHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWL 200
             GL    LKK P       E+K   + C +ICL +   GE  R LP C+H+FH++C+D WL
Sbjct:    79 GLKKRELKKFPVAEYGSGEVKIAATEC-AICLGEFADGERVRVLPPCNHSFHMSCIDTWL 137

Query:   201 IRHGSCPVCRRDV 213
             + H SCP CR  +
Sbjct:   138 VSHSSCPNCRHSL 150

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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8LBA0	NIPL2_ARATH	No assigned EC number	0.6119	0.9389	0.8968	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00016305001 SubName- Full=Chromosome chr17 scaffold_12, whole genome shotgun sequence; (217 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	213
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	1e-13
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	3e-10
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	4e-10
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	2e-07
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	4e-07
smart00184	40	smart00184, RING, Ring finger	2e-06
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	3e-05
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	4e-05
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	8e-05
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	1e-04
pfam13488	46	pfam13488, Gly-zipper_Omp, Glycine zipper	2e-04
pfam13436	116	pfam13436, Gly-zipper_OmpA, Glycine-zipper contain	6e-04
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	7e-04
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	0.001
pfam13441	45	pfam13441, Gly-zipper_YMGG, YMGG-like Gly-zipper	0.001
pfam05433	42	pfam05433, Rick_17kDa_Anti, Glycine zipper 2TM dom	0.001
pfam13441	45	pfam13441, Gly-zipper_YMGG, YMGG-like Gly-zipper	0.003

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

 Score = 62.8 bits (153), Expect = 1e-13
 Identities = 21/45 (46%), Positives = 25/45 (55%), Gaps = 1/45 (2%)

Query: 168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD 212
           C ICL +   GE    LP C H FH  C+DKWL    +CP+CR  
Sbjct: 3   CPICLDEFEPGEEVVVLP-CGHVFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

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

 Score = 53.6 bits (129), Expect = 3e-10
 Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 4/48 (8%)

Query: 167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWL-IRHGSCPVCRRDV 213
            C ICL++         L  C H F  +C+DKWL     +CP+CR  +
Sbjct: 1   ECPICLEEFRE---PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 58.1 bits (140), Expect = 4e-10
 Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 11/73 (15%)

Query: 151 LPCHVILDEIKP---------TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLI 201
           +P       +KP          +   C+IC+ + I  +  R LP C H FH+ CVDKWL+
Sbjct: 300 IPTTTTKGSLKPLSIERAVEADKGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLL 358

Query: 202 RHG-SCPVCRRDV 213
            +   CPVCR  +
Sbjct: 359 GYSNKCPVCRTAI 371

Length = 374

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

 Score = 47.0 bits (112), Expect = 2e-07
 Identities = 16/53 (30%), Positives = 21/53 (39%), Gaps = 9/53 (16%)

Query: 167 CCSICLQDIIVGELARSLP---------HCHHTFHLACVDKWLIRHGSCPVCR 210
            C+IC             P          C H FHL C+ +WL    +CP+CR
Sbjct: 21  VCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73

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

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

 Score = 48.6 bits (116), Expect = 4e-07
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 4/47 (8%)

Query: 168 CSICLQDIIVGELARS----LPHCHHTFHLACVDKWLIRHGSCPVCR 210
           C+IC++ +   E+       L +C+H F + C+D W     +CPVCR
Sbjct: 177 CAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCR 223

Length = 238

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

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 4/43 (9%)

Query: 168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWL-IRHGSCPVC 209
           C ICL++ +  +    LP C HTF  +C+ KWL   + +CP+C
Sbjct: 1   CPICLEEYL--KDPVILP-CGHTFCRSCIRKWLESGNNTCPIC 40

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

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

 Score = 39.8 bits (93), Expect = 3e-05
 Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 3/48 (6%)

Query: 164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRR 211
           +   C ICL  +        L  C H F   C+ ++L +   CP+CR 
Sbjct: 1   EELECPICLDLLRD---PVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 43.4 bits (102), Expect = 4e-05
 Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 11/56 (19%)

Query: 168 CSICLQDII----------VGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           C+IC+ ++           +    + LP C H  HL C+  WL R  +CP+CRR V
Sbjct: 290 CTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPV 344

Length = 491

>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 = 11/25 (44%), Positives = 16/25 (64%)

Query: 187 CHHTFHLACVDKWLIRHGSCPVCRR 211
           C+H FH  C+ +WL   G CP+ R+
Sbjct: 54  CNHAFHDHCIYRWLDTKGVCPLDRQ 78

Length = 88

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

 Score = 42.0 bits (98), Expect = 1e-04
 Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 9/50 (18%)

Query: 168  CSICLQDIIVGELARSLPH-----CHHTFHLACVDKWLIRHGS--CPVCR 210
            C+IC    ++  + RSLP      C + FH  C+ KW        CP+CR
Sbjct: 1472 CAICYS--VLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCR 1519

Length = 1525

>gnl|CDD|205666 pfam13488, Gly-zipper_Omp, Glycine zipper

 Score = 37.4 bits (88), Expect = 2e-04
 Identities = 19/36 (52%), Positives = 21/36 (58%), Gaps = 1/36 (2%)

Query: 32 ALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAV 67
          A  GA  GA  GA AG A   G L GA +GA+AGA 
Sbjct: 3  AAIGAAAGAAIGAAAGGAGK-GALIGAAVGALAGAA 37

Length = 46

>gnl|CDD|222127 pfam13436, Gly-zipper_OmpA, Glycine-zipper containing OmpA-like membrane domain

 Score = 38.1 bits (89), Expect = 6e-04
 Identities = 19/45 (42%), Positives = 20/45 (44%), Gaps = 3/45 (6%)

Query: 22 AISGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGA 66
          A      G  A  GA  GA  GA AG   D G   GA  GA+ GA
Sbjct: 46 AARSAAGG--AAVGAAAGAAAGAAAGGGGD-GAAIGAAAGALVGA 87

Length = 116

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

 Score = 35.9 bits (83), Expect = 7e-04
 Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 4/43 (9%)

Query: 168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLI-RHGSCPVC 209
           C ICL++    +    LP C H F   C+  WL   + +CP+C
Sbjct: 1   CPICLEEPK--DPVTILP-CGHLFCSKCILSWLESGNVTCPLC 40

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

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

 Score = 36.7 bits (85), Expect = 0.001
 Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 3/28 (10%)

Query: 187 CHHTFHLACVDKWLIRHGS---CPVCRR 211
           C H FH+ C+ KWL    S   CP+CR+
Sbjct: 52  CKHNFHMHCILKWLATETSKGLCPMCRQ 79

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|222132 pfam13441, Gly-zipper_YMGG, YMGG-like Gly-zipper

 Score = 35.2 bits (82), Expect = 0.001
 Identities = 19/36 (52%), Positives = 23/36 (63%), Gaps = 1/36 (2%)

Query: 32 ALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAV 67
          A+AGA  GA  GA  G A+  G  RGA +GA AGA+
Sbjct: 3  AVAGAAIGAAAGAAVGAATGGGG-RGAAIGAAAGAL 37

Length = 45

>gnl|CDD|203250 pfam05433, Rick_17kDa_Anti, Glycine zipper 2TM domain

 Score = 35.1 bits (82), Expect = 0.001
 Identities = 19/37 (51%), Positives = 22/37 (59%), Gaps = 2/37 (5%)

Query: 32 ALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVL 68
          AL GA  GA+ GA  G     G L GA +GA AGAV+
Sbjct: 3  ALIGAAAGAVAGAAIGGGD--GRLLGAVIGAAAGAVV 37

This family includes a putative two transmembrane alpha-helical region that contains glycine zipper motifs. This family includes several Rickettsia genus specific 17 kDa surface antigen proteins. Length = 42

>gnl|CDD|222132 pfam13441, Gly-zipper_YMGG, YMGG-like Gly-zipper

 Score = 34.4 bits (80), Expect = 0.003
 Identities = 18/44 (40%), Positives = 21/44 (47%), Gaps = 3/44 (6%)

Query: 24 SGTLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAV 67
          +G + G  A  GA  GA  GA  G     G   GA  GA+AGA 
Sbjct: 1  TGAVAG--AAIGAAAGAAVGAATGGGGR-GAAIGAAAGALAGAA 41

Length = 45

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	213
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.74
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.66
PHA02929	238	N1R/p28-like protein; Provisional	99.49
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.44
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.39
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.36
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.22
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.2
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.2
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.13
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.12
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.11
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.11
PHA02926	242	zinc finger-like protein; Provisional	99.08
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.04
PF14634	44	zf-RING_5: zinc-RING finger domain	99.01
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.95
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.93
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.9
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.89
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.88
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.85
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.81
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.71
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.64
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.61
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.61
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.48
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.48
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.47
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.38
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.37
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.32
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.31
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.31
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.27
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.16
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.14
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.06
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.91
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.9
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.88
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.83
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.75
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.58
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.52
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	97.5
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.4
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.39
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.35
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	97.25
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.16
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.09
PF13436	118	Gly-zipper_OmpA: Glycine-zipper containing OmpA-li	97.03
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	96.87
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.71
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	96.69
PF13441	45	Gly-zipper_YMGG: YMGG-like Gly-zipper	96.66
PF13488	46	Gly-zipper_Omp: Glycine zipper	96.65
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.64
PHA03096	284	p28-like protein; Provisional	96.58
PHA02825	162	LAP/PHD finger-like protein; Provisional	96.58
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	96.56
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	96.55
KOG2660	331	consensus Locus-specific chromosome binding protei	96.55
PF05433	42	Rick_17kDa_Anti: Glycine zipper 2TM domain; InterP	96.55
PF13441	45	Gly-zipper_YMGG: YMGG-like Gly-zipper	96.54
PF13488	46	Gly-zipper_Omp: Glycine zipper	96.49
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	96.49
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	96.42
PF13436	118	Gly-zipper_OmpA: Glycine-zipper containing OmpA-li	96.35
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.25
PRK10510	219	putative outer membrane lipoprotein; Provisional	96.24
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	96.03
COG5236	493	Uncharacterized conserved protein, contains RING Z	95.95
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	95.77
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	95.66
KOG3039	303	consensus Uncharacterized conserved protein [Funct	95.48
COG5152	259	Uncharacterized conserved protein, contains RING a	95.31
PRK10540	72	lipoprotein; Provisional	95.28
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	95.17
COG5222	427	Uncharacterized conserved protein, contains RING Z	94.99
KOG1940	276	consensus Zn-finger protein [General function pred	94.93
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	94.85
KOG1002	791	consensus Nucleotide excision repair protein RAD16	94.79
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	94.56
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	94.51
KOG3053	293	consensus Uncharacterized conserved protein [Funct	94.28
PRK11280	170	hypothetical protein; Provisional	93.95
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	93.8
PRK10540	72	lipoprotein; Provisional	93.51
PF04641	260	Rtf2: Rtf2 RING-finger	93.32
PF06897	102	DUF1269: Protein of unknown function (DUF1269); In	93.31
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	93.14
TIGR03789	239	pdsO proteobacterial sortase system OmpA family pr	93.13
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	92.92
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	92.14
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	92.04
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	91.73
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	91.61
KOG1001	674	consensus Helicase-like transcription factor HLTF/	91.25
COG5175	480	MOT2 Transcriptional repressor [Transcription]	91.19
KOG1609	323	consensus Protein involved in mRNA turnover and st	91.01
KOG0298	1394	consensus DEAD box-containing helicase-like transc	90.92
PF06897	102	DUF1269: Protein of unknown function (DUF1269); In	90.6
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	90.52
KOG3002	299	consensus Zn finger protein [General function pred	89.84
KOG3899	381	consensus Uncharacterized conserved protein [Funct	89.78
PF05433	42	Rick_17kDa_Anti: Glycine zipper 2TM domain; InterP	89.77
KOG0269	839	consensus WD40 repeat-containing protein [Function	89.28
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	89.21
PRK10510	219	putative outer membrane lipoprotein; Provisional	88.83
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	88.5
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	88.28
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	87.89
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	87.83
PLN02720	140	complex II	87.81
PF05818	215	TraT: Enterobacterial TraT complement resistance p	87.08
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	86.35
KOG0825	1134	consensus PHD Zn-finger protein [General function	85.72
KOG3005	276	consensus GIY-YIG type nuclease [General function	85.59
PRK09430	267	djlA Dna-J like membrane chaperone protein; Provis	85.46
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	85.34
PRK11280	170	hypothetical protein; Provisional	84.97
COG4803	170	Predicted membrane protein [Function unknown]	84.64
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	84.22
PRK10457	82	hypothetical protein; Provisional	84.01
PRK11677	134	hypothetical protein; Provisional	83.61
KOG1829	580	consensus Uncharacterized conserved protein, conta	83.3
COG4803	170	Predicted membrane protein [Function unknown]	82.42
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	81.89
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	80.76
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	80.24
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	80.22

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

Probab=99.74  E-value=1e-18  Score=154.83  Aligned_cols=74  Identities=39%  Similarity=0.855  Sum_probs=64.9

Q ss_pred             cCCCCCHHHHhcCCceeeeccCCCCCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCC-CcccCCCC
Q 028116          139 LSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGS-CPVCRRDV  213 (213)
Q Consensus       139 ~~~gls~~~i~~lp~~~~~~~~~~~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~s-CPlCR~~v  213 (213)
                      ....+.++.++++|..+|+....+.....|+||+|+|++||.+|.|| |+|.||.+|||+||.++.+ ||+||+++
T Consensus       203 ~~~r~~k~~l~~~p~~~f~~~~~~~~~~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di  277 (348)
T KOG4628|consen  203 RRNRLIKRLLKKLPVRTFTKGDDEDATDTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDI  277 (348)
T ss_pred             hhhhhHHHHHhhCCcEEeccccccCCCceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcC
Confidence            44678899999999999988765333369999999999999999999 9999999999999998865 99999864

>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=99.66  E-value=2.7e-17  Score=104.85  Aligned_cols=44  Identities=50%  Similarity=1.167  Sum_probs=40.7

Q ss_pred             CcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccC
Q 028116          166 SCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCR  210 (213)
Q Consensus       166 ~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR  210 (213)
                      ++|+||+++|..++.+..++ |+|.||.+||.+|++++++||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHhCCcCCccC
Confidence            47999999999999999999 999999999999999999999998

...

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.49  E-value=1.7e-14  Score=122.76  Aligned_cols=74  Identities=27%  Similarity=0.588  Sum_probs=57.9

Q ss_pred             CCCCCHHHHhcCCceeeeccCC--CCCCCcccccccccccCc----eeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          140 SRGLTGESLKKLPCHVILDEIK--PTQSSCCSICLQDIIVGE----LARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       140 ~~gls~~~i~~lp~~~~~~~~~--~~~~~~C~ICle~~~~ge----~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ..+.+++.++.+|.....-+..  ...+.+|+||++++...+    .+..++.|+|.||..||.+|++++.+||+||.++
T Consensus       147 k~~~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~  226 (238)
T PHA02929        147 KGKNYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPF  226 (238)
T ss_pred             hcchhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEe
Confidence            4566888899999886543322  245789999999987654    2345666999999999999999999999999864

>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=99.44  E-value=6.5e-14  Score=98.87  Aligned_cols=47  Identities=32%  Similarity=0.859  Sum_probs=36.2

Q ss_pred             CCCcccccccccccC---------ceeeecCCCCCcccHhhHHHHHhcCCCCcccC
Q 028116          164 QSSCCSICLQDIIVG---------ELARSLPHCHHTFHLACVDKWLIRHGSCPVCR  210 (213)
Q Consensus       164 ~~~~C~ICle~~~~g---------e~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR  210 (213)
                      .++.|+||+++|.+.         +....++.|+|.||..||.+||+++.+||+||
T Consensus        18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            455699999999332         22334444999999999999999999999998

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 ....

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

Probab=99.39  E-value=1.4e-13  Score=121.86  Aligned_cols=50  Identities=38%  Similarity=1.016  Sum_probs=44.4

Q ss_pred             CCCCcccccccc-cccC---------ceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQD-IIVG---------ELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~-~~~g---------e~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .++..|.||+++ |..+         .++++|| |||+||..|++.|++++.+||+||.||
T Consensus       285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~  344 (491)
T COG5243         285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPV  344 (491)
T ss_pred             CCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCcc
Confidence            578899999999 5554         2568999 999999999999999999999999985

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

Probab=99.36  E-value=3.6e-13  Score=116.59  Aligned_cols=50  Identities=44%  Similarity=1.106  Sum_probs=45.9

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHh-cCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLI-RHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~-~~~sCPlCR~~v  213 (213)
                      ....+|.||+++|..++.++.|| |+|.||..|+++|+. -+..||+||.++
T Consensus       321 ~~GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~i  371 (374)
T COG5540         321 DKGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAI  371 (374)
T ss_pred             CCCceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCC
Confidence            34588999999999999999999 999999999999998 577999999975

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

Probab=99.22  E-value=6.3e-12  Score=90.51  Aligned_cols=50  Identities=34%  Similarity=0.872  Sum_probs=39.7

Q ss_pred             CCCCccccccccccc--------C-ceeeecCCCCCcccHhhHHHHHhc---CCCCcccCCC
Q 028116          163 TQSSCCSICLQDIIV--------G-ELARSLPHCHHTFHLACVDKWLIR---HGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~--------g-e~v~~Lp~C~H~FH~~CI~~WL~~---~~sCPlCR~~  212 (213)
                      .+++.|.||...|..        | +.+..+.+|+|.||..||.+||.+   +++||+||++
T Consensus        19 ~~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~   80 (85)
T PF12861_consen   19 ANDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQP   80 (85)
T ss_pred             CCCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCe
Confidence            347889999988863        2 334456679999999999999986   4689999986

>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=99.20  E-value=9e-12  Score=81.36  Aligned_cols=45  Identities=33%  Similarity=0.838  Sum_probs=38.9

Q ss_pred             CCcccccccccccCceeeecCCCCCc-ccHhhHHHHHhcCCCCcccCCCC
Q 028116          165 SSCCSICLQDIIVGELARSLPHCHHT-FHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       165 ~~~C~ICle~~~~ge~v~~Lp~C~H~-FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      +..|.||++....   +..+| |+|. |+..|+.+|++++.+||+||+++
T Consensus         2 ~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i   47 (50)
T PF13920_consen    2 DEECPICFENPRD---VVLLP-CGHLCFCEECAERLLKRKKKCPICRQPI   47 (50)
T ss_dssp             HSB-TTTSSSBSS---EEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-
T ss_pred             cCCCccCCccCCc---eEEeC-CCChHHHHHHhHHhcccCCCCCcCChhh
Confidence            5789999998554   77888 9999 99999999999999999999975

...

>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=99.20  E-value=1.4e-11  Score=76.88  Aligned_cols=44  Identities=43%  Similarity=1.079  Sum_probs=37.0

Q ss_pred             cccccccccccCceeeecCCCCCcccHhhHHHHHhc-CCCCcccCCCC
Q 028116          167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR-HGSCPVCRRDV  213 (213)
Q Consensus       167 ~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~-~~sCPlCR~~v  213 (213)
                      +|+||++.+  .+.+...+ |+|.||..|+++|+.+ +.+||+||+++
T Consensus         1 ~C~iC~~~~--~~~~~~~~-C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEF--REPVVLLP-CGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhh--hCceEecC-CCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            599999998  23455555 9999999999999998 77899999875

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

Probab=99.13  E-value=2.2e-11  Score=104.94  Aligned_cols=47  Identities=30%  Similarity=0.846  Sum_probs=41.9

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      +.+..|.+||+..+.   +..+| |||+||+.||..|...+..||+||.++
T Consensus       237 ~a~~kC~LCLe~~~~---pSaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~  283 (293)
T KOG0317|consen  237 EATRKCSLCLENRSN---PSATP-CGHIFCWSCILEWCSEKAECPLCREKF  283 (293)
T ss_pred             CCCCceEEEecCCCC---CCcCc-CcchHHHHHHHHHHccccCCCcccccC
Confidence            567899999997655   77899 999999999999999999999999863

>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=99.12  E-value=4.3e-11  Score=74.24  Aligned_cols=39  Identities=38%  Similarity=1.000  Sum_probs=32.9

Q ss_pred             ccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCccc
Q 028116          168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVC  209 (213)
Q Consensus       168 C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlC  209 (213)
                      |+||++.+.+  .+..++ |||.|+.+|+.+|++++.+||+|
T Consensus         1 C~iC~~~~~~--~~~~~~-CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTP-CGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECT-TSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC--cCEECC-CCCchhHHHHHHHHHCcCCCcCC
Confidence            8999998776  345676 99999999999999999999998

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

Probab=99.11  E-value=1.5e-11  Score=116.32  Aligned_cols=49  Identities=37%  Similarity=0.955  Sum_probs=44.7

Q ss_pred             CCCCcccccccccccCce--eeecCCCCCcccHhhHHHHHhcCCCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGEL--ARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~--v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~  212 (213)
                      ..+..|+||+|++..++.  +.+|| |+|+||..|+.+|++++++||+||..
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~  339 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTV  339 (543)
T ss_pred             hcCCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhh
Confidence            457899999999998765  78999 99999999999999999999999973

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.11  E-value=5.7e-11  Score=97.82  Aligned_cols=47  Identities=34%  Similarity=0.776  Sum_probs=38.7

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc----------------CCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR----------------HGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~----------------~~sCPlCR~~v  213 (213)
                      .++.+|+||++.+++   +..++ |+|.||..||.+|+..                +.+||+||+++
T Consensus        16 ~~~~~CpICld~~~d---PVvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~I   78 (193)
T PLN03208         16 GGDFDCNICLDQVRD---PVVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDV   78 (193)
T ss_pred             CCccCCccCCCcCCC---cEEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcC
Confidence            456889999998765   45666 9999999999999852                34799999875

>PHA02926 zinc finger-like protein; Provisional

Probab=99.08  E-value=6.8e-11  Score=98.82  Aligned_cols=50  Identities=26%  Similarity=0.773  Sum_probs=39.9

Q ss_pred             CCCCcccccccccccC-----ceeeecCCCCCcccHhhHHHHHhcC------CCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVG-----ELARSLPHCHHTFHLACVDKWLIRH------GSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~g-----e~v~~Lp~C~H~FH~~CI~~WL~~~------~sCPlCR~~  212 (213)
                      ..+.+|+||+|...+.     .....|+.|+|.||..||.+|...+      .+||+||..
T Consensus       168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~  228 (242)
T PHA02926        168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTR  228 (242)
T ss_pred             cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcce
Confidence            5679999999986332     2356787899999999999999753      469999975

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

Probab=99.04  E-value=1.4e-10  Score=97.28  Aligned_cols=48  Identities=31%  Similarity=0.661  Sum_probs=38.4

Q ss_pred             CCCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC---CCCcccCCCC
Q 028116          162 PTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH---GSCPVCRRDV  213 (213)
Q Consensus       162 ~~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~---~sCPlCR~~v  213 (213)
                      +...-+|.|||+.-++   +.+.. |||.||+.||.+||..+   ..||+||..|
T Consensus        44 ~~~~FdCNICLd~akd---PVvTl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~V   94 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKD---PVVTL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEV   94 (230)
T ss_pred             CCCceeeeeeccccCC---CEEee-cccceehHHHHHHHhhcCCCeeCCcccccc
Confidence            3667889999997544   44554 99999999999999854   4689999865

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.01  E-value=2.2e-10  Score=72.96  Aligned_cols=44  Identities=30%  Similarity=0.711  Sum_probs=38.3

Q ss_pred             cccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCC
Q 028116          167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRR  211 (213)
Q Consensus       167 ~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~  211 (213)
                      .|+||+++|.+.+..+.++ |+|+|+..|+.++......||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~-CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTS-CGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcc-cCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            5999999996656777777 9999999999999866778999985

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

Probab=98.95  E-value=4.8e-10  Score=90.66  Aligned_cols=49  Identities=27%  Similarity=0.651  Sum_probs=41.4

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      +....|+|||+.+.+...  .-.+|||+||..||+.-++....||+||+.|
T Consensus       129 ~~~~~CPiCl~~~sek~~--vsTkCGHvFC~~Cik~alk~~~~CP~C~kkI  177 (187)
T KOG0320|consen  129 EGTYKCPICLDSVSEKVP--VSTKCGHVFCSQCIKDALKNTNKCPTCRKKI  177 (187)
T ss_pred             ccccCCCceecchhhccc--cccccchhHHHHHHHHHHHhCCCCCCccccc
Confidence            556789999999887433  3346999999999999999999999999764

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

Probab=98.93  E-value=6.4e-10  Score=78.61  Aligned_cols=48  Identities=31%  Similarity=0.717  Sum_probs=37.8

Q ss_pred             CCcccccccccccC-ceeeecCCCCCcccHhhHHHHHhcCCCCcccCCC
Q 028116          165 SSCCSICLQDIIVG-ELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD  212 (213)
Q Consensus       165 ~~~C~ICle~~~~g-e~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~  212 (213)
                      ...|+-|+....++ |.+.....|+|.||..||.+||..++.||++|++
T Consensus        31 m~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~   79 (88)
T COG5194          31 MGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQT   79 (88)
T ss_pred             cCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCce
Confidence            45566665554444 4566666799999999999999999999999985

>smart00184 RING Ring finger

Probab=98.90  E-value=1.1e-09  Score=65.92  Aligned_cols=38  Identities=45%  Similarity=1.140  Sum_probs=32.8

Q ss_pred             ccccccccccCceeeecCCCCCcccHhhHHHHHh-cCCCCccc
Q 028116          168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLI-RHGSCPVC  209 (213)
Q Consensus       168 C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~-~~~sCPlC  209 (213)
                      |+||++.   .+.+..+| |+|.||..|+++|+. .+.+||+|
T Consensus         1 C~iC~~~---~~~~~~~~-C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEE---LKDPVVLP-CGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccC---CCCcEEec-CCChHHHHHHHHHHHhCcCCCCCC
Confidence            8999988   34577888 999999999999998 67789998

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)

>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=98.89  E-value=9.9e-10  Score=68.46  Aligned_cols=39  Identities=41%  Similarity=0.973  Sum_probs=33.1

Q ss_pred             ccccccccccCceeeecCCCCCcccHhhHHHHHh--cCCCCccc
Q 028116          168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLI--RHGSCPVC  209 (213)
Q Consensus       168 C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~--~~~sCPlC  209 (213)
                      |+||++.+...  +..++ |+|.||..|+.+|++  ....||+|
T Consensus         1 C~iC~~~~~~~--~~~~~-C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDP--VILLP-CGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSE--EEETT-TSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCC--CEEec-CCCcchHHHHHHHHHhcCCccCCcC
Confidence            89999987763  35676 999999999999999  45679998

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

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

Probab=98.88  E-value=1.3e-09  Score=68.83  Aligned_cols=38  Identities=39%  Similarity=0.866  Sum_probs=29.7

Q ss_pred             ccccccccccCceeeecCCCCCcccHhhHHHHHhcC----CCCccc
Q 028116          168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH----GSCPVC  209 (213)
Q Consensus       168 C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~----~sCPlC  209 (213)
                      |+||++-|.+   +..|+ |||.|+..||.+|.+++    ..||.|
T Consensus         1 CpiC~~~~~~---Pv~l~-CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKD---PVSLP-CGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SS---EEE-S-SSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCC---ccccC-CcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            8999999887   77888 99999999999999754    369998

>smart00504 Ubox Modified RING finger domain

Probab=98.85  E-value=3.2e-09  Score=71.90  Aligned_cols=44  Identities=30%  Similarity=0.595  Sum_probs=38.7

Q ss_pred             CcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          166 SCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       166 ~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ..|+||++.+.+   +..+| |||+|+..||.+|++++.+||+|++++
T Consensus         2 ~~Cpi~~~~~~~---Pv~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~   45 (63)
T smart00504        2 FLCPISLEVMKD---PVILP-SGQTYERRAIEKWLLSHGTDPVTGQPL   45 (63)
T ss_pred             cCCcCCCCcCCC---CEECC-CCCEEeHHHHHHHHHHCCCCCCCcCCC
Confidence            469999998876   45677 999999999999999999999999864

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=98.81  E-value=6.4e-10  Score=77.95  Aligned_cols=50  Identities=32%  Similarity=0.763  Sum_probs=39.4

Q ss_pred             CCCCccccccccccc---------CceeeecCCCCCcccHhhHHHHHhc---CCCCcccCCC
Q 028116          163 TQSSCCSICLQDIIV---------GELARSLPHCHHTFHLACVDKWLIR---HGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~---------ge~v~~Lp~C~H~FH~~CI~~WL~~---~~sCPlCR~~  212 (213)
                      ..++.|-||.-.|..         ++.+-++..|.|.||..||.+|+..   +..||+||++
T Consensus        18 ~~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~   79 (84)
T KOG1493|consen   18 APDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQT   79 (84)
T ss_pred             CCCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchhe
Confidence            456688888877753         3455567779999999999999974   5579999985

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.71  E-value=8.5e-09  Score=93.83  Aligned_cols=47  Identities=32%  Similarity=0.650  Sum_probs=40.6

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      +....|+||++.|..   +..+| |+|.||..||..|+..+..||+||.++
T Consensus        24 e~~l~C~IC~d~~~~---Pvitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~   70 (397)
T TIGR00599        24 DTSLRCHICKDFFDV---PVLTS-CSHTFCSLCIRRCLSNQPKCPLCRAED   70 (397)
T ss_pred             ccccCCCcCchhhhC---ccCCC-CCCchhHHHHHHHHhCCCCCCCCCCcc
Confidence            456899999998865   44677 999999999999999988999999864

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

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

Probab=98.64  E-value=2.2e-08  Score=65.30  Aligned_cols=42  Identities=24%  Similarity=0.704  Sum_probs=33.3

Q ss_pred             cccccccccccCceeeecCCCC-----CcccHhhHHHHHhcC--CCCcccC
Q 028116          167 CCSICLQDIIVGELARSLPHCH-----HTFHLACVDKWLIRH--GSCPVCR  210 (213)
Q Consensus       167 ~C~ICle~~~~ge~v~~Lp~C~-----H~FH~~CI~~WL~~~--~sCPlCR  210 (213)
                      .|.||++ ..+++.....| |.     |.+|..|+.+|+..+  .+||+|+
T Consensus         1 ~CrIC~~-~~~~~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHD-EGDEGDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCC-CCCCCCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4899999 33445556888 85     999999999999754  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

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

Probab=98.61  E-value=2.9e-08  Score=62.98  Aligned_cols=38  Identities=32%  Similarity=0.762  Sum_probs=23.0

Q ss_pred             ccccccccccC-ceeeecCCCCCcccHhhHHHHHhcCC----CCc
Q 028116          168 CSICLQDIIVG-ELARSLPHCHHTFHLACVDKWLIRHG----SCP  207 (213)
Q Consensus       168 C~ICle~~~~g-e~v~~Lp~C~H~FH~~CI~~WL~~~~----sCP  207 (213)
                      |+||.| |... ..+..|| |||+|+.+|++++++++.    +||
T Consensus         1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 7554 4668899 999999999999998542    687

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

Probab=98.61  E-value=1.7e-08  Score=86.22  Aligned_cols=47  Identities=34%  Similarity=0.807  Sum_probs=39.9

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHH-HHhcCCC-CcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDK-WLIRHGS-CPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~-WL~~~~s-CPlCR~~v  213 (213)
                      ..+..|+||++....   +..+| |||+||..||.. |-+++.. ||+||+.+
T Consensus       213 ~~d~kC~lC~e~~~~---ps~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~  261 (271)
T COG5574         213 LADYKCFLCLEEPEV---PSCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKV  261 (271)
T ss_pred             ccccceeeeecccCC---ccccc-ccchhhHHHHHHHHHhhccccCchhhhhc
Confidence            457889999987554   77888 999999999999 9887776 99999864

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

Probab=98.48  E-value=2.8e-08  Score=85.26  Aligned_cols=50  Identities=34%  Similarity=0.791  Sum_probs=41.3

Q ss_pred             CCCCcccccccccccCc-------eeeecCCCCCcccHhhHHHHH--hcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGE-------LARSLPHCHHTFHLACVDKWL--IRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge-------~v~~Lp~C~H~FH~~CI~~WL--~~~~sCPlCR~~v  213 (213)
                      -++.-|.||-+.+...+       ..-+|. |+|.||..||.-|-  -++++||.|++.|
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekV  280 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKV  280 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHh
Confidence            45688999998876553       566887 99999999999995  4788999999764

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

Probab=98.48  E-value=2.8e-08  Score=69.50  Aligned_cols=49  Identities=33%  Similarity=0.889  Sum_probs=23.2

Q ss_pred             CCcccccccccc-cCcee-ee--cCCCCCcccHhhHHHHHhc-----------CCCCcccCCCC
Q 028116          165 SSCCSICLQDII-VGELA-RS--LPHCHHTFHLACVDKWLIR-----------HGSCPVCRRDV  213 (213)
Q Consensus       165 ~~~C~ICle~~~-~ge~v-~~--Lp~C~H~FH~~CI~~WL~~-----------~~sCPlCR~~v  213 (213)
                      +.+|.||++... .++.+ ..  -++|++.||..|+.+||..           ..+||.|+++|
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i   65 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPI   65 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEE
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCee
Confidence            478999999866 43332 22  2479999999999999973           12599999864

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

Probab=98.47  E-value=6.7e-08  Score=71.59  Aligned_cols=50  Identities=28%  Similarity=0.769  Sum_probs=40.2

Q ss_pred             CCCCcccccccccc-------------cCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCC
Q 028116          163 TQSSCCSICLQDII-------------VGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~-------------~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~  212 (213)
                      -.-+.|+||...+.             .+|.......|+|.||..||.+||++++.||+|.++
T Consensus        44 i~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~e  106 (114)
T KOG2930|consen   44 IVVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKE  106 (114)
T ss_pred             eeechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcc
Confidence            45677999875542             235566777799999999999999999999999764

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

Probab=98.38  E-value=1.2e-07  Score=87.17  Aligned_cols=50  Identities=34%  Similarity=0.814  Sum_probs=38.6

Q ss_pred             CCCCcccccccccccCc-----e---------eeecCCCCCcccHhhHHHHHhc-CCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGE-----L---------ARSLPHCHHTFHLACVDKWLIR-HGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge-----~---------v~~Lp~C~H~FH~~CI~~WL~~-~~sCPlCR~~v  213 (213)
                      .....|+||++++.--.     .         ....| |.|+||..|+.+|... +-.||.||.++
T Consensus       569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tP-C~HifH~~CL~~WMd~ykl~CPvCR~pL  633 (636)
T KOG0828|consen  569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTP-CHHIFHRQCLLQWMDTYKLICPVCRCPL  633 (636)
T ss_pred             hccccceEeccccceeeccCcchhhhhhhhccccccc-hHHHHHHHHHHHHHhhhcccCCccCCCC
Confidence            45678999999875311     1         12457 9999999999999995 55999999975

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

Probab=98.37  E-value=1.7e-07  Score=86.51  Aligned_cols=45  Identities=31%  Similarity=0.700  Sum_probs=35.0

Q ss_pred             CCcccccccccccCceeeecCCCCCcccHhhHHHHHhc-----CCCCcccCCCC
Q 028116          165 SSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR-----HGSCPVCRRDV  213 (213)
Q Consensus       165 ~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~-----~~sCPlCR~~v  213 (213)
                      +..|||||+....   +..+ .|||+||.+||.+.+..     ...||+||..|
T Consensus       186 ~~~CPICL~~~~~---p~~t-~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I  235 (513)
T KOG2164|consen  186 DMQCPICLEPPSV---PVRT-NCGHIFCGPCILQYWNYSAIKGPCSCPICRSTI  235 (513)
T ss_pred             CCcCCcccCCCCc---cccc-ccCceeeHHHHHHHHhhhcccCCccCCchhhhc
Confidence            6789999998544   3334 49999999999888753     45899999753

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

Probab=98.32  E-value=4.2e-07  Score=80.78  Aligned_cols=47  Identities=28%  Similarity=0.723  Sum_probs=41.2

Q ss_pred             CCCCcccccccccccCceeeecCCCCCc-ccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHT-FHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~-FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ++..+|.||+.+-++   ..+|| |.|+ .|..|-+..--+++.||+||+++
T Consensus       288 ~~gkeCVIClse~rd---t~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi  335 (349)
T KOG4265|consen  288 ESGKECVICLSESRD---TVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPI  335 (349)
T ss_pred             cCCCeeEEEecCCcc---eEEec-chhhehhHhHHHHHHHhhcCCCccccch
Confidence            456889999998665   77999 9999 99999999877899999999975

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

Probab=98.31  E-value=1.6e-07  Score=91.77  Aligned_cols=51  Identities=25%  Similarity=0.789  Sum_probs=39.4

Q ss_pred             CCCCcccccccccccCc---eeeecCCCCCcccHhhHHHHHhc--CCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGE---LARSLPHCHHTFHLACVDKWLIR--HGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge---~v~~Lp~C~H~FH~~CI~~WL~~--~~sCPlCR~~v  213 (213)
                      ...++|+||+.-+..-|   .-.+.|.|.|.||..|+-+|++.  +++||+||.++
T Consensus      1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRsei 1522 (1525)
T COG5219        1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEI 1522 (1525)
T ss_pred             CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCcccccc
Confidence            56789999987765211   22355669999999999999986  45899999864

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

Probab=98.31  E-value=4.3e-07  Score=63.88  Aligned_cols=46  Identities=24%  Similarity=0.482  Sum_probs=36.3

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc-CCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR-HGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~-~~sCPlCR~~v  213 (213)
                      +...|+|+.+-|.+   +..+| +||+|...||.+||.+ +.+||+||.++
T Consensus         3 ~~f~CpIt~~lM~d---PVi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l   49 (73)
T PF04564_consen    3 DEFLCPITGELMRD---PVILP-SGHTYERSAIERWLEQNGGTDPFTRQPL   49 (73)
T ss_dssp             GGGB-TTTSSB-SS---EEEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-
T ss_pred             cccCCcCcCcHhhC---ceeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcC
Confidence            35689999998876   67888 9999999999999998 88999998864

Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....

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

Probab=98.27  E-value=2.9e-07  Score=83.77  Aligned_cols=46  Identities=37%  Similarity=0.907  Sum_probs=38.0

Q ss_pred             CCCCcccccccccccCc-eeeecCCCCCcccHhhHHHHHhcCCCCcccCC
Q 028116          163 TQSSCCSICLQDIIVGE-LARSLPHCHHTFHLACVDKWLIRHGSCPVCRR  211 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge-~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~  211 (213)
                      .+-.+||||||.+...- .++..+ |.|.||..|+.+|  ...+||+||.
T Consensus       173 tELPTCpVCLERMD~s~~gi~t~~-c~Hsfh~~cl~~w--~~~scpvcR~  219 (493)
T KOG0804|consen  173 TELPTCPVCLERMDSSTTGILTIL-CNHSFHCSCLMKW--WDSSCPVCRY  219 (493)
T ss_pred             ccCCCcchhHhhcCccccceeeee-cccccchHHHhhc--ccCcChhhhh
Confidence            45688999999987653 344555 9999999999999  6789999995

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

Probab=98.16  E-value=6.5e-07  Score=79.15  Aligned_cols=46  Identities=33%  Similarity=0.724  Sum_probs=40.5

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .-..|-||.+-|..   +...| |+|.||.-||.+.|..+..||.|+.++
T Consensus        22 ~lLRC~IC~eyf~i---p~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~   67 (442)
T KOG0287|consen   22 DLLRCGICFEYFNI---PMITP-CSHTFCSLCIRKFLSYKPQCPTCCVTV   67 (442)
T ss_pred             HHHHHhHHHHHhcC---ceecc-ccchHHHHHHHHHhccCCCCCceeccc
Confidence            34679999998876   66788 999999999999999999999999764

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

Probab=98.14  E-value=1.1e-06  Score=76.39  Aligned_cols=46  Identities=35%  Similarity=0.682  Sum_probs=39.0

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~  212 (213)
                      +....|-||-+-|..   ....+ |||.||.-||...|..|.-||+||.+
T Consensus        23 Ds~lrC~IC~~~i~i---p~~Tt-CgHtFCslCIR~hL~~qp~CP~Cr~~   68 (391)
T COG5432          23 DSMLRCRICDCRISI---PCETT-CGHTFCSLCIRRHLGTQPFCPVCRED   68 (391)
T ss_pred             hhHHHhhhhhheeec---ceecc-cccchhHHHHHHHhcCCCCCcccccc
Confidence            345779999887765   44555 99999999999999999999999975

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

Probab=98.06  E-value=1.9e-06  Score=77.28  Aligned_cols=50  Identities=36%  Similarity=0.854  Sum_probs=39.5

Q ss_pred             CCCCcccccccccccCc----eeeecCCCCCcccHhhHHHHH--hc-----CCCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGE----LARSLPHCHHTFHLACVDKWL--IR-----HGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge----~v~~Lp~C~H~FH~~CI~~WL--~~-----~~sCPlCR~~  212 (213)
                      ..+..|.||++...+.-    ..+.||+|.|.||.+||.+|-  .+     ..+||.||.+
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~  219 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVP  219 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCc
Confidence            45789999999865432    235678899999999999997  44     4789999975

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

Probab=97.91  E-value=2.1e-06  Score=82.79  Aligned_cols=48  Identities=25%  Similarity=0.424  Sum_probs=42.6

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD  212 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~  212 (213)
                      ....|++|+..+.++......+ |+|+||..||+.|-+.-.+||+||..
T Consensus       122 ~~~~CP~Ci~s~~DqL~~~~k~-c~H~FC~~Ci~sWsR~aqTCPiDR~E  169 (1134)
T KOG0825|consen  122 VENQCPNCLKSCNDQLEESEKH-TAHYFCEECVGSWSRCAQTCPVDRGE  169 (1134)
T ss_pred             hhhhhhHHHHHHHHHhhccccc-cccccHHHHhhhhhhhcccCchhhhh
Confidence            3467999999998887777776 99999999999999999999999975

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

Probab=97.90  E-value=2.6e-06  Score=56.22  Aligned_cols=45  Identities=33%  Similarity=0.721  Sum_probs=33.8

Q ss_pred             CCcccccccccccCceeeecCCCCCc-ccHhhHHHHHh-cCCCCcccCCCC
Q 028116          165 SSCCSICLQDIIVGELARSLPHCHHT-FHLACVDKWLI-RHGSCPVCRRDV  213 (213)
Q Consensus       165 ~~~C~ICle~~~~ge~v~~Lp~C~H~-FH~~CI~~WL~-~~~sCPlCR~~v  213 (213)
                      +.+|.||+|.-.+  .+  |-.|||+ .+..|-.+.++ .+..||+||+++
T Consensus         7 ~dECTICye~pvd--sV--lYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi   53 (62)
T KOG4172|consen    7 SDECTICYEHPVD--SV--LYTCGHMCMCYACGLRLKKALHGCCPICRAPI   53 (62)
T ss_pred             ccceeeeccCcch--HH--HHHcchHHhHHHHHHHHHHccCCcCcchhhHH
Confidence            4889999987443  23  2239998 78899765554 789999999874

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

Probab=97.88  E-value=2.8e-06  Score=58.07  Aligned_cols=43  Identities=30%  Similarity=0.686  Sum_probs=22.4

Q ss_pred             CCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCC
Q 028116          165 SSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD  212 (213)
Q Consensus       165 ~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~  212 (213)
                      --.|++|.+-++.   +..+.+|.|+|+..||.+-+.  ..||+|+.|
T Consensus         7 lLrCs~C~~~l~~---pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~P   49 (65)
T PF14835_consen    7 LLRCSICFDILKE---PVCLGGCEHIFCSSCIRDCIG--SECPVCHTP   49 (65)
T ss_dssp             TTS-SSS-S--SS----B---SSS--B-TTTGGGGTT--TB-SSS--B
T ss_pred             hcCCcHHHHHhcC---CceeccCccHHHHHHhHHhcC--CCCCCcCCh
Confidence            3679999887665   555667999999999987544  349999976

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

Probab=97.83  E-value=2e-06  Score=76.43  Aligned_cols=48  Identities=29%  Similarity=0.674  Sum_probs=39.7

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc-CCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR-HGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~-~~sCPlCR~~v  213 (213)
                      ..+..|+|||+-++.   ....+.|.|-||.+||.+-++. +++||.||+.+
T Consensus        41 ~~~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l   89 (381)
T KOG0311|consen   41 DIQVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKL   89 (381)
T ss_pred             hhhhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhc
Confidence            456889999998766   4455679999999999999975 67899999863

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

Probab=97.75  E-value=8.8e-06  Score=71.03  Aligned_cols=38  Identities=26%  Similarity=0.627  Sum_probs=34.0

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHh
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLI  201 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~  201 (213)
                      -....|.|||-.|..++...+.+ |-|+||..|+.++|.
T Consensus       113 ~p~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~  150 (368)
T KOG4445|consen  113 HPNGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLT  150 (368)
T ss_pred             CCCCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHH
Confidence            45678999999999999888998 999999999988864

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

Probab=97.58  E-value=2.4e-05  Score=75.48  Aligned_cols=45  Identities=29%  Similarity=0.606  Sum_probs=36.6

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHh-cCCCCcccCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLI-RHGSCPVCRRD  212 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~-~~~sCPlCR~~  212 (213)
                      .-..||+|-..+++   + ++++|+|.||.+||.+-+. ++..||.|-++
T Consensus       642 ~~LkCs~Cn~R~Kd---~-vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~a  687 (698)
T KOG0978|consen  642 ELLKCSVCNTRWKD---A-VITKCGHVFCEECVQTRYETRQRKCPKCNAA  687 (698)
T ss_pred             hceeCCCccCchhh---H-HHHhcchHHHHHHHHHHHHHhcCCCCCCCCC
Confidence            34789999877665   2 4557999999999999886 67899999764

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

Probab=97.52  E-value=2.7e-05  Score=70.21  Aligned_cols=47  Identities=38%  Similarity=0.870  Sum_probs=39.0

Q ss_pred             CCCcccccccccccC-ceeeecCCCCCcccHhhHHHHHhcC--CCCcccCC
Q 028116          164 QSSCCSICLQDIIVG-ELARSLPHCHHTFHLACVDKWLIRH--GSCPVCRR  211 (213)
Q Consensus       164 ~~~~C~ICle~~~~g-e~v~~Lp~C~H~FH~~CI~~WL~~~--~sCPlCR~  211 (213)
                      -+.-|-.|=|.+-.. |....|| |.|+||..|+.+.|.++  .+||.||+
T Consensus       364 ~~L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  364 TELYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             HhhhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            346699998887543 5788999 99999999999999875  48999994

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

Probab=97.50  E-value=2.7e-05  Score=62.53  Aligned_cols=42  Identities=29%  Similarity=0.604  Sum_probs=35.1

Q ss_pred             CceeeeccCCCCCCCcccccccccccCceeeecCCCCCcccHh
Q 028116          152 PCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLA  194 (213)
Q Consensus       152 p~~~~~~~~~~~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~  194 (213)
                      |+..|.++...++..+|.||||+++.|+++.+|| |-.+||+.
T Consensus       164 PrlsYNdDVL~ddkGECvICLEdL~~GdtIARLP-CLCIYHK~  205 (205)
T KOG0801|consen  164 PRLSYNDDVLKDDKGECVICLEDLEAGDTIARLP-CLCIYHKQ  205 (205)
T ss_pred             cccccccchhcccCCcEEEEhhhccCCCceeccc-eEEEeecC
Confidence            4555655555577889999999999999999999 99999963

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

Probab=97.40  E-value=8.7e-05  Score=49.82  Aligned_cols=43  Identities=35%  Similarity=0.556  Sum_probs=28.1

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc--CCCCcc
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR--HGSCPV  208 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~--~~sCPl  208 (213)
                      .....|||.++.|++  .++.. +|+|+|-...|.+||.+  +..||+
T Consensus         9 ~~~~~CPiT~~~~~~--PV~s~-~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen    9 TISLKCPITLQPFED--PVKSK-KCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             B--SB-TTTSSB-SS--EEEES-SS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             EeccCCCCcCChhhC--CcCcC-CCCCeecHHHHHHHHHhcCCCCCCC
Confidence            345789999999875  35555 59999999999999954  446998

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

Probab=97.39  E-value=8.2e-05  Score=68.05  Aligned_cols=47  Identities=30%  Similarity=0.786  Sum_probs=40.2

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ..+.+|.||..-+..   +..+| |||.|+..||++-+.+...||.||.++
T Consensus        82 ~sef~c~vc~~~l~~---pv~tp-cghs~c~~Cl~r~ld~~~~cp~Cr~~l  128 (398)
T KOG4159|consen   82 RSEFECCVCSRALYP---PVVTP-CGHSFCLECLDRSLDQETECPLCRDEL  128 (398)
T ss_pred             cchhhhhhhHhhcCC---Ccccc-ccccccHHHHHHHhccCCCCccccccc
Confidence            457889999887766   56778 999999999999888888999999763

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

Probab=97.35  E-value=5.9e-05  Score=68.28  Aligned_cols=46  Identities=26%  Similarity=0.749  Sum_probs=37.3

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc--CCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR--HGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~--~~sCPlCR~~v  213 (213)
                      .-..|-||-|.   +..++.-| |||..|..|+..|-..  .++||.||.++
T Consensus       368 TFeLCKICaen---dKdvkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEI  415 (563)
T KOG1785|consen  368 TFELCKICAEN---DKDVKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEI  415 (563)
T ss_pred             hHHHHHHhhcc---CCCccccc-ccchHHHHHHHhhcccCCCCCCCceeeEe
Confidence            34669999775   34488899 9999999999999754  46899999764

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

Probab=97.25  E-value=0.00018  Score=46.30  Aligned_cols=40  Identities=30%  Similarity=0.884  Sum_probs=27.6

Q ss_pred             ccccccccccCceeeecCCCC-----CcccHhhHHHHHhc--CCCCccc
Q 028116          168 CSICLQDIIVGELARSLPHCH-----HTFHLACVDKWLIR--HGSCPVC  209 (213)
Q Consensus       168 C~ICle~~~~ge~v~~Lp~C~-----H~FH~~CI~~WL~~--~~sCPlC  209 (213)
                      |-||+++-.+.+ .-..| |.     .+.|..|+.+|+..  +.+|++|
T Consensus         1 CrIC~~~~~~~~-~li~p-C~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISP-CRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-S-SS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecc-cccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            789999877655 44566 54     37899999999984  5679988

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

Probab=97.16  E-value=0.00024  Score=72.74  Aligned_cols=50  Identities=32%  Similarity=0.786  Sum_probs=38.4

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC----------CCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH----------GSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~----------~sCPlCR~~v  213 (213)
                      +.++.|-||+.+--.......|. |+|+||..|..+-|++.          -+||+|+.++
T Consensus      3484 D~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~I 3543 (3738)
T KOG1428|consen 3484 DADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKI 3543 (3738)
T ss_pred             ccCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchh
Confidence            56788999988754445556776 99999999998766542          2899999864

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

Probab=97.09  E-value=0.00025  Score=64.90  Aligned_cols=48  Identities=29%  Similarity=0.724  Sum_probs=39.8

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      +++..|++|...+.+.  +... .|+|.||..|+.+|+..+..||.||.++
T Consensus        19 ~~~l~C~~C~~vl~~p--~~~~-~cgh~fC~~C~~~~~~~~~~cp~~~~~~   66 (391)
T KOG0297|consen   19 DENLLCPICMSVLRDP--VQTT-TCGHRFCAGCLLESLSNHQKCPVCRQEL   66 (391)
T ss_pred             cccccCccccccccCC--CCCC-CCCCcccccccchhhccCcCCccccccc
Confidence            5678999999987763  2223 4999999999999999999999998753

>PF13436 Gly-zipper_OmpA: Glycine-zipper containing OmpA-like membrane domain

Probab=97.03  E-value=0.00053  Score=52.64  Aligned_cols=39  Identities=38%  Similarity=0.503  Sum_probs=27.6

Q ss_pred             HhhhHHHHHHHHhhhcccccccccchhhhhhhhhHHHHHH
Q 028116           32 ALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVE   71 (213)
Q Consensus        32 a~~g~~~ga~~ga~~g~~~~~g~~rGa~~GaiaGav~sve   71 (213)
                      +++|+++||++|++.|- ...|.+.||++||+.|++....
T Consensus        56 a~~GA~~GA~~Ga~~G~-~~~ga~~GAa~Ga~~G~~~g~~   94 (118)
T PF13436_consen   56 AAIGAAAGAAIGAIIGG-NGRGAAIGAAAGAAVGAAAGAA   94 (118)
T ss_pred             HHHHHHHHHHHHhhcCC-CccchHHHHHHHHHHHHHhhhh
Confidence            45667777777777766 4557788888888888776654

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

Probab=96.87  E-value=0.00082  Score=56.80  Aligned_cols=49  Identities=24%  Similarity=0.718  Sum_probs=40.4

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc--------CCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR--------HGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~--------~~sCPlCR~~v  213 (213)
                      +.+.-|..|-..+..||.+|..  |=|.||..|++.|-..        -.+||.|..+|
T Consensus        48 DY~pNC~LC~t~La~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~ei  104 (299)
T KOG3970|consen   48 DYNPNCRLCNTPLASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEI  104 (299)
T ss_pred             CCCCCCceeCCccccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCcc
Confidence            3456799999999999988654  9999999999999763        23799998765

>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=96.71  E-value=0.00063  Score=50.28  Aligned_cols=33  Identities=30%  Similarity=0.713  Sum_probs=27.7

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHH
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVD  197 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~  197 (213)
                      +++..|++|-+.+.. ......| |+|+||..|++
T Consensus        76 ~~~~~C~vC~k~l~~-~~f~~~p-~~~v~H~~C~~  108 (109)
T PF10367_consen   76 TESTKCSVCGKPLGN-SVFVVFP-CGHVVHYSCIK  108 (109)
T ss_pred             CCCCCccCcCCcCCC-ceEEEeC-CCeEEeccccc
Confidence            346789999999987 5667888 99999999975

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

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

Probab=96.69  E-value=0.0028  Score=56.23  Aligned_cols=44  Identities=23%  Similarity=0.561  Sum_probs=35.7

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCccc
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVC  209 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlC  209 (213)
                      .+...|+||+..-++..   ++.-=|-+||.+||.+.+.+++.||+=
T Consensus       298 ~~~~~CpvClk~r~Npt---vl~vSGyVfCY~Ci~~Yv~~~~~CPVT  341 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQNPT---VLEVSGYVFCYPCIFSYVVNYGHCPVT  341 (357)
T ss_pred             CccccChhHHhccCCCc---eEEecceEEeHHHHHHHHHhcCCCCcc
Confidence            56788999999877632   232258999999999999999999974

>PF13441 Gly-zipper_YMGG: YMGG-like Gly-zipper

Probab=96.66  E-value=0.0021  Score=41.02  Aligned_cols=33  Identities=45%  Similarity=0.602  Sum_probs=20.6

Q ss_pred             HHhhhHHHHHHHHhhhcccccccccchhhhhhhhhHHH
Q 028116           31 FALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVL   68 (213)
Q Consensus        31 ~a~~g~~~ga~~ga~~g~~~~~g~~rGa~~GaiaGav~   68 (213)
                      -|+.|+.+|+++|+++|     .--+||.+||.+|++.
T Consensus         6 GA~iGA~~GA~iG~~~g-----~~~~GA~iGA~~Ga~~   38 (45)
T PF13441_consen    6 GAAIGAAAGAVIGAIIG-----NGGKGAAIGAAAGALA   38 (45)
T ss_pred             HHHHHHHHHHHHHHhhC-----CCcccchhhhhhhhhh
Confidence            46677788888888877     2234555555555543

>PF13488 Gly-zipper_Omp: Glycine zipper

Probab=96.65  E-value=0.0019  Score=41.45  Aligned_cols=35  Identities=43%  Similarity=0.611  Sum_probs=18.9

Q ss_pred             hHHHHHHHHhhhcccc---cccccchhhhhhhhhHHHH
Q 028116           35 GAFTGAITGALAGRAS---DCGVLRGAGLGAIAGAVLS   69 (213)
Q Consensus        35 g~~~ga~~ga~~g~~~---~~g~~rGa~~GaiaGav~s   69 (213)
                      |+.+||++|+++|..+   ..|-+-|+++|++.|+...
T Consensus         2 Ga~iGA~~Ga~iG~~~g~~~~ga~iGa~vGa~~G~~ig   39 (46)
T PF13488_consen    2 GAAIGAAAGAAIGAATGGPGKGAAIGAAVGAAVGAAIG   39 (46)
T ss_pred             cHHHHHHHHHHHHHHhCCchhhHHHHHHHHHHHHHHHH
Confidence            4445555555555444   3455666666666665543

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

Probab=96.64  E-value=0.0013  Score=42.48  Aligned_cols=44  Identities=23%  Similarity=0.521  Sum_probs=22.9

Q ss_pred             ccccccccccCc-eeeecCCCCCcccHhhHHHHHh-cCCCCcccCCC
Q 028116          168 CSICLQDIIVGE-LARSLPHCHHTFHLACVDKWLI-RHGSCPVCRRD  212 (213)
Q Consensus       168 C~ICle~~~~ge-~v~~Lp~C~H~FH~~CI~~WL~-~~~sCPlCR~~  212 (213)
                      |++|.+++...+ ...--+ |++.++..|..+-+. ..+.||-||++
T Consensus         1 cp~C~e~~d~~d~~~~PC~-Cgf~IC~~C~~~i~~~~~g~CPgCr~~   46 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCE-CGFQICRFCYHDILENEGGRCPGCREP   46 (48)
T ss_dssp             -TTTS-B--CCCTT--SST-TS----HHHHHHHTTSS-SB-TTT--B
T ss_pred             CCCcccccccCCCccccCc-CCCcHHHHHHHHHHhccCCCCCCCCCC
Confidence            799999984433 333344 899999999888886 47899999986

>PHA03096 p28-like protein; Provisional

Probab=96.58  E-value=0.0011  Score=58.22  Aligned_cols=46  Identities=28%  Similarity=0.665  Sum_probs=35.0

Q ss_pred             CcccccccccccC----ceeeecCCCCCcccHhhHHHHHhc---CCCCcccCC
Q 028116          166 SCCSICLQDIIVG----ELARSLPHCHHTFHLACVDKWLIR---HGSCPVCRR  211 (213)
Q Consensus       166 ~~C~ICle~~~~g----e~v~~Lp~C~H~FH~~CI~~WL~~---~~sCPlCR~  211 (213)
                      ..|.||++.....    ..-..|+.|.|.|+..||..|-..   ..+||.||.
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            6799999986643    245679999999999999999753   235666553

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=96.58  E-value=0.0019  Score=51.88  Aligned_cols=48  Identities=21%  Similarity=0.611  Sum_probs=31.9

Q ss_pred             CCCCcccccccccccCceeeecC--CCCCcccHhhHHHHHhc--CCCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLP--HCHHTFHLACVDKWLIR--HGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp--~C~H~FH~~CI~~WL~~--~~sCPlCR~~  212 (213)
                      ..+..|-||.++-.  +...--.  .=--..|.+|+++|+..  ..+||+|+.+
T Consensus         6 ~~~~~CRIC~~~~~--~~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~   57 (162)
T PHA02825          6 LMDKCCWICKDEYD--VVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGP   57 (162)
T ss_pred             CCCCeeEecCCCCC--CccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCe
Confidence            45688999998843  2222111  00016799999999975  4579999875

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

Probab=96.56  E-value=0.0019  Score=56.04  Aligned_cols=48  Identities=21%  Similarity=0.515  Sum_probs=36.0

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC--CCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH--GSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~--~sCPlCR~~v  213 (213)
                      ..+.+|++|-+.-..  .....+ |+|+||-.||.+=+...  -+||.|-.++
T Consensus       237 t~~~~C~~Cg~~Pti--P~~~~~-C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~  286 (298)
T KOG2879|consen  237 TSDTECPVCGEPPTI--PHVIGK-CGHIYCYYCIATSRLWDASFTCPLCGENV  286 (298)
T ss_pred             cCCceeeccCCCCCC--Ceeecc-ccceeehhhhhhhhcchhhcccCccCCCC
Confidence            667999999876332  233444 99999999999876643  5899997753

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

Probab=96.55  E-value=0.0012  Score=51.62  Aligned_cols=37  Identities=19%  Similarity=0.368  Sum_probs=30.8

Q ss_pred             CCCcccccccccccCceeeecCCCC------CcccHhhHHHHHh
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCH------HTFHLACVDKWLI  201 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~------H~FH~~CI~~WL~  201 (213)
                      ...+|.||++.+...+-+..++ |+      |+||..|+.+|-+
T Consensus        25 ~~~EC~IC~~~I~~~~GvV~vt-~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   25 CTVECQICFDRIDNNDGVVYVT-DGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             cCeeehhhhhhhhcCCCEEEEe-cCCeehHHHHHHHHHHHHHHh
Confidence            3688999999998855677777 76      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.

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

Probab=96.55  E-value=0.00056  Score=60.55  Aligned_cols=47  Identities=28%  Similarity=0.636  Sum_probs=37.5

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~  212 (213)
                      ....+|.+|---|.+..   ..+.|-|.||..||.+.|....+||.|...
T Consensus        13 n~~itC~LC~GYliDAT---TI~eCLHTFCkSCivk~l~~~~~CP~C~i~   59 (331)
T KOG2660|consen   13 NPHITCRLCGGYLIDAT---TITECLHTFCKSCIVKYLEESKYCPTCDIV   59 (331)
T ss_pred             ccceehhhccceeecch---hHHHHHHHHHHHHHHHHHHHhccCCcccee
Confidence            34688999976555532   334599999999999999999999999754

>PF05433 Rick_17kDa_Anti: Glycine zipper 2TM domain; InterPro: IPR008816 This domain includes a putative two transmembrane alpha-helical region that contains glycine zipper motifs []

Probab=96.55  E-value=0.0018  Score=40.80  Aligned_cols=37  Identities=43%  Similarity=0.614  Sum_probs=26.2

Q ss_pred             hHHHHHHHHhhhcccc--cccccchhhhhhhhhHHHHHH
Q 028116           35 GAFTGAITGALAGRAS--DCGVLRGAGLGAIAGAVLSVE   71 (213)
Q Consensus        35 g~~~ga~~ga~~g~~~--~~g~~rGa~~GaiaGav~sve   71 (213)
                      |+++|+++|+++|...  .++=..|+.+||+.|+++.-+
T Consensus         2 G~~~Ga~~Ga~~G~~ig~~~g~~~g~~~Ga~~Ga~~G~~   40 (42)
T PF05433_consen    2 GALIGAAVGAVAGSQIGGGNGRTLGAVAGAVAGALIGNQ   40 (42)
T ss_pred             chHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHHhh
Confidence            5566666666666655  567788889999999887643

The domain is found in several Rickettsia genus specific 17 kDa surface antigen proteins [].; GO: 0019867 outer membrane

>PF13441 Gly-zipper_YMGG: YMGG-like Gly-zipper

Probab=96.54  E-value=0.0017  Score=41.43  Aligned_cols=31  Identities=52%  Similarity=0.684  Sum_probs=20.7

Q ss_pred             HhhhHHHHHHHH-hhhcccccccccchhhhhhhhhHHH
Q 028116           32 ALAGAFTGAITG-ALAGRASDCGVLRGAGLGAIAGAVL   68 (213)
Q Consensus        32 a~~g~~~ga~~g-a~~g~~~~~g~~rGa~~GaiaGav~   68 (213)
                      |.+|+++|+++| .-.|-      +-|+++|+++|++.
T Consensus        11 A~~GA~iG~~~g~~~~GA------~iGA~~Ga~~G~~~   42 (45)
T PF13441_consen   11 AAAGAVIGAIIGNGGKGA------AIGAAAGALAGAAI   42 (45)
T ss_pred             HHHHHHHHHhhCCCcccc------hhhhhhhhhhhhhh
Confidence            567777777777 55442      35777777777764

>PF13488 Gly-zipper_Omp: Glycine zipper

Probab=96.49  E-value=0.002  Score=41.29  Aligned_cols=17  Identities=41%  Similarity=0.483  Sum_probs=7.7

Q ss_pred             hhhHHHHHHHHhhhccc
Q 028116           33 LAGAFTGAITGALAGRA   49 (213)
Q Consensus        33 ~~g~~~ga~~ga~~g~~   49 (213)
                      +.|+.+|+++|+.+|+.
T Consensus        25 ~iGa~vGa~~G~~ig~~   41 (46)
T PF13488_consen   25 AIGAAVGAAVGAAIGNY   41 (46)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            34444444444444443

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

Probab=96.49  E-value=0.0017  Score=58.17  Aligned_cols=47  Identities=28%  Similarity=0.646  Sum_probs=39.1

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .++..||||.-.--   .....| |+|.=|..||.+.|...+.|=.|+..+
T Consensus       420 sEd~lCpICyA~pi---~Avf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv  466 (489)
T KOG4692|consen  420 SEDNLCPICYAGPI---NAVFAP-CSHRSCYGCITQHLMNCKRCFFCKTTV  466 (489)
T ss_pred             cccccCcceecccc---hhhccC-CCCchHHHHHHHHHhcCCeeeEeccee
Confidence            67889999986522   244677 999999999999999999999998753

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

Probab=96.42  E-value=0.0015  Score=64.14  Aligned_cols=49  Identities=33%  Similarity=0.722  Sum_probs=41.3

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC-------CCCcccCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH-------GSCPVCRR  211 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~-------~sCPlCR~  211 (213)
                      .+..+|.||++.+.....+..-..|=|+||..||.+|-++.       =.||-|+.
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs  244 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS  244 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence            46788999999999988888777799999999999998641       15999983

>PF13436 Gly-zipper_OmpA: Glycine-zipper containing OmpA-like membrane domain

Probab=96.35  E-value=0.0038  Score=47.93  Aligned_cols=40  Identities=38%  Similarity=0.455  Sum_probs=34.7

Q ss_pred             HhhhHHHHHHHHhhhcccccccccchhhhhhhhhHHHHHHH
Q 028116           32 ALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVEL   72 (213)
Q Consensus        32 a~~g~~~ga~~ga~~g~~~~~g~~rGa~~GaiaGav~sve~   72 (213)
                      +..|+++||++||++|...+. --+|+++||.+||++..-.
T Consensus        52 ~~~ga~~GA~~GA~~Ga~~G~-~~~ga~~GAa~Ga~~G~~~   91 (118)
T PF13436_consen   52 TAGGAAIGAAAGAAIGAIIGG-NGRGAAIGAAAGAAVGAAA   91 (118)
T ss_pred             HHHHHHHHHHHHHHHHhhcCC-CccchHHHHHHHHHHHHHh
Confidence            459999999999999998777 7889999999999987543

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

Probab=96.25  E-value=0.0026  Score=57.91  Aligned_cols=47  Identities=23%  Similarity=0.569  Sum_probs=38.3

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc--------CCCCcccC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR--------HGSCPVCR  210 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~--------~~sCPlCR  210 (213)
                      ..--.|.||+++....+....+| |+|+||..|...++..        .-.||-++
T Consensus       182 ~slf~C~ICf~e~~G~~c~~~lp-C~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~  236 (445)
T KOG1814|consen  182 NSLFDCCICFEEQMGQHCFKFLP-CSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPK  236 (445)
T ss_pred             hhcccceeeehhhcCcceeeecc-cchHHHHHHHHHHHHHhhhcceeeeecCCCCC
Confidence            34578999999877668899999 9999999999999863        22687664

>PRK10510 putative outer membrane lipoprotein; Provisional

Probab=96.24  E-value=0.0052  Score=52.01  Aligned_cols=38  Identities=37%  Similarity=0.452  Sum_probs=22.3

Q ss_pred             HhhhHHHHHHHHhhhccc--ccccccchhhhhhhhhHHHH
Q 028116           32 ALAGAFTGAITGALAGRA--SDCGVLRGAGLGAIAGAVLS   69 (213)
Q Consensus        32 a~~g~~~ga~~ga~~g~~--~~~g~~rGa~~GaiaGav~s   69 (213)
                      |++|+++||++|++.|-.  ...|-+-||++|+.+|+...
T Consensus        39 a~~Ga~~Ga~~G~~~g~~~~~~~~a~~ga~~G~~~G~~~g   78 (219)
T PRK10510         39 AGIGSLVGAGIGALSSSKKDRGKGALIGAAAGAALGGGVG   78 (219)
T ss_pred             hHHHHHHHHHHHhhhcCCCcccchhhhHhHHHhhhhhhhh
Confidence            455566666666655521  12356667777777777665

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

Probab=96.03  E-value=0.00048  Score=62.21  Aligned_cols=49  Identities=27%  Similarity=0.646  Sum_probs=42.9

Q ss_pred             CCCcccccccccccC-ceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVG-ELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~g-e~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      -...|+||.+.++.. +....+- |+|.+|..|+.+||.+...||.||+++
T Consensus       195 lv~sl~I~~~slK~~y~k~~~~~-~g~~~~~~kL~k~L~~~~kl~~~~rel  244 (465)
T KOG0827|consen  195 LVGSLSICFESLKQNYDKISAIV-CGHIYHHGKLSKWLATKRKLPSCRREL  244 (465)
T ss_pred             HHhhhHhhHHHHHHHHHHHHHHh-hcccchhhHHHHHHHHHHHhHHHHhhh
Confidence            457899999999876 6677776 999999999999999999999999864

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

Probab=95.95  E-value=0.0062  Score=54.55  Aligned_cols=47  Identities=28%  Similarity=0.698  Sum_probs=37.8

Q ss_pred             CCCCCcccccccccccCceeeecCCCCCcccHhhHHHH--HhcCCCCcccCCC
Q 028116          162 PTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKW--LIRHGSCPVCRRD  212 (213)
Q Consensus       162 ~~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~W--L~~~~sCPlCR~~  212 (213)
                      ++++.-|-||-+.+.-   ...+| |+|..|..|-.+.  |-.+..||+||.+
T Consensus        58 DEen~~C~ICA~~~TY---s~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE  106 (493)
T COG5236          58 DEENMNCQICAGSTTY---SARYP-CGHQICHACAVRLRALYMQKGCPLCRTE  106 (493)
T ss_pred             ccccceeEEecCCceE---EEecc-CCchHHHHHHHHHHHHHhccCCCccccc
Confidence            3566779999887654   67899 9999999998654  4578899999975

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

Probab=95.77  E-value=0.0033  Score=55.02  Aligned_cols=43  Identities=26%  Similarity=0.444  Sum_probs=36.7

Q ss_pred             CcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCC
Q 028116          166 SCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD  212 (213)
Q Consensus       166 ~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~  212 (213)
                      ..|-||.+.|..   ..+. +|+|+||..|-.+-+++...|++|-++
T Consensus       242 f~c~icr~~f~~---pVvt-~c~h~fc~~ca~~~~qk~~~c~vC~~~  284 (313)
T KOG1813|consen  242 FKCFICRKYFYR---PVVT-KCGHYFCEVCALKPYQKGEKCYVCSQQ  284 (313)
T ss_pred             cccccccccccc---chhh-cCCceeehhhhccccccCCcceecccc
Confidence            459999999987   3344 499999999999999999999999764

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

Probab=95.66  E-value=0.0054  Score=55.02  Aligned_cols=43  Identities=33%  Similarity=0.672  Sum_probs=32.1

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~  212 (213)
                      .....|.||+++.++   ...+| |||+=+  |..-- +...+||+||+.
T Consensus       303 ~~p~lcVVcl~e~~~---~~fvp-cGh~cc--ct~cs-~~l~~CPvCR~r  345 (355)
T KOG1571|consen  303 PQPDLCVVCLDEPKS---AVFVP-CGHVCC--CTLCS-KHLPQCPVCRQR  345 (355)
T ss_pred             CCCCceEEecCCccc---eeeec-CCcEEE--chHHH-hhCCCCchhHHH
Confidence            556789999998766   66888 999966  55432 234569999975

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.48  E-value=0.019  Score=49.35  Aligned_cols=50  Identities=16%  Similarity=0.276  Sum_probs=43.1

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ....||||.+.+.+.-....|..|||+|...|+++....-..||+|-+++
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~pl  269 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPL  269 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcC
Confidence            45669999999988776667767999999999999999999999997764

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

Probab=95.31  E-value=0.0091  Score=49.69  Aligned_cols=43  Identities=26%  Similarity=0.553  Sum_probs=36.2

Q ss_pred             CcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCC
Q 028116          166 SCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD  212 (213)
Q Consensus       166 ~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~  212 (213)
                      -.|-||-++|+.   +.+.. |||.||..|..+=.+....|-+|-+.
T Consensus       197 F~C~iCKkdy~s---pvvt~-CGH~FC~~Cai~~y~kg~~C~~Cgk~  239 (259)
T COG5152         197 FLCGICKKDYES---PVVTE-CGHSFCSLCAIRKYQKGDECGVCGKA  239 (259)
T ss_pred             eeehhchhhccc---hhhhh-cchhHHHHHHHHHhccCCcceecchh
Confidence            479999999987   44554 99999999999888888999999653

>PRK10540 lipoprotein; Provisional

Probab=95.28  E-value=0.05  Score=38.20  Aligned_cols=34  Identities=35%  Similarity=0.411  Sum_probs=20.5

Q ss_pred             hhHHHHHHHHhhhcccccccccchhhhhhhhhHHHHHH
Q 028116           34 AGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVE   71 (213)
Q Consensus        34 ~g~~~ga~~ga~~g~~~~~g~~rGa~~GaiaGav~sve   71 (213)
                      .|++.|+++|++.|    .|-..|+.+||+.|+++.=+
T Consensus        36 ~Ga~~Ga~~Ga~~g----~g~~~g~~~Ga~~G~~~G~~   69 (72)
T PRK10540         36 IGAGAGALGGAVLT----DGSTLGTLGGAAVGGVIGHQ   69 (72)
T ss_pred             HHHHHHHHHHHHhc----CCcHHHHHHHHHHHHHHhHh
Confidence            45555555555554    34446777788887776533

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

Probab=95.17  E-value=0.016  Score=47.45  Aligned_cols=28  Identities=36%  Similarity=1.077  Sum_probs=23.5

Q ss_pred             CCCCcccHhhHHHHHhc-----C------CCCcccCCCC
Q 028116          186 HCHHTFHLACVDKWLIR-----H------GSCPVCRRDV  213 (213)
Q Consensus       186 ~C~H~FH~~CI~~WL~~-----~------~sCPlCR~~v  213 (213)
                      .|+.-||.-|+..||+.     +      ..||.|..||
T Consensus       189 qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pi  227 (234)
T KOG3268|consen  189 QCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPI  227 (234)
T ss_pred             ccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcc
Confidence            49999999999999973     2      3699998875

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

Probab=94.99  E-value=0.02  Score=50.40  Aligned_cols=43  Identities=30%  Similarity=0.630  Sum_probs=33.6

Q ss_pred             CcccccccccccCceeeecCCCCCcccHhhHHHHHh-cCCCCcccCC
Q 028116          166 SCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLI-RHGSCPVCRR  211 (213)
Q Consensus       166 ~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~-~~~sCPlCR~  211 (213)
                      ..|+.|-.-+..   ..+.|.|+|.||..||..-|. ....||.|.+
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            779999776544   334477999999999997776 4568999965

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

Probab=94.93  E-value=0.014  Score=51.11  Aligned_cols=45  Identities=27%  Similarity=0.663  Sum_probs=38.0

Q ss_pred             CcccccccccccCc-eeeecCCCCCcccHhhHHHHHhcCCCCcccCC
Q 028116          166 SCCSICLQDIIVGE-LARSLPHCHHTFHLACVDKWLIRHGSCPVCRR  211 (213)
Q Consensus       166 ~~C~ICle~~~~ge-~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~  211 (213)
                      .-||||.+.+..+. .+..++ |+|.-|..|...-...+-+||+|.+
T Consensus       159 ~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  159 FNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             CCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccc
Confidence            33999999976664 566777 9999999999998888899999976

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

Probab=94.85  E-value=0.02  Score=36.10  Aligned_cols=41  Identities=24%  Similarity=0.715  Sum_probs=23.1

Q ss_pred             ccccccccccCceeeecCCCCCcccHhhHHHHHhcCC--CCccc
Q 028116          168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG--SCPVC  209 (213)
Q Consensus       168 C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~--sCPlC  209 (213)
                      |.+|.+-...|..=... .|+=.+|..|++.+++.+.  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~-~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNR-DCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS---S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCC-ccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            66777766665433222 4888999999999998765  79988

; PDB: 3NW0_A 2CT0_A.

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

Probab=94.79  E-value=0.013  Score=55.21  Aligned_cols=46  Identities=24%  Similarity=0.611  Sum_probs=35.1

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc-----CCCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR-----HGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~-----~~sCPlCR~~  212 (213)
                      .+...|-+|-+.-++   ..... |.|.||.-||.++...     +-+||.|-..
T Consensus       534 k~~~~C~lc~d~aed---~i~s~-ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~  584 (791)
T KOG1002|consen  534 KGEVECGLCHDPAED---YIESS-CHHKFCRLCIKEYVESFMENNNVTCPVCHIG  584 (791)
T ss_pred             cCceeecccCChhhh---hHhhh-hhHHHHHHHHHHHHHhhhcccCCCCcccccc
Confidence            456789999886433   44554 9999999999988763     4589999764

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=94.56  E-value=0.016  Score=38.39  Aligned_cols=32  Identities=28%  Similarity=0.590  Sum_probs=25.6

Q ss_pred             ceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          179 ELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       179 e~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ..-..+| |+|+.+..|.+-+  +-+-||+|-+++
T Consensus        18 ~~~~~~p-CgH~I~~~~f~~~--rYngCPfC~~~~   49 (55)
T PF14447_consen   18 TKGTVLP-CGHLICDNCFPGE--RYNGCPFCGTPF   49 (55)
T ss_pred             ccccccc-ccceeeccccChh--hccCCCCCCCcc
Confidence            3445788 9999999997764  778899998764

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

Probab=94.51  E-value=0.055  Score=49.06  Aligned_cols=50  Identities=28%  Similarity=0.676  Sum_probs=31.9

Q ss_pred             CCCCccccccccccc-------------CceeeecCC-----CCCcccHhhHHHHHhc-------------CCCCcccCC
Q 028116          163 TQSSCCSICLQDIIV-------------GELARSLPH-----CHHTFHLACVDKWLIR-------------HGSCPVCRR  211 (213)
Q Consensus       163 ~~~~~C~ICle~~~~-------------ge~v~~Lp~-----C~H~FH~~CI~~WL~~-------------~~sCPlCR~  211 (213)
                      ++.+.|-=|++.-..             |......|.     |.-++|.+|+-+|+..             +..||+||+
T Consensus       269 ~e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa  348 (358)
T PF10272_consen  269 QELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRA  348 (358)
T ss_pred             cccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcc
Confidence            566789999875322             101111122     4466789999999863             337999998


Q ss_pred             C
Q 028116          212 D  212 (213)
Q Consensus       212 ~  212 (213)
                      +
T Consensus       349 ~  349 (358)
T PF10272_consen  349 K  349 (358)
T ss_pred             c
Confidence            6

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

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.28  E-value=0.016  Score=49.91  Aligned_cols=49  Identities=31%  Similarity=0.773  Sum_probs=35.0

Q ss_pred             CCCCcccccccccccCcee-eecCCCC-----CcccHhhHHHHHhcC--------CCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELA-RSLPHCH-----HTFHLACVDKWLIRH--------GSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v-~~Lp~C~-----H~FH~~CI~~WL~~~--------~sCPlCR~~  212 (213)
                      +.+..|-||+..=++.... .+-| |.     |..|..|+..|+..+        -+||-|+++
T Consensus        18 e~eR~CWiCF~TdeDn~~a~WV~P-CrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTE   80 (293)
T KOG3053|consen   18 ELERCCWICFATDEDNRLAAWVHP-CRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTE   80 (293)
T ss_pred             ccceeEEEEeccCcccchhhhccc-ccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcch
Confidence            5678899998764433222 3456 63     899999999999642        269999874

>PRK11280 hypothetical protein; Provisional

Probab=93.95  E-value=0.048  Score=44.43  Aligned_cols=40  Identities=25%  Similarity=0.376  Sum_probs=28.7

Q ss_pred             hhHHHHHHHHhhhcccccccc--cchhhhhhhhhHHHHHHHh
Q 028116           34 AGAFTGAITGALAGRASDCGV--LRGAGLGAIAGAVLSVELL   73 (213)
Q Consensus        34 ~g~~~ga~~ga~~g~~~~~g~--~rGa~~GaiaGav~sve~~   73 (213)
                      .|+++||++|+++|..-..|=  .-++.+||++|+++.=++-
T Consensus        66 ~Gtv~Gav~Gg~~G~~iGgG~Gr~~at~~Ga~~G~~~G~~i~  107 (170)
T PRK11280         66 AGSVLGAVAGGVLGHQFGGGRGKDVATVAGALGGGYAGNQIQ  107 (170)
T ss_pred             hhHHHHHHHHHHhhhhccCCCccHHHHHHHHHHHHHHHHHHH
Confidence            678888888888887765542  3467888888888876643

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

Probab=93.80  E-value=0.0098  Score=52.14  Aligned_cols=41  Identities=27%  Similarity=0.668  Sum_probs=30.1

Q ss_pred             CCcccccccccccCceeeecCCCCCc-ccHhhHHHHHhcCCCCcccCCCC
Q 028116          165 SSCCSICLQDIIVGELARSLPHCHHT-FHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       165 ~~~C~ICle~~~~ge~v~~Lp~C~H~-FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      +..|.||++.-.+   -..|+ |||. -|..|-.+    -+.||+||+.|
T Consensus       300 ~~LC~ICmDaP~D---CvfLe-CGHmVtCt~CGkr----m~eCPICRqyi  341 (350)
T KOG4275|consen  300 RRLCAICMDAPRD---CVFLE-CGHMVTCTKCGKR----MNECPICRQYI  341 (350)
T ss_pred             HHHHHHHhcCCcc---eEEee-cCcEEeehhhccc----cccCchHHHHH
Confidence            5679999987443   45787 9998 46777544    34899999753

>PRK10540 lipoprotein; Provisional

Probab=93.51  E-value=0.13  Score=36.11  Aligned_cols=13  Identities=46%  Similarity=0.598  Sum_probs=5.4

Q ss_pred             hHHHHHHHHhhhc
Q 028116           35 GAFTGAITGALAG   47 (213)
Q Consensus        35 g~~~ga~~ga~~g   47 (213)
                      |+.+|+.+|++.|
T Consensus        33 g~~~Ga~~Ga~~G   45 (72)
T PRK10540         33 NTAIGAGAGALGG   45 (72)
T ss_pred             hhHHHHHHHHHHH
Confidence            3344444444433

>PF04641 Rtf2: Rtf2 RING-finger

Probab=93.32  E-value=0.085  Score=45.66  Aligned_cols=49  Identities=16%  Similarity=0.322  Sum_probs=37.4

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~  212 (213)
                      .....|||...+|........+-.|||+|-..++.+- .....||+|-.+
T Consensus       111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~  159 (260)
T PF04641_consen  111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKP  159 (260)
T ss_pred             CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-cccccccccCCc
Confidence            4567799999999655444444339999999999997 235679999765

>PF06897 DUF1269: Protein of unknown function (DUF1269); InterPro: IPR009200 There are currently no experimental data for members of this group or their homologues

Probab=93.31  E-value=0.085  Score=39.46  Aligned_cols=21  Identities=57%  Similarity=0.803  Sum_probs=11.0

Q ss_pred             hhHHHHHHHHhhhcccccccc
Q 028116           34 AGAFTGAITGALAGRASDCGV   54 (213)
Q Consensus        34 ~g~~~ga~~ga~~g~~~~~g~   54 (213)
                      +|+++||.+||+.|..++.|+
T Consensus        20 ~G~~~GA~~Gal~G~l~d~gI   40 (102)
T PF06897_consen   20 LGAAVGAAAGALAGALSDYGI   40 (102)
T ss_pred             HHHHHHHHHHHHHhHHhhCCC
Confidence            555555555555555554443

However, these proteins are predicted to contain two or more transmembrane segments.

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

Probab=93.14  E-value=0.04  Score=54.68  Aligned_cols=36  Identities=22%  Similarity=0.623  Sum_probs=29.3

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHH
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWL  200 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL  200 (213)
                      +.+++|.+|-..+... .-.+-| |||.||.+|+.+-.
T Consensus       815 ep~d~C~~C~~~ll~~-pF~vf~-CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  815 EPQDSCDHCGRPLLIK-PFYVFP-CGHCFHRDCLIRHV  850 (911)
T ss_pred             cCccchHHhcchhhcC-cceeee-ccchHHHHHHHHHH
Confidence            5679999999887764 455677 99999999998764

>TIGR03789 pdsO proteobacterial sortase system OmpA family protein

Probab=93.13  E-value=0.063  Score=46.14  Aligned_cols=35  Identities=34%  Similarity=0.510  Sum_probs=19.3

Q ss_pred             hHHHHHHHHhhhcccccccccchhhhhhhhhHHHHHH
Q 028116           35 GAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVE   71 (213)
Q Consensus        35 g~~~ga~~ga~~g~~~~~g~~rGa~~GaiaGav~sve   71 (213)
                      |+.+|+.+||++|-.-. |. -|+.+|++.|+++.-+
T Consensus        42 ~~~~g~~~ga~~g~~~g-g~-~G~~~G~~~G~~~g~~   76 (239)
T TIGR03789        42 EALIGLGSGALLGALVG-GP-VGAIIGGITGGLIGQA   76 (239)
T ss_pred             chhhhHHHHHHHhhhhc-cH-HHHHHHHHHHHHhhhh
Confidence            44444444444443221 33 4777777777777654

A newly defined histidine kinase (TIGR03785) and response regulator (TIGR03787) gene pair occurs exclusively in Proteobacteria, mostly of marine origin, nearly all of which contain a subfamily 6 sortase (TIGR03784) and its single dedicated target protein (TIGR03788) adjacent to to the sortase. This protein family shows up in only in those species with the histidine kinase/response regulator gene pair, and often adjacent to that pair. It belongs to the OmpA protein family (pfam00691). Its function is unknown. We assign the gene symbol pdsO, for Proteobacterial Dedicated Sortase system OmpA family protein.

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=92.92  E-value=0.12  Score=34.23  Aligned_cols=41  Identities=24%  Similarity=0.596  Sum_probs=33.4

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcc
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPV  208 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPl  208 (213)
                      ....|++|-+.|.+++.+.+-|.|+-.+|..|-++    ...|-.
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~----~g~C~~   44 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK----AGGCIN   44 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh----CCceEe
Confidence            45789999999998888889999999999999544    445543

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

Probab=92.14  E-value=0.061  Score=53.21  Aligned_cols=42  Identities=29%  Similarity=0.668  Sum_probs=31.4

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRR  211 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~  211 (213)
                      ....|+.|--.++-.  ...- .|+|.||..|+.   .+...||-|+.
T Consensus       839 q~skCs~C~~~LdlP--~VhF-~CgHsyHqhC~e---~~~~~CP~C~~  880 (933)
T KOG2114|consen  839 QVSKCSACEGTLDLP--FVHF-LCGHSYHQHCLE---DKEDKCPKCLP  880 (933)
T ss_pred             eeeeecccCCccccc--eeee-ecccHHHHHhhc---cCcccCCccch
Confidence            346899997665542  3344 499999999998   45678999986

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

Probab=92.04  E-value=0.073  Score=47.19  Aligned_cols=44  Identities=30%  Similarity=0.729  Sum_probs=29.5

Q ss_pred             CCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          165 SSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       165 ~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .-.|--|-  |-..---|..| |+|+||.+|-..  ..-+.||.|-.+|
T Consensus        90 VHfCd~Cd--~PI~IYGRmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen   90 VHFCDRCD--FPIAIYGRMIP-CKHVFCLECARS--DSDKICPLCDDRV  133 (389)
T ss_pred             eEeecccC--Ccceeeecccc-cchhhhhhhhhc--CccccCcCcccHH
Confidence            34577773  33323446788 999999999643  2356899997653

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

Probab=91.73  E-value=0.077  Score=44.61  Aligned_cols=37  Identities=30%  Similarity=0.716  Sum_probs=28.5

Q ss_pred             ccccccccccCceeeecCCCCCc-ccHhhHHHHHhcCCCCcccCCC
Q 028116          168 CSICLQDIIVGELARSLPHCHHT-FHLACVDKWLIRHGSCPVCRRD  212 (213)
Q Consensus       168 C~ICle~~~~ge~v~~Lp~C~H~-FH~~CI~~WL~~~~sCPlCR~~  212 (213)
                      |-.|-+.   +-.|..+| |.|. +|..|-..    -..||+|+.+
T Consensus       161 Cr~C~~~---~~~VlllP-CrHl~lC~~C~~~----~~~CPiC~~~  198 (207)
T KOG1100|consen  161 CRKCGER---EATVLLLP-CRHLCLCGICDES----LRICPICRSP  198 (207)
T ss_pred             ceecCcC---CceEEeec-ccceEeccccccc----CccCCCCcCh
Confidence            8888665   34588999 9887 88889554    4569999975

>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=91.61  E-value=0.053  Score=34.91  Aligned_cols=27  Identities=33%  Similarity=0.909  Sum_probs=21.4

Q ss_pred             C-CCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          187 C-HHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       187 C-~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      | .|+.+..|+..-|.+...||+|.+++
T Consensus        18 C~dHYLCl~CLt~ml~~s~~C~iC~~~L   45 (50)
T PF03854_consen   18 CSDHYLCLNCLTLMLSRSDRCPICGKPL   45 (50)
T ss_dssp             -SS-EEEHHHHHHT-SSSSEETTTTEE-
T ss_pred             ecchhHHHHHHHHHhccccCCCcccCcC
Confidence            6 49999999999999999999998764

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.

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

Probab=91.25  E-value=0.073  Score=52.10  Aligned_cols=42  Identities=29%  Similarity=0.687  Sum_probs=32.7

Q ss_pred             CcccccccccccCceeeecCCCCCcccHhhHHHHHhcC--CCCcccCCC
Q 028116          166 SCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH--GSCPVCRRD  212 (213)
Q Consensus       166 ~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~--~sCPlCR~~  212 (213)
                      ..|+||++    -+.....+ |+|.||..|+.+-+...  ..||+||..
T Consensus       455 ~~c~ic~~----~~~~~it~-c~h~~c~~c~~~~i~~~~~~~~~~cr~~  498 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITR-CGHDFCVECLKKSIQQSENAPCPLCRNV  498 (674)
T ss_pred             cccccccc----cccceeec-ccchHHHHHHHhccccccCCCCcHHHHH
Confidence            78999999    23455565 99999999998877642  369999964

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=91.19  E-value=0.14  Score=45.92  Aligned_cols=49  Identities=22%  Similarity=0.636  Sum_probs=34.3

Q ss_pred             CCCCcccccccccccCcee-eecCCCCCcccHhhHHHHHh-cCCCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELA-RSLPHCHHTFHLACVDKWLI-RHGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v-~~Lp~C~H~FH~~CI~~WL~-~~~sCPlCR~~  212 (213)
                      ++++.||.|+|++...++- .-.| ||-..|.-|-..--+ -+..||-||+.
T Consensus        12 deed~cplcie~mditdknf~pc~-cgy~ic~fc~~~irq~lngrcpacrr~   62 (480)
T COG5175          12 DEEDYCPLCIEPMDITDKNFFPCP-CGYQICQFCYNNIRQNLNGRCPACRRK   62 (480)
T ss_pred             cccccCcccccccccccCCcccCC-cccHHHHHHHHHHHhhccCCChHhhhh
Confidence            4455699999998776543 3456 998877777544322 36799999974

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

Probab=91.01  E-value=0.12  Score=45.01  Aligned_cols=48  Identities=23%  Similarity=0.598  Sum_probs=35.5

Q ss_pred             CCCcccccccccccCce-eeecCCCC-----CcccHhhHHHHHh--cCCCCcccCCC
Q 028116          164 QSSCCSICLQDIIVGEL-ARSLPHCH-----HTFHLACVDKWLI--RHGSCPVCRRD  212 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~-v~~Lp~C~-----H~FH~~CI~~WL~--~~~sCPlCR~~  212 (213)
                      ++..|-||.++...... .-..| |.     +..|..|+++|+.  .+..|.+|...
T Consensus        77 ~~~~cRIc~~~~~~~~~~~l~~p-C~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~  132 (323)
T KOG1609|consen   77 SGPICRICHEEDEESNGLLLISP-CSCKGSLAYVHRSCLEKWFSIKGNITCEICKSF  132 (323)
T ss_pred             CCCcEEEEecccccccccccccC-ccccCcHHHHHHHHHHhhhccccCeeeeccccc
Confidence            35789999998655332 34555 65     6789999999998  45679999763

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

Probab=90.92  E-value=0.059  Score=55.42  Aligned_cols=45  Identities=27%  Similarity=0.651  Sum_probs=36.2

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRR  211 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~  211 (213)
                      .-..|+||++.+..-. . +- .|+|.++..|...|+..+..||+|+.
T Consensus      1152 ~~~~c~ic~dil~~~~-~-I~-~cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQG-G-IA-GCGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred             cccchHHHHHHHHhcC-C-ee-eechhHhhhHHHHHHHHhccCcchhh
Confidence            3457999999877421 2 22 49999999999999999999999973

>PF06897 DUF1269: Protein of unknown function (DUF1269); InterPro: IPR009200 There are currently no experimental data for members of this group or their homologues

Probab=90.60  E-value=0.11  Score=38.92  Aligned_cols=35  Identities=46%  Similarity=0.639  Sum_probs=20.2

Q ss_pred             HhhhHHHHHHHHhhhcccccccccchhhhhhhhhHH
Q 028116           32 ALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAV   67 (213)
Q Consensus        32 a~~g~~~ga~~ga~~g~~~~~g~~rGa~~GaiaGav   67 (213)
                      |+.|++.|.++|.+.+. ---|++=||+.||++|++
T Consensus         1 A~~G~~~G~LiGll~~~-pl~G~~~GA~~Gal~G~l   35 (102)
T PF06897_consen    1 ALSGALWGLLIGLLFGP-PLLGAAVGAAAGALAGAL   35 (102)
T ss_pred             CcchhHHHHHHHHHhhh-HHHHHHHHHHHHHHHhHH
Confidence            45566666666666443 123445566667777753

However, these proteins are predicted to contain two or more transmembrane segments.

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

Probab=90.52  E-value=0.12  Score=47.39  Aligned_cols=39  Identities=26%  Similarity=0.445  Sum_probs=28.9

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHh
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLI  201 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~  201 (213)
                      ....+|.||..+....+......+|+|.||.+|..+.+.
T Consensus       144 ~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~ie  182 (384)
T KOG1812|consen  144 LPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIE  182 (384)
T ss_pred             cccccCccCccccccHhhhHHHhcccchhhhHHhHHHhh
Confidence            346889999955555433333446999999999998886

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

Probab=89.84  E-value=0.24  Score=43.95  Aligned_cols=43  Identities=21%  Similarity=0.552  Sum_probs=32.8

Q ss_pred             CCCCcccccccccccCceeeecCCC--CCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHC--HHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C--~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .+-.+||||.+.+...    .. +|  ||+-|..|-.   +.++.||.||.++
T Consensus        46 ~~lleCPvC~~~l~~P----i~-QC~nGHlaCssC~~---~~~~~CP~Cr~~~   90 (299)
T KOG3002|consen   46 LDLLDCPVCFNPLSPP----IF-QCDNGHLACSSCRT---KVSNKCPTCRLPI   90 (299)
T ss_pred             hhhccCchhhccCccc----ce-ecCCCcEehhhhhh---hhcccCCcccccc
Confidence            4568899999998774    22 25  6999999865   3588999999874

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.78  E-value=0.17  Score=44.53  Aligned_cols=26  Identities=27%  Similarity=0.888  Sum_probs=20.9

Q ss_pred             CCCcccHhhHHHHHh-------------cCCCCcccCCC
Q 028116          187 CHHTFHLACVDKWLI-------------RHGSCPVCRRD  212 (213)
Q Consensus       187 C~H~FH~~CI~~WL~-------------~~~sCPlCR~~  212 (213)
                      |.-++|..|+-+|+.             .+.+||+||++
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~  363 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKN  363 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhc
Confidence            567788999999985             34589999986

>PF05433 Rick_17kDa_Anti: Glycine zipper 2TM domain; InterPro: IPR008816 This domain includes a putative two transmembrane alpha-helical region that contains glycine zipper motifs []

Probab=89.77  E-value=0.21  Score=31.33  Aligned_cols=33  Identities=39%  Similarity=0.643  Sum_probs=16.2

Q ss_pred             hhhHHHHHHHHhhh--cccccccccchhhhhhhhh
Q 028116           33 LAGAFTGAITGALA--GRASDCGVLRGAGLGAIAG   65 (213)
Q Consensus        33 ~~g~~~ga~~ga~~--g~~~~~g~~rGa~~GaiaG   65 (213)
                      ++|+++|+++|...  +.-.-.+.+=|+.+|++.|
T Consensus         4 ~~Ga~~Ga~~G~~ig~~~g~~~g~~~Ga~~Ga~~G   38 (42)
T PF05433_consen    4 LIGAAVGAVAGSQIGGGNGRTLGAVAGAVAGALIG   38 (42)
T ss_pred             HHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHH
Confidence            34455555555444  3444444455555555544

The domain is found in several Rickettsia genus specific 17 kDa surface antigen proteins [].; GO: 0019867 outer membrane

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

Probab=89.28  E-value=0.32  Score=47.80  Aligned_cols=42  Identities=24%  Similarity=0.469  Sum_probs=31.3

Q ss_pred             CCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcc
Q 028116          165 SSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPV  208 (213)
Q Consensus       165 ~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPl  208 (213)
                      ...|.+|-..+. |..+ ..+.|+|.-|..|+.+|+..+.-||.
T Consensus       779 ~~~CtVC~~vi~-G~~~-~c~~C~H~gH~sh~~sw~~~~s~ca~  820 (839)
T KOG0269|consen  779 SAKCTVCDLVIR-GVDV-WCQVCGHGGHDSHLKSWFFKASPCAK  820 (839)
T ss_pred             hcCceeecceee-eeEe-ecccccccccHHHHHHHHhcCCCCcc
Confidence            346888855433 3333 34569999999999999999988876

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

Probab=89.21  E-value=0.25  Score=48.92  Aligned_cols=50  Identities=20%  Similarity=0.544  Sum_probs=35.9

Q ss_pred             CCCCcccccccccccCceeeecCCCC---CcccHhhHHHHHhcC--CCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCH---HTFHLACVDKWLIRH--GSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~---H~FH~~CI~~WL~~~--~sCPlCR~~  212 (213)
                      +++..|.||..+=.+++..-.--+|.   .+.|..|+.+|+...  ..|-+|..+
T Consensus        10 ~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~   64 (1175)
T COG5183          10 EDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYE   64 (1175)
T ss_pred             ccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecce
Confidence            55689999998755555443322343   569999999999854  469999875

>PRK10510 putative outer membrane lipoprotein; Provisional

Probab=88.83  E-value=0.52  Score=39.87  Aligned_cols=37  Identities=41%  Similarity=0.431  Sum_probs=29.7

Q ss_pred             hhHHHHHHHHhhhccccccc--ccchhhhhhhhhHHHHH
Q 028116           34 AGAFTGAITGALAGRASDCG--VLRGAGLGAIAGAVLSV   70 (213)
Q Consensus        34 ~g~~~ga~~ga~~g~~~~~g--~~rGa~~GaiaGav~sv   70 (213)
                      .|+.+||++||++|..++..  --+|+++||..||.+.-
T Consensus        37 ~ga~~Ga~~Ga~~G~~~g~~~~~~~~a~~ga~~G~~~G~   75 (219)
T PRK10510         37 IGAGIGSLVGAGIGALSSSKKDRGKGALIGAAAGAALGG   75 (219)
T ss_pred             hhhHHHHHHHHHHHhhhcCCCcccchhhhHhHHHhhhhh
Confidence            48999999999999998653  35688889988876654

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

Probab=88.50  E-value=0.58  Score=30.31  Aligned_cols=43  Identities=23%  Similarity=0.618  Sum_probs=18.8

Q ss_pred             CcccccccccccCceeeecCCCCCcccHhhHHHHHhc---CC--CCcccCCC
Q 028116          166 SCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR---HG--SCPVCRRD  212 (213)
Q Consensus       166 ~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~---~~--sCPlCR~~  212 (213)
                      ..|+|..+.+..  .+|-. .|.|.-+.+ ++.||..   ++  .||+|.++
T Consensus         3 L~CPls~~~i~~--P~Rg~-~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRI--PVRGK-NCKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SS--EEEET-T--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEEEe--CccCC-cCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            468888887755  34444 599983322 2345542   22  59999875

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.

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

Probab=88.28  E-value=0.13  Score=50.06  Aligned_cols=44  Identities=32%  Similarity=0.725  Sum_probs=35.5

Q ss_pred             CCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCC---CCcccCCC
Q 028116          165 SSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG---SCPVCRRD  212 (213)
Q Consensus       165 ~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~---sCPlCR~~  212 (213)
                      ..+|+||++.+...    .+-+|.|.|+.-|+..-|..++   .||+|+..
T Consensus        21 ~lEc~ic~~~~~~p----~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~   67 (684)
T KOG4362|consen   21 ILECPICLEHVKEP----SLLKCDHIFLKFCLNKLFESKKGPKQCALCKSD   67 (684)
T ss_pred             hccCCceeEEeecc----chhhhhHHHHhhhhhceeeccCccccchhhhhh
Confidence            58899999998874    3346999999999987776544   79999854

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

Probab=87.89  E-value=0.41  Score=43.73  Aligned_cols=47  Identities=15%  Similarity=0.268  Sum_probs=38.8

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC---CCCcccCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH---GSCPVCRR  211 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~---~sCPlCR~  211 (213)
                      .--.|||=.|.-.+.+.+..|. |||+...+=+++..+..   -.||.|=.
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~  382 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYCPV  382 (394)
T ss_pred             ceeecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence            3456999988888888899998 99999999999987653   36999943

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

Probab=87.83  E-value=0.3  Score=48.03  Aligned_cols=25  Identities=28%  Similarity=0.709  Sum_probs=22.4

Q ss_pred             ecCCCCCcccHhhHHHHHhcCCCCcc
Q 028116          183 SLPHCHHTFHLACVDKWLIRHGSCPV  208 (213)
Q Consensus       183 ~Lp~C~H~FH~~CI~~WL~~~~sCPl  208 (213)
                      ... |+|..|..|...|+.....||.
T Consensus      1045 Cg~-C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1045 CGT-CGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             hcc-ccccccHHHHHHHHhcCCcCCC
Confidence            454 9999999999999999999984

>PLN02720 complex II

Probab=87.81  E-value=0.37  Score=37.49  Aligned_cols=54  Identities=24%  Similarity=0.307  Sum_probs=35.7

Q ss_pred             HHHhhhHHHHHHH-Hhhhcccccccccchh----hhhhhhhHHHHHHHhhhcccceeccCC
Q 028116           30 LFALAGAFTGAIT-GALAGRASDCGVLRGA----GLGAIAGAVLSVELLEASRAYWCLERT   85 (213)
Q Consensus        30 ~~a~~g~~~ga~~-ga~~g~~~~~g~~rGa----~~GaiaGav~sve~~e~s~~~W~~d~~   85 (213)
                      -||++|+++||+- |+++=.-+.+  .+||    +-|+|-|..+.-|+.+.-..+.+.|.-
T Consensus        67 ~fa~~Ga~vGa~~tag~a~kysk~--phga~lsfl~G~~~G~~~G~EvAnh~lqLYk~d~m  125 (140)
T PLN02720         67 TFAVTGAAVGAVSTAGVAWKYSKS--PHGAALAFLGGGVFGWAFGQEVANHWLQLYKFDTM  125 (140)
T ss_pred             HHHhhhhhhhhhhhhHHHHHhhcC--CchHHHHHhccchhhhhHhHHHHHHHHHHHhcccc
Confidence            3788999999874 3332222222  4555    457888888888888888777766643

>PF05818 TraT: Enterobacterial TraT complement resistance protein; InterPro: IPR008874 The traT gene is one of the F factor transfer genes and encodes an outer membrane protein which is involved in interactions between Escherichia coli and its surroundings []

Probab=87.08  E-value=0.53  Score=39.80  Aligned_cols=36  Identities=39%  Similarity=0.615  Sum_probs=20.5

Q ss_pred             hhHHHHHHHHhhhcccccccccchhhhh-hhhhHHHHHH
Q 028116           34 AGAFTGAITGALAGRASDCGVLRGAGLG-AIAGAVLSVE   71 (213)
Q Consensus        34 ~g~~~ga~~ga~~g~~~~~g~~rGa~~G-aiaGav~sve   71 (213)
                      .|++.||.+|+.+|-.+  +--+|+.+| .++||.++.-
T Consensus        88 gga~~Ga~~G~~~g~~~--~~~~g~~~G~GlaGalig~~  124 (215)
T PF05818_consen   88 GGALAGAATGAAIGAYN--SGSAGAAIGAGLAGALIGMI  124 (215)
T ss_pred             hhHHHHhHHhhhhcccc--CCccchhhhhhHHHhHHHHH
Confidence            46666777776666443  223455566 5666555543

The protein plays a role in preventing unproductive conjugation between bacteria carrying like plasmids.; GO: 0046999 regulation of conjugation, 0019867 outer membrane

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

Probab=86.35  E-value=0.33  Score=46.32  Aligned_cols=42  Identities=38%  Similarity=0.972  Sum_probs=35.4

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~  212 (213)
                      +....|.||+++.    ..+..+ |.   |..|..+|+..+..||+|++.
T Consensus       477 ~~~~~~~~~~~~~----~~~~~~-~~---~~~~l~~~~~~~~~~pl~~~~  518 (543)
T KOG0802|consen  477 EPNDVCAICYQEM----SARITP-CS---HALCLRKWLYVQEVCPLCHTY  518 (543)
T ss_pred             cccCcchHHHHHH----Hhcccc-cc---chhHHHhhhhhccccCCCchh
Confidence            4567899999997    355666 88   999999999999999999864

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

Probab=85.72  E-value=0.47  Score=46.95  Aligned_cols=49  Identities=10%  Similarity=0.150  Sum_probs=35.4

Q ss_pred             CCCCcccccccccccCc---eeeecCCCCCcccHhhHHHHHhc------CCCCcccCC
Q 028116          163 TQSSCCSICLQDIIVGE---LARSLPHCHHTFHLACVDKWLIR------HGSCPVCRR  211 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge---~v~~Lp~C~H~FH~~CI~~WL~~------~~sCPlCR~  211 (213)
                      ....+|.+|.-++...+   ..-.+..|.|.||..||.+|+.+      +-.||+|..
T Consensus        94 a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~  151 (1134)
T KOG0825|consen   94 AESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEE  151 (1134)
T ss_pred             ccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHH
Confidence            45677888888887732   22223369999999999999864      446899865

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

Probab=85.59  E-value=0.69  Score=40.25  Aligned_cols=46  Identities=30%  Similarity=0.800  Sum_probs=33.6

Q ss_pred             CcccccccccccCceee---ecCCCCCcccHhhHHHHHh---------cCCCCcccCC
Q 028116          166 SCCSICLQDIIVGELAR---SLPHCHHTFHLACVDKWLI---------RHGSCPVCRR  211 (213)
Q Consensus       166 ~~C~ICle~~~~ge~v~---~Lp~C~H~FH~~CI~~WL~---------~~~sCPlCR~  211 (213)
                      .+|.+|.+++.+.+..+   .-|.|.-.+|..|+..-+.         ....||.|++
T Consensus       183 ~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~  240 (276)
T KOG3005|consen  183 VECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEK  240 (276)
T ss_pred             hhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhc
Confidence            68999999994433333   2346899999999988443         2357999986

>PRK09430 djlA Dna-J like membrane chaperone protein; Provisional

Probab=85.46  E-value=0.75  Score=40.08  Aligned_cols=37  Identities=30%  Similarity=0.396  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHhhhcccccccccch
Q 028116           18 FIAGAISGTLTGLFALAGAFTGAITGALAGRASDCGVLRG   57 (213)
Q Consensus        18 ~~~~~~~~~~~~~~a~~g~~~ga~~ga~~g~~~~~g~~rG   57 (213)
                      +.++++.+++-++|   |...||+.|++.|+.-+.|..++
T Consensus         3 ~~gki~g~~~G~~~---~g~~Ga~~G~~~Gh~~d~~~~~~   39 (267)
T PRK09430          3 YWGKILGFAFGFLF---GGFFGALLGLLIGHMFDKARSRK   39 (267)
T ss_pred             hHHHHHHHHHHHHH---hhHHHHHHHHHHHhHHhhhhhhc
Confidence            34566666666655   55899999999999998876543

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

Probab=85.34  E-value=0.51  Score=26.48  Aligned_cols=23  Identities=30%  Similarity=0.639  Sum_probs=16.5

Q ss_pred             cccccccccccCceeeecCCCCCcc
Q 028116          167 CCSICLQDIIVGELARSLPHCHHTF  191 (213)
Q Consensus       167 ~C~ICle~~~~ge~v~~Lp~C~H~F  191 (213)
                      .||-|...+..  ..+.-|.|||.|
T Consensus         2 ~CP~C~~~V~~--~~~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCPECGAEVPE--SAKFCPHCGYDF   24 (26)
T ss_pred             cCCCCcCCchh--hcCcCCCCCCCC
Confidence            58888777644  355677788887

Several members are annotated as putative helicases.

>PRK11280 hypothetical protein; Provisional

Probab=84.97  E-value=0.67  Score=37.81  Aligned_cols=43  Identities=26%  Similarity=0.369  Sum_probs=29.6

Q ss_pred             HhhhHHHHHHHHhhhccccc--ccccchhhhhhhhhHHHHHHHhh
Q 028116           32 ALAGAFTGAITGALAGRASD--CGVLRGAGLGAIAGAVLSVELLE   74 (213)
Q Consensus        32 a~~g~~~ga~~ga~~g~~~~--~g~~rGa~~GaiaGav~sve~~e   74 (213)
                      +++|+++|++.|...|--+.  .+-+=||++|+++|..+.=.+-+
T Consensus        68 tv~Gav~Gg~~G~~iGgG~Gr~~at~~Ga~~G~~~G~~i~~~~~~  112 (170)
T PRK11280         68 SVLGAVAGGVLGHQFGGGRGKDVATVAGALGGGYAGNQIQGGMQE  112 (170)
T ss_pred             HHHHHHHHHHhhhhccCCCccHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            34566666666666655543  56677999999999998865544

>COG4803 Predicted membrane protein [Function unknown]

Probab=84.64  E-value=0.98  Score=36.15  Aligned_cols=14  Identities=57%  Similarity=0.838  Sum_probs=5.9

Q ss_pred             hhHHHHHHHHhhhc
Q 028116           34 AGAFTGAITGALAG   47 (213)
Q Consensus        34 ~g~~~ga~~ga~~g   47 (213)
                      +|++-|++-|.++|
T Consensus        60 aGa~sGafWG~LiG   73 (170)
T COG4803          60 AGAVSGAFWGMLIG   73 (170)
T ss_pred             hccccccHHHHHHH
Confidence            34444444444444

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

Probab=84.22  E-value=0.79  Score=29.99  Aligned_cols=43  Identities=23%  Similarity=0.478  Sum_probs=22.1

Q ss_pred             ccccccccccC------ceeeecCCCCCcccHhhHHHHHhcCCCCcccC
Q 028116          168 CSICLQDIIVG------ELARSLPHCHHTFHLACVDKWLIRHGSCPVCR  210 (213)
Q Consensus       168 C~ICle~~~~g------e~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR  210 (213)
                      |-=|+..|..+      ...-.-|+|++.|+.+|=.--=+.-..||-|-
T Consensus         2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~   50 (51)
T PF07975_consen    2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGCE   50 (51)
T ss_dssp             ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred             CccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCCC
Confidence            55677777665      24556788999999999322112345799884

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

>PRK10457 hypothetical protein; Provisional

Probab=84.01  E-value=3.2  Score=29.80  Aligned_cols=49  Identities=20%  Similarity=0.270  Sum_probs=34.2

Q ss_pred             HHHHHHHhhhHHHHHHHHhhhcccccccccchhhhhhhhhHHHHHHHhh
Q 028116           26 TLTGLFALAGAFTGAITGALAGRASDCGVLRGAGLGAIAGAVLSVELLE   74 (213)
Q Consensus        26 ~~~~~~a~~g~~~ga~~ga~~g~~~~~g~~rGa~~GaiaGav~sve~~e   74 (213)
                      +.|-+..++|+++|..++.+-|.....|+=-+.-+.|+.||++-+-+..
T Consensus        30 ~~tiilGiiGA~iGg~l~~~~g~~~~~g~~~~~~i~aviGAiill~i~~   78 (82)
T PRK10457         30 FMTIILGIVGAVVGGWISTFFGFGKVDGFNFGSFVVAVIGAIVVLFIYR   78 (82)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHH
Confidence            4677778888888888877666654455423467888888887766543

>PRK11677 hypothetical protein; Provisional

Probab=83.61  E-value=0.85  Score=35.80  Aligned_cols=25  Identities=36%  Similarity=0.478  Sum_probs=20.8

Q ss_pred             HHHhhhHHHHHHHHhhhcccccccc
Q 028116           30 LFALAGAFTGAITGALAGRASDCGV   54 (213)
Q Consensus        30 ~~a~~g~~~ga~~ga~~g~~~~~g~   54 (213)
                      ++|++|-++|+|+|+++++.+..+.
T Consensus         4 ~~a~i~livG~iiG~~~~R~~~~~~   28 (134)
T PRK11677          4 EYALIGLVVGIIIGAVAMRFGNRKL   28 (134)
T ss_pred             HHHHHHHHHHHHHHHHHHhhccchh
Confidence            5788999999999999998866554

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

Probab=83.30  E-value=0.4  Score=46.06  Aligned_cols=44  Identities=23%  Similarity=0.670  Sum_probs=28.0

Q ss_pred             CCCCcccccccc-----cccCceeeecCCCCCcccHhhHHHHHhcCCCCcccC
Q 028116          163 TQSSCCSICLQD-----IIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCR  210 (213)
Q Consensus       163 ~~~~~C~ICle~-----~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR  210 (213)
                      ....-|.+|...     |+.....+.. .|+++||..|..+   ++.-||-|-
T Consensus       509 ~~gfiCe~Cq~~~iiyPF~~~~~~rC~-~C~avfH~~C~~r---~s~~CPrC~  557 (580)
T KOG1829|consen  509 GKGFICELCQHNDIIYPFETRNTRRCS-TCLAVFHKKCLRR---KSPCCPRCE  557 (580)
T ss_pred             cCeeeeeeccCCCcccccccccceeHH-HHHHHHHHHHHhc---cCCCCCchH
Confidence            445668888432     3322333444 4999999999654   455599994

>COG4803 Predicted membrane protein [Function unknown]

Probab=82.42  E-value=0.24  Score=39.63  Aligned_cols=22  Identities=45%  Similarity=0.777  Sum_probs=13.8

Q ss_pred             hhhHHHHHHHHhhhcccccccc
Q 028116           33 LAGAFTGAITGALAGRASDCGV   54 (213)
Q Consensus        33 ~~g~~~ga~~ga~~g~~~~~g~   54 (213)
                      +.|..+||.+|||.|--++-|.
T Consensus        80 l~G~avGAa~GAl~g~l~DvGI  101 (170)
T COG4803          80 LLGMAVGAASGALSGSLTDVGI  101 (170)
T ss_pred             HHHHHHHHhhhhhccceeecCc
Confidence            3666666666666666665554

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

Probab=81.89  E-value=1.2  Score=35.00  Aligned_cols=49  Identities=20%  Similarity=0.423  Sum_probs=33.2

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHh---cCCCCcccCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLI---RHGSCPVCRRD  212 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~---~~~sCPlCR~~  212 (213)
                      .-.+|.||.|.-.+.....----||-..|..|--...+   .++.||.|+..
T Consensus        79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTS  130 (140)
T PF05290_consen   79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTS  130 (140)
T ss_pred             CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccc
Confidence            45889999887554333322224898899998654333   47899999975

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=80.76  E-value=0.94  Score=27.39  Aligned_cols=27  Identities=26%  Similarity=0.535  Sum_probs=18.7

Q ss_pred             CcccccccccccCce-------eeecCCCCCccc
Q 028116          166 SCCSICLQDIIVGEL-------ARSLPHCHHTFH  192 (213)
Q Consensus       166 ~~C~ICle~~~~ge~-------v~~Lp~C~H~FH  192 (213)
                      ..||-|...|+..+.       ...-|+|+|.|+
T Consensus         3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~   36 (37)
T PF13719_consen    3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR   36 (37)
T ss_pred             EECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence            468888888865542       335667999886

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

Probab=80.24  E-value=0.9  Score=38.32  Aligned_cols=43  Identities=30%  Similarity=0.781  Sum_probs=35.0

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCccc
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVC  209 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlC  209 (213)
                      +-..|.+|..-.-.|  +|.- .|+=.+|..|+.+.+.+.+.||-|
T Consensus       180 nlk~Cn~Ch~LvIqg--~rCg-~c~i~~h~~c~qty~q~~~~cphc  222 (235)
T KOG4718|consen  180 NLKNCNLCHCLVIQG--IRCG-SCNIQYHRGCIQTYLQRRDICPHC  222 (235)
T ss_pred             HHHHHhHhHHHhhee--eccC-cccchhhhHHHHHHhcccCcCCch
Confidence            456799998865543  4444 499999999999999999999999

>smart00249 PHD PHD zinc finger

Probab=80.22  E-value=1.1  Score=27.03  Aligned_cols=31  Identities=29%  Similarity=0.586  Sum_probs=22.6

Q ss_pred             cccccccccccCceeeecCCCCCcccHhhHHH
Q 028116          167 CCSICLQDIIVGELARSLPHCHHTFHLACVDK  198 (213)
Q Consensus       167 ~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~  198 (213)
                      .|.+|.+....+..+.-- .|...||..|+..
T Consensus         1 ~C~~C~~~~~~~~~i~C~-~C~~~~H~~C~~~   31 (47)
T smart00249        1 YCSVCGKPDDGGELLQCD-GCDRWYHQTCLGP   31 (47)
T ss_pred             CcccCCCcCCCCCEEECC-CCCchhhhhhCCC
Confidence            478898876454445444 5999999999854

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	213
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		4e-08
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		4e-08
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		2e-07
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		2e-07
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		4e-07

>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 = 54.7 bits (130), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCR 210
           Q  CC IC  + + G++A  LP CHH FH  CV  WL + G+CPVCR
Sbjct: 39  QEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCR 84

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 24/46 (52%), Positives = 30/46 (65%)
Query: 168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           C++CL ++  GE AR LP C H FH  CVD WL  H +CP+CR  V
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>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 = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 22/46 (47%), Positives = 31/46 (67%), Gaps = 1/46 (2%)
Query: 168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           C +C +D  +GE  R LP C+H FH +C+  WL +H SCPVCR+ +
Sbjct: 18  CPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSL 62

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/46 (52%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           C+ICL  +  GE  R LP C H FH  CVD+WLI +  CP+CR D+
Sbjct: 17  CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDI 61

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 142 GLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLI 201
           G +G S  +LP +        ++ + C +C+ D    +L R LP C+H FH  CVDKWL 
Sbjct: 1   GSSGSS-GQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLK 58
Query: 202 RHGSCPVCRRD 212
            + +CP+CR D
Sbjct: 59  ANRTCPICRAD 69

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	213
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	9e-23
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	3e-22
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	2e-20
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	8e-20
2ect_A	78	Ring finger protein 126; metal binding protein, st	8e-19
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	2e-18
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	9e-17
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	5e-16
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	6e-14
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	8e-14
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	1e-11
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	2e-10
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	2e-10
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	3e-10
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	7e-10
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	2e-09
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	2e-09
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	2e-08
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	4e-08
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	7e-08
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	2e-07
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	2e-07
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	3e-07
3nw0_A	238	Non-structural maintenance of chromosomes element	3e-07
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	5e-07
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	8e-07
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	3e-06
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	1e-05
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	1e-05
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	5e-05
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	7e-05
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	9e-05
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	2e-04
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	4e-04
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	4e-04
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	6e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-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 = 87.0 bits (216), Expect = 9e-23
 Identities = 29/88 (32%), Positives = 44/88 (50%), Gaps = 2/88 (2%)

Query: 127 MSYDVNDTDCRALSRGLTGESLKKLPCHVILDE-IKPTQSSCCSICLQDIIVGELARSLP 185
           M +  +       +   + ES+  LP  ++ ++     Q  CC IC  + + G++A  LP
Sbjct: 1   MGHHHHHHSHMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP 60

Query: 186 HCHHTFHLACVDKWLIRHGSCPVCRRDV 213
            CHH FH  CV  WL + G+CPVCR   
Sbjct: 61  -CHHYFHKPCVSIWLQKSGTCPVCRCMF 87

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

 Score = 85.1 bits (211), Expect = 3e-22
 Identities = 25/70 (35%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 144 TGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH 203
           +  S  +LP +        ++ + C +C+ D    +L R LP C+H FH  CVDKWL  +
Sbjct: 2   SSGSSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKAN 60

Query: 204 GSCPVCRRDV 213
            +CP+CR D 
Sbjct: 61  RTCPICRADS 70

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

 Score = 79.9 bits (198), Expect = 2e-20
 Identities = 24/48 (50%), Positives = 30/48 (62%)

Query: 166 SCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
             C++CL ++  GE AR LP C H FH  CVD WL  H +CP+CR  V
Sbjct: 6   VECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens} Length = 69

 Score = 78.6 bits (194), Expect = 8e-20
 Identities = 24/56 (42%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 158 DEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           +  +      C+ICL  +  GE  R LP C H FH  CVD+WLI +  CP+CR D+
Sbjct: 7   EGTEEDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDI 61

>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 = 76.3 bits (188), Expect = 8e-19
 Identities = 22/48 (45%), Positives = 31/48 (64%), Gaps = 1/48 (2%)

Query: 166 SCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
             C +C +D  +GE  R LP C+H FH +C+  WL +H SCPVCR+ +
Sbjct: 16  LECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSL 62

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

 Score = 75.2 bits (185), Expect = 2e-18
 Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 158 DEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
              +      C++CL+D    +     P C H FH  C+ KWL     CP+C   V
Sbjct: 8   KVKELNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPV 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 = 70.4 bits (173), Expect = 9e-17
 Identities = 16/49 (32%), Positives = 22/49 (44%)

Query: 165 SSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           SS C ICL+DI    +   +  C H  H  C ++ L     CP+C    
Sbjct: 5   SSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPS 53

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

 Score = 69.2 bits (169), Expect = 5e-16
 Identities = 14/60 (23%), Positives = 27/60 (45%), Gaps = 7/60 (11%)

Query: 153 CHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD 212
           C V + +        C  C  +    +       C+H+FH  C+  W+ ++  CP+C++D
Sbjct: 21  CRVQVMD-------ACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQD 73

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

 Score = 63.2 bits (154), Expect = 6e-14
 Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 3/52 (5%)

Query: 162 PTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
            T +  C ICL+D      + +LP C H F   C+ +W+ ++ +CP+C+  V
Sbjct: 2   ATVAERCPICLEDPS--NYSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPV 50

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

 Score = 62.8 bits (153), Expect = 8e-14
 Identities = 19/46 (41%), Positives = 25/46 (54%), Gaps = 5/46 (10%)

Query: 168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           C IC+     G     LP C H+F   C+DKW  RH +CP+CR  +
Sbjct: 18  CCICMD----GRADLILP-CAHSFCQKCIDKWSDRHRNCPICRLQM 58

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

 Score = 57.2 bits (138), Expect = 1e-11
 Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 3/59 (5%)

Query: 158 DEIKPTQSSCCSICLQDIIVGELARSLP---HCHHTFHLACVDKWLIRHGSCPVCRRDV 213
             ++P+ +  C IC+           L     C H F   C+   L    +CP CR+ +
Sbjct: 8   TGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66

>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 = 54.8 bits (131), Expect = 2e-10
 Identities = 12/54 (22%), Positives = 18/54 (33%)

Query: 159 EIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD 212
                    C          E   +   C+H FH  C+ +WL     CP+  R+
Sbjct: 45  NHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 98

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

 Score = 55.2 bits (132), Expect = 2e-10
 Identities = 12/54 (22%), Positives = 18/54 (33%)

Query: 159 EIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD 212
                    C          E   +   C+H FH  C+ +WL     CP+  R+
Sbjct: 56  NHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 109

>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 = 53.7 bits (129), Expect = 3e-10
 Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 3/59 (5%)

Query: 158 DEIKPTQSSCCSICL---QDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
             ++P+ +  C IC+    +I+          C H F   C+   L    +CP CR+ +
Sbjct: 3   TGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61

>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 = 53.4 bits (128), Expect = 7e-10
 Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 4/47 (8%)

Query: 168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR-HGSCPVCRRDV 213
           C IC++ +     AR  PHC      +C+ +WL      CP CR  +
Sbjct: 25  CFICMEKL---RDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPL 68

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

 Score = 50.9 bits (122), Expect = 2e-09
 Identities = 13/49 (26%), Positives = 18/49 (36%), Gaps = 3/49 (6%)

Query: 168 CSICLQDIIVGELARSLP---HCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           C IC+           L     C H F   C+   L    +CP CR+ +
Sbjct: 6   CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54

>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 = 51.1 bits (122), Expect = 2e-09
 Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 5/47 (10%)

Query: 168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGS--CPVCRRD 212
           C+IC   +I G   +S   C    HL CV K+   +    CP C   
Sbjct: 18  CNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDY 61

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

 Score = 49.4 bits (118), Expect = 2e-08
 Identities = 14/47 (29%), Positives = 19/47 (40%), Gaps = 3/47 (6%)

Query: 167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
            C IC  +      A  +P C H +   C+ K+L     CP C   V
Sbjct: 24  RCGICF-EYFNI--AMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTV 67

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

 Score = 47.8 bits (114), Expect = 4e-08
 Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 3/46 (6%)

Query: 168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           CSIC   +I    A ++  C HTF  +C+ +       CP C   V
Sbjct: 18  CSICKGYLID---ATTITECLHTFCKSCIVRHFYYSNRCPKCNIVV 60

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

 Score = 48.3 bits (115), Expect = 7e-08
 Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 3/47 (6%)

Query: 167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
            C +C    I    A ++  C H+F   C+ ++L     CP+C   V
Sbjct: 17  MCVLCGGYFID---ATTIIECLHSFCKTCIVRYLETSKYCPICDVQV 60

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

 Score = 47.7 bits (113), Expect = 2e-07
 Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%)

Query: 167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
            C IC +  I         +C H+F   C+++W+ R   CP+CR+D+
Sbjct: 66  QCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDI 108

>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 = 46.8 bits (110), Expect = 2e-07
 Identities = 16/74 (21%), Positives = 24/74 (32%), Gaps = 19/74 (25%)

Query: 157 LDEIKPTQSSCCSICLQDIIVG--------------ELARSLPHCHHTFHLACVDKWLIR 202
            +E+K      C IC++ + V                +   L  C H FHL C+      
Sbjct: 17  TEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCN 76

Query: 203 -----HGSCPVCRR 211
                   CP C+ 
Sbjct: 77  GNKDGSLQCPSCKT 90

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

 Score = 45.6 bits (108), Expect = 3e-07
 Identities = 10/46 (21%), Positives = 15/46 (32%), Gaps = 4/46 (8%)

Query: 168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           C IC Q          +  C H F  +C  +       C +C +  
Sbjct: 18  CFICRQAFQNP----VVTKCRHYFCESCALEHFRATPRCYICDQPT 59

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

 Score = 48.2 bits (114), Expect = 3e-07
 Identities = 15/48 (31%), Positives = 20/48 (41%), Gaps = 5/48 (10%)

Query: 167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGS--CPVCRRD 212
            C+IC   +I G+   S   C    HL CV K+   +    CP C   
Sbjct: 182 ICNICHSLLIQGQ---SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDY 226

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

 Score = 44.8 bits (106), Expect = 5e-07
 Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 4/46 (8%)

Query: 168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           C+ICLQ         SLP C H F   CV         C +CR+++
Sbjct: 18  CAICLQTC---VHPVSLP-CKHVFCYLCVKGASWLGKRCALCRQEI 59

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

 Score = 47.9 bits (113), Expect = 8e-07
 Identities = 12/61 (19%), Positives = 21/61 (34%), Gaps = 15/61 (24%)

Query: 168 CSICLQDIIVGELARSL----PHCHHTFHLACVDKWL-----------IRHGSCPVCRRD 212
           C+IC    + G     +      C    H  C+++W            +  G CP C+  
Sbjct: 311 CNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAK 370

Query: 213 V 213
           +
Sbjct: 371 L 371

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

 Score = 45.9 bits (108), Expect = 3e-06
 Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 5/56 (8%)

Query: 159 EIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG-SCPVCRRDV 213
               +    C IC ++       +  P C H    +C+  W    G  CP CR ++
Sbjct: 326 CEMGSTFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEI 377

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

 Score = 41.3 bits (97), Expect = 1e-05
 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 5/47 (10%)

Query: 167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG--SCPVCRR 211
            C IC  DI+    A  +P C +++   C+   L+     +CP C +
Sbjct: 17  LCLICK-DIMTD--AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQ 60

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

 Score = 41.3 bits (97), Expect = 1e-05
 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 5/47 (10%)

Query: 167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG--SCPVCRR 211
            C IC  DI+    A  +P C +++   C+   L+     +CP C +
Sbjct: 15  LCLICK-DIMTD--AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQ 58

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

 Score = 40.9 bits (95), Expect = 5e-05
 Identities = 13/49 (26%), Positives = 18/49 (36%), Gaps = 3/49 (6%)

Query: 168 CSICLQDIIVGELARSLP---HCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           C IC+           L     C H F   C+   L    +CP CR+ +
Sbjct: 10  CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 58

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

 Score = 39.9 bits (93), Expect = 7e-05
 Identities = 13/47 (27%), Positives = 15/47 (31%), Gaps = 5/47 (10%)

Query: 167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
            CS C   +        L  C H F   CV   +     CPVC    
Sbjct: 24  RCSRCTNIL---REPVCLGGCEHIFCSNCVSDCIGT--GCPVCYTPA 65

>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 = 40.3 bits (94), Expect = 9e-05
 Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 4/48 (8%)

Query: 167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG-SCPVCRRDV 213
            C ICL D++      +   C H F   C+   L      CP CR+ +
Sbjct: 56  MCPICL-DMLKN--TMTTKECLHRFCADCIITALRSGNKECPTCRKKL 100

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

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 3/49 (6%)

Query: 168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG---SCPVCRRDV 213
           C IC++     +L   L HC HT    C++K L        CP C +  
Sbjct: 18  CPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKIT 66

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

 Score = 36.6 bits (85), Expect = 4e-04
 Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 7/47 (14%)

Query: 167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
            C  C  +    +  + LP C HT    C++   ++   CP+C+   
Sbjct: 8   RCQQCQAEA---KCPKLLP-CLHTLCSGCLEASGMQ---CPICQAPW 47

>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 = 38.0 bits (88), Expect = 4e-04
 Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 7/49 (14%)

Query: 167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG--SCPVCRRDV 213
            C  C +   +     +   C H     C+D+   R    SCP CR D+
Sbjct: 54  QCICCQE---LVFRPITTV-CQHNVCKDCLDRSF-RAQVFSCPACRYDL 97

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

 Score = 36.6 bits (84), Expect = 6e-04
 Identities = 9/48 (18%), Positives = 20/48 (41%), Gaps = 1/48 (2%)

Query: 166 SCCSICLQDIIVGELARSLPHCHHTFHLACVDKWL-IRHGSCPVCRRD 212
             C +C++ + + ++      C +     C  +     +G CP CR+ 
Sbjct: 12  VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKP 59

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 39.1 bits (90), Expect = 9e-04
 Identities = 25/156 (16%), Positives = 51/156 (32%), Gaps = 43/156 (27%)

Query: 71  ELLEASRAYWCLERTGSRGSSSMADFVEDLLRGRFIEEQFTPAILGAYHWQVRIASMSYD 130
            +    R +W L    S+    +  FVE++LR  +        ++     + R  SM   
Sbjct: 60  AVSGTLRLFWTLL---SKQEEMVQKFVEEVLRINY------KFLMSPIKTEQRQPSMMTR 110

Query: 131 V---------NDTDC---RALSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQ----- 173
           +         ND        +SR      L++      L E++P +    ++ +      
Sbjct: 111 MYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQA-----LLELRPAK----NVLIDGVLGS 161

Query: 174 --DIIVGELARSLP-HCHHTFHLACVDKWLIRHGSC 206
               +  ++  S    C   F +     W +   +C
Sbjct: 162 GKTWVALDVCLSYKVQCKMDFKIF----W-LNLKNC 192

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	213
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.8
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.77
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.69
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.64
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.63
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.62
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.61
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.57
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.56
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.54
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.53
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.53
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.51
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.48
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.48
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.46
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.46
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.45
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.44
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.43
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.41
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.4
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.37
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.37
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.36
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.34
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.33
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.33
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.32
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.31
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.3
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.29
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.29
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.29
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.28
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.28
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.28
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.25
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.25
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.24
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.23
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.2
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.17
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.16
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.16
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.14
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.14
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.1
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.09
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.08
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	99.06
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.05
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.05
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.03
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.03
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.0
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.0
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.99
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.9
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.88
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.88
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.86
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.84
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.83
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.74
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.73
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.7
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.57
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.56
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.38
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.36
3nw0_A	238	Non-structural maintenance of chromosomes element	98.07
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	95.87
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	95.54
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	95.39
1we9_A	64	PHD finger family protein; structural genomics, PH	95.31
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	94.78
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	93.45
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	91.96
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	91.93
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	91.79
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	91.78
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	91.56
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	91.1
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	90.86
1weu_A	91	Inhibitor of growth family, member 4; structural g	90.4
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	89.96
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	89.9
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	89.71
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	89.59
1wem_A	76	Death associated transcription factor 1; structura	89.45
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	88.33
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	87.8
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	87.8
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	86.62
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	86.49
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	86.38
1wew_A	78	DNA-binding family protein; structural genomics, P	86.26
1wee_A	72	PHD finger family protein; structural genomics, PH	86.08
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	85.46
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	85.22
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	85.05
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	84.71
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	84.28
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	84.03
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	82.5
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	82.05
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	81.97

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

Probab=99.80  E-value=5.4e-20  Score=133.61  Aligned_cols=78  Identities=36%  Similarity=0.795  Sum_probs=68.8

Q ss_pred             cCcccCCCCCHHHHhcCCceeeeccCC-CCCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          135 DCRALSRGLTGESLKKLPCHVILDEIK-PTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       135 ~~~~~~~gls~~~i~~lp~~~~~~~~~-~~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ......++++++.+++||...+..... ...+..|+||+++|..++.++.+| |+|.||..||++|++++.+||+||+++
T Consensus         9 ~~~~~~~~~s~~~i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~   87 (91)
T 2l0b_A            9 SHMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCMF   87 (91)
T ss_dssp             CCSSCCCCCCHHHHHTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTTTCCBS
T ss_pred             CCCcCCCCCCHHHHHhCCCeeecccccccCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcCcCccC
Confidence            344567899999999999998876554 356788999999999999999999 999999999999999999999999875

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

Probab=99.77  E-value=1.5e-19  Score=126.23  Aligned_cols=68  Identities=37%  Similarity=0.807  Sum_probs=59.9

Q ss_pred             HHHHhcCCceeeeccCCCCCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          145 GESLKKLPCHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       145 ~~~i~~lp~~~~~~~~~~~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .+.++++|..++.......++..|+||+++|..++.++.+| |+|.||..||.+|++++.+||+||+++
T Consensus         3 ~~~i~~lp~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~   70 (75)
T 1x4j_A            3 SGSSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADS   70 (75)
T ss_dssp             CCCCSSCCCEEBCSSSCSSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCC
T ss_pred             HhhHhhCCcEEecCccccCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcC
Confidence            34567888888876655567788999999999999999999 999999999999999999999999875

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

Probab=99.69  E-value=1.2e-17  Score=109.58  Aligned_cols=51  Identities=47%  Similarity=1.024  Sum_probs=47.0

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      +++.+|+||+++|..++.+..+|.|+|.||..||.+|++++.+||+||+++
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~   53 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV   53 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCS
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEe
Confidence            356889999999999998889988999999999999999999999999875

>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=99.64  E-value=1.4e-16  Score=109.07  Aligned_cols=50  Identities=48%  Similarity=1.072  Sum_probs=46.3

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ..+..|+||++.|..++.++.+| |+|.||..||.+|+.++.+||+||+++
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~   61 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDI   61 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBS
T ss_pred             CCCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccc
Confidence            56688999999999888899999 999999999999999999999999875

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

Probab=99.63  E-value=1.6e-16  Score=110.23  Aligned_cols=50  Identities=34%  Similarity=0.804  Sum_probs=46.3

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ..+..|+||+++|..++.+..+| |+|.||..||.+|++++.+||+||+++
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~   62 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPV   62 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBC
T ss_pred             CCCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCccc
Confidence            45688999999999988888998 999999999999999999999999875

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

Probab=99.62  E-value=9e-17  Score=114.21  Aligned_cols=50  Identities=26%  Similarity=0.822  Sum_probs=41.1

Q ss_pred             CCCcccccccccc-----------cCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          164 QSSCCSICLQDII-----------VGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~-----------~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ++..|+||+++|.           .++.++.+|.|+|.||..||++||+++++||+||+++
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~   74 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDW   74 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBC
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCc
Confidence            4556777777664           4566777777999999999999999999999999875

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

Probab=99.61  E-value=3.3e-16  Score=109.78  Aligned_cols=50  Identities=44%  Similarity=1.051  Sum_probs=46.2

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ..+..|+||++.|..++.++.+| |+|.||..||.+|++++.+||+||+++
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~   62 (78)
T 2ect_A           13 GSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSL   62 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSCEEECT-TSCEEETTTTHHHHTTTCSCTTTCCCC
T ss_pred             CCCCCCeeCCccccCCCCEEEeC-CCCeecHHHHHHHHHcCCcCcCcCCcc
Confidence            55788999999999988888998 999999999999999999999999875

>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=99.57  E-value=1.5e-15  Score=99.23  Aligned_cols=50  Identities=38%  Similarity=0.781  Sum_probs=43.6

Q ss_pred             CCCCcccccccccccC-ceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVG-ELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~g-e~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ..+..|+||+++|..+ +.+..+| |+|.||..||.+|++.+.+||+||+++
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~   53 (55)
T 2ecm_A            3 SGSSGCPICLEDIHTSRVVAHVLP-CGHLLHRTCYEEMLKEGYRCPLCSGPS   53 (55)
T ss_dssp             SCCCSCTTTCCCCCTTTSCEEECT-TSCEEETTHHHHHHHHTCCCTTSCCSS
T ss_pred             CCCCcCcccChhhcCCCcCeEecC-CCCcccHHHHHHHHHcCCcCCCCCCcC
Confidence            4568899999999665 4567787 999999999999999999999999875

>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=99.56  E-value=1.9e-15  Score=113.24  Aligned_cols=50  Identities=28%  Similarity=0.662  Sum_probs=40.3

Q ss_pred             CCCCcccccccccccCc---------------eeeecCCCCCcccHhhHHHHHh-----cCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGE---------------LARSLPHCHHTFHLACVDKWLI-----RHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge---------------~v~~Lp~C~H~FH~~CI~~WL~-----~~~sCPlCR~~v  213 (213)
                      ..+..|+||+++|..++               .++.+| |+|.||..||++|+.     .+.+||+||+.+
T Consensus        23 ~~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~   92 (114)
T 1v87_A           23 APEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIY   92 (114)
T ss_dssp             CCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBS
T ss_pred             CCCCcCccCChhhcCcccccccccccccCcccceecCC-CCCcccHHHHHHHHHcccCCCCCcCCCCCCcc
Confidence            34578999999997643               334666 999999999999994     567999999863

>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=99.54  E-value=4e-15  Score=111.17  Aligned_cols=49  Identities=31%  Similarity=0.716  Sum_probs=42.2

Q ss_pred             CCCCcccccccccccC--------------c-eeeecCCCCCcccHhhHHHHHhcCCCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVG--------------E-LARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~g--------------e-~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~  212 (213)
                      .++..|+||+++|...              + .++.+| |+|.||..||++||.++.+||+||++
T Consensus        35 ~~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~Cr~~   98 (106)
T 3dpl_R           35 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNRE   98 (106)
T ss_dssp             SCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSB
T ss_pred             CCCCCCccCChhHhCcCchhhccccccCCccceEeecc-cCcEECHHHHHHHHHcCCcCcCCCCc
Confidence            5678899999999854              1 355676 99999999999999999999999986

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

Probab=99.53  E-value=4.2e-15  Score=101.15  Aligned_cols=50  Identities=28%  Similarity=0.667  Sum_probs=43.4

Q ss_pred             CCCCcccccccccccC----ceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVG----ELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~g----e~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .+...|+||++.|...    +.+..++ |+|.||..||++|+.++.+||+||+++
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~   66 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKI   66 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEECS-SSCEEEHHHHHHHHHHCSSCTTTCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeCC-CCChhcHHHHHHHHHcCCCCCCCCCcc
Confidence            5578899999998763    3446777 999999999999999999999999875

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

Probab=99.53  E-value=2.8e-15  Score=102.80  Aligned_cols=50  Identities=28%  Similarity=0.667  Sum_probs=43.4

Q ss_pred             CCCCcccccccccccC----ceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVG----ELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~g----e~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .++..|+||++.|...    +.+..+| |+|.||..||.+|++++.+||+||+++
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~   61 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKI   61 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBC
T ss_pred             CCCCCCcccChhhhccccccCCeEeCC-CCChHhHHHHHHHHHcCCCCCCCCCcc
Confidence            5678899999998763    4556777 999999999999999999999999874

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

Probab=99.51  E-value=5.2e-15  Score=99.23  Aligned_cols=49  Identities=29%  Similarity=0.656  Sum_probs=42.5

Q ss_pred             CCCcccccccccccC----ceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVG----ELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~g----e~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ++..|+||++.+...    +.+..++ |+|.||..||.+|++++.+||+||+++
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~   54 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKI   54 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEET-TSCEEEHHHHHHHHHHCSBCTTTCCBC
T ss_pred             CCCCCCccChhhhCccccCCCEEeCC-CCCchhHHHHHHHHHcCCCCCCCCccC
Confidence            457899999998763    4456777 999999999999999999999999875

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

Probab=99.48  E-value=1.7e-14  Score=102.50  Aligned_cols=49  Identities=27%  Similarity=0.696  Sum_probs=42.3

Q ss_pred             CCCCcccccccccccCceeeecCCCC-----CcccHhhHHHHHhcCC--CCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCH-----HTFHLACVDKWLIRHG--SCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~-----H~FH~~CI~~WL~~~~--sCPlCR~~v  213 (213)
                      .++..|.||+++|.+++.+ .+| |+     |.||..||++||..++  +||+||+++
T Consensus        13 ~~~~~C~IC~~~~~~~~~l-~~p-C~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~   68 (80)
T 2d8s_A           13 SSQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEF   68 (80)
T ss_dssp             TTSCCCSSSCCCCCSSSCE-ECS-SSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBC
T ss_pred             CCCCCCeEcCccccCCCee-Eec-cccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCee
Confidence            5668899999999887766 688 96     9999999999998764  899999864

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

Probab=99.48  E-value=2e-14  Score=97.89  Aligned_cols=48  Identities=35%  Similarity=0.942  Sum_probs=41.8

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      +.+..|+||++.+..  .+..+| |+|.||..|+.+|+.++.+||+||+++
T Consensus         3 ~~~~~C~IC~~~~~~--~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~   50 (68)
T 1chc_A            3 TVAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPV   50 (68)
T ss_dssp             CCCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCC
T ss_pred             CCCCCCeeCCccccC--CcEecC-CCCeeHHHHHHHHHhCcCcCcCCChhh
Confidence            346789999999864  356788 999999999999999999999999875

>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=99.46  E-value=3.6e-15  Score=113.31  Aligned_cols=50  Identities=30%  Similarity=0.737  Sum_probs=1.9

Q ss_pred             CCCCcccccccccccC--------------ceeeecCCCCCcccHhhHHHHHhcCCCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVG--------------ELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~g--------------e~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~  212 (213)
                      .+++.|+||+++|...              +....++.|+|.||..||++||+++++||+||++
T Consensus        46 ~~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~  109 (117)
T 4a0k_B           46 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE  109 (117)
T ss_dssp             CCC-------------------------------------------------------------
T ss_pred             CCCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCe
Confidence            5678999999999752              2223333499999999999999999999999986

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

Probab=99.46  E-value=2.6e-14  Score=98.52  Aligned_cols=47  Identities=34%  Similarity=0.735  Sum_probs=41.6

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .++..|+||++.+..   ...+| |+|.||..||.+|+..+.+||+||+++
T Consensus        13 ~~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~   59 (71)
T 2d8t_A           13 LTVPECAICLQTCVH---PVSLP-CKHVFCYLCVKGASWLGKRCALCRQEI   59 (71)
T ss_dssp             SSCCBCSSSSSBCSS---EEEET-TTEEEEHHHHHHCTTCSSBCSSSCCBC
T ss_pred             CCCCCCccCCcccCC---CEEcc-CCCHHHHHHHHHHHHCCCcCcCcCchh
Confidence            556889999999865   46778 999999999999999999999999875

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

Probab=99.45  E-value=1.6e-14  Score=99.01  Aligned_cols=46  Identities=41%  Similarity=0.979  Sum_probs=41.1

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .++..|+||++.+..    ..+| |+|.||..||.+|+.++.+||+||+++
T Consensus        13 ~~~~~C~IC~~~~~~----~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~   58 (70)
T 2ecn_A           13 TDEEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQM   58 (70)
T ss_dssp             CCCCCCSSSCCSCCS----EEET-TTEEECHHHHHHSSCCCSSCHHHHHCT
T ss_pred             CCCCCCeeCCcCccC----cccC-CCCcccHHHHHHHHHCcCcCCCcCCcc
Confidence            456889999999876    6788 999999999999999999999999864

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

Probab=99.44  E-value=6.7e-14  Score=99.64  Aligned_cols=50  Identities=28%  Similarity=0.654  Sum_probs=43.6

Q ss_pred             CCCCcccccccccccCce-eeecCCCCCcccHhhHHHHHhcC---CCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGEL-ARSLPHCHHTFHLACVDKWLIRH---GSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~-v~~Lp~C~H~FH~~CI~~WL~~~---~sCPlCR~~v  213 (213)
                      .+...|+||++.|...+. +..+| |+|.||..||.+|+..+   .+||+||+++
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~   66 (88)
T 2ct2_A           13 REVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKIT   66 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSSCEEECS-SSCEEEHHHHHHHHHHCSSCBCCTTTCCCB
T ss_pred             cCCCCCccCCccccccCCCeEECC-CCChhhHHHHHHHHHcCCCCcCCCCCCCcc
Confidence            456889999999988764 77887 99999999999999986   7999999863

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

Probab=99.43  E-value=7.9e-14  Score=96.30  Aligned_cols=47  Identities=34%  Similarity=0.663  Sum_probs=40.7

Q ss_pred             CCCCcccccccccccCceeeec-CCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSL-PHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~L-p~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .++..|+||++.+.+   ...+ + |+|.||..||.+|+..+.+||+||+++
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~   60 (72)
T 2djb_A           13 TPYILCSICKGYLID---ATTITE-CLHTFCKSCIVRHFYYSNRCPKCNIVV   60 (72)
T ss_dssp             CGGGSCTTTSSCCSS---CEECSS-SCCEECHHHHHHHHHHCSSCTTTCCCC
T ss_pred             CCCCCCCCCChHHHC---cCEECC-CCCHHHHHHHHHHHHcCCcCCCcCccc
Confidence            456889999999876   3444 6 999999999999999999999999875

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

Probab=99.41  E-value=1.7e-13  Score=96.59  Aligned_cols=47  Identities=21%  Similarity=0.417  Sum_probs=41.2

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .....|+||++.|..   +..+| |+|.||..||.+|+..+.+||+||+++
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~   59 (81)
T 2csy_A           13 EIPFRCFICRQAFQN---PVVTK-CRHYFCESCALEHFRATPRCYICDQPT   59 (81)
T ss_dssp             CCCSBCSSSCSBCCS---EEECT-TSCEEEHHHHHHHHHHCSBCSSSCCBC
T ss_pred             CCCCCCcCCCchhcC---eeEcc-CCCHhHHHHHHHHHHCCCcCCCcCccc
Confidence            456789999999865   45687 999999999999999999999999874

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

Probab=99.40  E-value=7e-14  Score=108.49  Aligned_cols=45  Identities=38%  Similarity=0.949  Sum_probs=40.5

Q ss_pred             CCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          165 SSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       165 ~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      +..|+||++.|..   +..+| |||.||..||.+|+.++.+||+||+++
T Consensus        53 ~~~C~iC~~~~~~---~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~   97 (138)
T 4ayc_A           53 ELQCIICSEYFIE---AVTLN-CAHSFCSYCINEWMKRKIECPICRKDI   97 (138)
T ss_dssp             HSBCTTTCSBCSS---EEEET-TSCEEEHHHHHHHTTTCSBCTTTCCBC
T ss_pred             cCCCcccCcccCC---ceECC-CCCCccHHHHHHHHHcCCcCCCCCCcC
Confidence            4679999999865   56788 999999999999999999999999875

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

Probab=99.37  E-value=2.9e-13  Score=93.19  Aligned_cols=47  Identities=28%  Similarity=0.675  Sum_probs=40.0

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHh---cCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLI---RHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~---~~~sCPlCR~~v  213 (213)
                      .++..|+||++.+..   +..+| |+|.||..||.+|++   .+.+||+||+++
T Consensus        18 ~~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~   67 (73)
T 2ysl_A           18 QEEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLCKTSV   67 (73)
T ss_dssp             CCCCBCTTTCSBCSS---EEECT-TCCEEEHHHHHHHCSSSCSCCCCSSSCCCC
T ss_pred             ccCCEeccCCcccCC---eEEcC-CCChhhHHHHHHHHHcCCCCCCCCCCCCcC
Confidence            456889999999875   55677 999999999999997   456899999875

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

Probab=99.37  E-value=2.8e-13  Score=94.12  Aligned_cols=47  Identities=23%  Similarity=0.641  Sum_probs=40.5

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC--CCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH--GSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~--~sCPlCR~~  212 (213)
                      .++..|+||++.|..   +..+|.|+|.||..||.+|+..+  .+||+||++
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~   61 (74)
T 2yur_A           13 PDELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQN   61 (74)
T ss_dssp             CGGGSCSSSCCCCTT---CEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCS
T ss_pred             CCCCCCcCCChHHhC---CeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCc
Confidence            456889999999876   45577799999999999999876  689999986

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

Probab=99.36  E-value=2.9e-13  Score=91.77  Aligned_cols=47  Identities=19%  Similarity=0.523  Sum_probs=39.3

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHh-cCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLI-RHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~-~~~sCPlCR~~v  213 (213)
                      .++..|+||++.+..   +..++ |||.||..||.+|+. .+.+||+||+++
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~   60 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCS---PKQTE-CGHRFCESCMAALLSSSSPKCTACQESI   60 (66)
T ss_dssp             CCCEECTTTCCEESS---CCCCS-SSCCCCHHHHHHHHTTSSCCCTTTCCCC
T ss_pred             CcCCCCCCCChHhcC---eeECC-CCCHHHHHHHHHHHHhCcCCCCCCCcCC
Confidence            456889999999875   33477 999999999999995 567899999875

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

Probab=99.34  E-value=3.7e-13  Score=102.19  Aligned_cols=50  Identities=28%  Similarity=0.667  Sum_probs=43.2

Q ss_pred             CCCCcccccccccccC----ceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVG----ELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~g----e~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .++..|+||++.|.+.    +.+..++ |||.||..||.+|++.+.+||+||+++
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~   58 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKI   58 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEET-TCCEEEHHHHHHHHTTCSBCTTTCCBC
T ss_pred             CCCCCCcccChhhhCccccccCeEecC-CCChhhHHHHHHHHHhCCCCCCCCCcC
Confidence            3568899999998763    4557787 999999999999999999999999864

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

Probab=99.33  E-value=8e-13  Score=100.34  Aligned_cols=50  Identities=28%  Similarity=0.667  Sum_probs=43.0

Q ss_pred             CCCCcccccccccccC----ceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVG----ELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~g----e~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ++...|+||++.|...    ..+..++ |+|.||..||++|++.+.+||+||+++
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~  123 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKI  123 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEET-TSBEEEHHHHHHHHHHCSBCTTTCCBC
T ss_pred             CCCCCCCCCCCccccccccCcceEeCC-CCChhhHHHHHHHHHcCCCCCCCCCcC
Confidence            5678899999998763    3446676 999999999999999999999999875

>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=99.33  E-value=4.4e-13  Score=98.54  Aligned_cols=47  Identities=28%  Similarity=0.758  Sum_probs=40.4

Q ss_pred             CCCCcccccccccccCceeee-cCCCCCcccHhhHHHHHhcC-CCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARS-LPHCHHTFHLACVDKWLIRH-GSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~-Lp~C~H~FH~~CI~~WL~~~-~sCPlCR~~v  213 (213)
                      .++..|+||++.|..   +.. ++ |||.||..||.+|+..+ .+||+||+++
T Consensus        20 ~~~~~C~IC~~~~~~---p~~~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~   68 (100)
T 3lrq_A           20 AEVFRCFICMEKLRD---ARLCPH-CSKLCCFSCIRRWLTEQRAQCPHCRAPL   68 (100)
T ss_dssp             HHHTBCTTTCSBCSS---EEECTT-TCCEEEHHHHHHHHHHTCSBCTTTCCBC
T ss_pred             CCCCCCccCCccccC---ccccCC-CCChhhHHHHHHHHHHCcCCCCCCCCcC
Confidence            346889999999875   445 77 99999999999999988 6999999874

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

Probab=99.32  E-value=8.2e-13  Score=92.25  Aligned_cols=47  Identities=21%  Similarity=0.453  Sum_probs=40.9

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc-CCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR-HGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~-~~sCPlCR~~v  213 (213)
                      .++..|+||++.|.+   +..+| |||.||..||.+|+.+ +.+||+||+++
T Consensus         6 ~~~~~C~IC~~~~~~---Pv~~~-CgH~fc~~Ci~~~~~~~~~~CP~C~~~~   53 (78)
T 1t1h_A            6 PEYFRCPISLELMKD---PVIVS-TGQTYERSSIQKWLDAGHKTCPKSQETL   53 (78)
T ss_dssp             SSSSSCTTTSCCCSS---EEEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBC
T ss_pred             cccCCCCCccccccC---CEEcC-CCCeecHHHHHHHHHHCcCCCCCCcCCC
Confidence            457889999999875   55678 9999999999999987 78999999864

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

Probab=99.31  E-value=1.2e-12  Score=92.07  Aligned_cols=47  Identities=34%  Similarity=0.724  Sum_probs=40.4

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc------CCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR------HGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~------~~sCPlCR~~v  213 (213)
                      .++..|+||++.|..   ...+| |+|.||..||.+|+..      +.+||+||+++
T Consensus        17 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~   69 (85)
T 2ecw_A           17 KEEVTCPICLELLKE---PVSAD-CNHSFCRACITLNYESNRNTDGKGNCPVCRVPY   69 (85)
T ss_dssp             CTTTSCTTTCSCCSS---CEECT-TSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCC
T ss_pred             ccCCCCcCCChhhCc---ceeCC-CCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcC
Confidence            456889999999876   34678 9999999999999988      67899999874

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

Probab=99.30  E-value=1.3e-12  Score=91.96  Aligned_cols=47  Identities=36%  Similarity=0.743  Sum_probs=40.6

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc------CCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR------HGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~------~~sCPlCR~~v  213 (213)
                      .++..|+||++.+..   +..+| |+|.||..|+.+|+..      +.+||+||+++
T Consensus        17 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~   69 (85)
T 2ecv_A           17 KEEVTCPICLELLTQ---PLSLD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISY   69 (85)
T ss_dssp             CCCCCCTTTCSCCSS---CBCCS-SSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSS
T ss_pred             cCCCCCCCCCcccCC---ceeCC-CCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCcc
Confidence            456889999999865   45677 9999999999999987      78999999864

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

Probab=99.29  E-value=3.7e-13  Score=93.94  Aligned_cols=47  Identities=32%  Similarity=0.639  Sum_probs=40.3

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc-------CCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR-------HGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~-------~~sCPlCR~~v  213 (213)
                      .++..|+||++.|..   +..+| |||.||..||.+|+..       +.+||+||+++
T Consensus        10 ~~~~~C~IC~~~~~~---p~~l~-CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~   63 (79)
T 2egp_A           10 QEEVTCPICLELLTE---PLSLD-CGHSLCRACITVSNKEAVTSMGGKSSCPVCGISY   63 (79)
T ss_dssp             CCCCEETTTTEECSS---CCCCS-SSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCC
T ss_pred             ccCCCCcCCCcccCC---eeECC-CCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcC
Confidence            456889999999876   45678 9999999999999987       66899999874

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

Probab=99.29  E-value=1.4e-12  Score=95.30  Aligned_cols=46  Identities=28%  Similarity=0.688  Sum_probs=39.9

Q ss_pred             CCCcccccccccccCceeeec-CCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSL-PHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~L-p~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      +...|+||++.|..   ...+ | |||.||..||.+|+..+.+||+||+++
T Consensus        21 ~~~~C~IC~~~~~~---p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~   67 (99)
T 2y43_A           21 DLLRCGICFEYFNI---AMIIPQ-CSHNYCSLCIRKFLSYKTQCPTCCVTV   67 (99)
T ss_dssp             HHTBCTTTCSBCSS---EEECTT-TCCEEEHHHHHHHHTTCCBCTTTCCBC
T ss_pred             CCCCcccCChhhCC---cCEECC-CCCHhhHHHHHHHHHCCCCCCCCCCcC
Confidence            45789999999875   4455 6 999999999999999999999999864

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

Probab=99.29  E-value=1.9e-12  Score=90.60  Aligned_cols=47  Identities=30%  Similarity=0.700  Sum_probs=40.4

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC--CCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH--GSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~--~sCPlCR~~  212 (213)
                      +....|.||++.+..++.-.   .|+|.||..||.+||+++  .+||+||++
T Consensus        13 ~~i~~C~IC~~~i~~g~~C~---~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~   61 (74)
T 2ct0_A           13 DAVKICNICHSLLIQGQSCE---TCGIRMHLPCVAKYFQSNAEPRCPHCNDY   61 (74)
T ss_dssp             SSSCBCSSSCCBCSSSEECS---SSCCEECHHHHHHHSTTCSSCCCTTTCSC
T ss_pred             CCCCcCcchhhHcccCCccC---CCCchhhHHHHHHHHHhcCCCCCCCCcCc
Confidence            45688999999998765332   599999999999999987  899999986

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

Probab=99.28  E-value=2.5e-12  Score=86.24  Aligned_cols=43  Identities=28%  Similarity=0.688  Sum_probs=36.9

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHh---cCCCCccc
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLI---RHGSCPVC  209 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~---~~~sCPlC  209 (213)
                      .++..|+||++.+.+   +..+| |+|.||..||.+|++   .+.+||+|
T Consensus        18 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           18 QEEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCBCTTTCSBCSS---CEECT-TSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             ccCCCCCcCCchhCC---eEEeC-CCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            456889999999875   55677 999999999999998   45689998

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

Probab=99.28  E-value=2e-12  Score=87.39  Aligned_cols=49  Identities=29%  Similarity=0.598  Sum_probs=38.9

Q ss_pred             CCCccccccc-ccccCcee-eecCCCCCcccHhhHHHHHhc-CCCCcccCCCC
Q 028116          164 QSSCCSICLQ-DIIVGELA-RSLPHCHHTFHLACVDKWLIR-HGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle-~~~~ge~v-~~Lp~C~H~FH~~CI~~WL~~-~~sCPlCR~~v  213 (213)
                      ++..|+||++ .+...... ..+| |||.||..||++|+.+ +.+||+||+++
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~   53 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPL   53 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCC
T ss_pred             CCCcCCcCCCCccCCCccCeecCC-CCCHhHHHHHHHHHHcCCCcCCCCCCcc
Confidence            3578999999 67665433 3466 9999999999999765 46899999875

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

Probab=99.28  E-value=1.6e-12  Score=96.51  Aligned_cols=47  Identities=28%  Similarity=0.675  Sum_probs=40.6

Q ss_pred             CCCCcccccccccccCceeeec-CCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSL-PHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~L-p~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .++..|+||++.|.+   ...+ | |||.||..||.+|+..+.+||+||+++
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~   60 (108)
T 2ckl_A           13 NPHLMCVLCGGYFID---ATTIIE-CLHSFCKTCIVRYLETSKYCPICDVQV   60 (108)
T ss_dssp             GGGTBCTTTSSBCSS---EEEETT-TCCEEEHHHHHHHHTSCSBCTTTCCBS
T ss_pred             CCcCCCccCChHHhC---cCEeCC-CCChhhHHHHHHHHHhCCcCcCCCccc
Confidence            456889999999875   4455 7 999999999999999999999999864

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

Probab=99.25  E-value=3.6e-12  Score=91.70  Aligned_cols=48  Identities=23%  Similarity=0.608  Sum_probs=40.5

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC--CCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH--GSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~--~sCPlCR~~v  213 (213)
                      .++..|+||++.|.+   +..+|.|||.||..||.+|+..+  .+||+||+++
T Consensus        11 ~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~   60 (92)
T 3ztg_A           11 PDELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQND   60 (92)
T ss_dssp             CTTTEETTTTEECSS---CEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSS
T ss_pred             CcCCCCCCCChhhcC---ceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcC
Confidence            556889999999875   55677699999999999999764  5899999863

>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=99.25  E-value=3.1e-12  Score=97.19  Aligned_cols=46  Identities=26%  Similarity=0.615  Sum_probs=39.4

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCC-CCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG-SCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~-sCPlCR~~v  213 (213)
                      ++..|+||++.|..   +..+| |||.||..||.+|+..+. +||+||+++
T Consensus        51 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~   97 (124)
T 3fl2_A           51 ETFQCICCQELVFR---PITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDL   97 (124)
T ss_dssp             HHTBCTTTSSBCSS---EEECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBC
T ss_pred             cCCCCCcCChHHcC---cEEee-CCCcccHHHHHHHHhHCcCCCCCCCccC
Confidence            45789999999885   56678 999999999999998655 899999864

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

Probab=99.24  E-value=3.8e-12  Score=83.61  Aligned_cols=43  Identities=35%  Similarity=0.881  Sum_probs=36.2

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHh---cCCCCccc
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLI---RHGSCPVC  209 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~---~~~sCPlC  209 (213)
                      .++..|+||++.+.+   ...+| |+|.||..||.+|+.   ++.+||+|
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLKE---PVIIE-CGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCSS---CCCCS-SCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccCCCCccCCcccCc---cEeCC-CCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            456889999999876   35677 999999999999954   56789998

>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=99.23  E-value=7.7e-12  Score=99.44  Aligned_cols=47  Identities=28%  Similarity=0.644  Sum_probs=39.3

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc-CCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR-HGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~-~~sCPlCR~~v  213 (213)
                      +...|+||++.|..  .+..+| |||.||..||.+|+.. +.+||+||.++
T Consensus        53 ~~~~C~IC~~~~~~--p~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~  100 (165)
T 2ckl_B           53 SELMCPICLDMLKN--TMTTKE-CLHRFCADCIITALRSGNKECPTCRKKL  100 (165)
T ss_dssp             HHHBCTTTSSBCSS--EEEETT-TCCEEEHHHHHHHHHTTCCBCTTTCCBC
T ss_pred             CCCCCcccChHhhC--cCEeCC-CCChhHHHHHHHHHHhCcCCCCCCCCcC
Confidence            45689999999875  333447 9999999999999997 77899999864

>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=99.20  E-value=6.8e-12  Score=93.10  Aligned_cols=46  Identities=35%  Similarity=0.711  Sum_probs=38.9

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCC---CCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG---SCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~---sCPlCR~~v  213 (213)
                      +...|+||++.+..   +..+| |||.||..||.+|+..+.   +||+||.++
T Consensus        20 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~   68 (112)
T 1jm7_A           20 KILECPICLELIKE---PVSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDI   68 (112)
T ss_dssp             HHTSCSSSCCCCSS---CCBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCC
T ss_pred             CCCCCcccChhhcC---eEECC-CCCHHHHHHHHHHHHhCCCCCCCcCCCCcC
Confidence            35789999999865   44577 999999999999998764   899999864

>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=99.17  E-value=9.7e-12  Score=93.77  Aligned_cols=47  Identities=34%  Similarity=0.620  Sum_probs=40.4

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCC-CCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG-SCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~-sCPlCR~~v  213 (213)
                      .++..|+||++.+..   ...+| |||.||..||.+|+..+. +||+||+++
T Consensus        16 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~   63 (118)
T 3hct_A           16 ESKYECPICLMALRE---AVQTP-CGHRFCKACIIKSIRDAGHKCPVDNEIL   63 (118)
T ss_dssp             CGGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBC
T ss_pred             CCCCCCCcCChhhcC---eEECC-cCChhhHHHHHHHHhhCCCCCCCCCCCc
Confidence            456889999999875   45677 999999999999998765 999999874

>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=1.6e-11  Score=96.78  Aligned_cols=46  Identities=28%  Similarity=0.630  Sum_probs=39.5

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCC-CCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG-SCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~-sCPlCR~~v  213 (213)
                      +...|+||++.|..   +..+| |+|.||..||.+|+.... +||+||.++
T Consensus        77 ~~~~C~IC~~~~~~---pv~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~  123 (150)
T 1z6u_A           77 QSFMCVCCQELVYQ---PVTTE-CFHNVCKDCLQRSFKAQVFSCPACRHDL  123 (150)
T ss_dssp             HHTBCTTTSSBCSS---EEECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBC
T ss_pred             cCCEeecCChhhcC---CEEcC-CCCchhHHHHHHHHHhCCCcCCCCCccC
Confidence            45789999999875   45688 999999999999998765 899999875

>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=99.16  E-value=1.6e-11  Score=83.25  Aligned_cols=47  Identities=26%  Similarity=0.450  Sum_probs=39.6

Q ss_pred             CCCCcccccccccccCceeee--cCCCCCc-ccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARS--LPHCHHT-FHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~--Lp~C~H~-FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .++..|+||++.+.+   +..  +| |||. |+..|+.+|.+++.+||+||+++
T Consensus         6 ~~~~~C~IC~~~~~~---~~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i   55 (64)
T 2vje_A            6 NAIEPCVICQGRPKN---GCIVHGK-TGHLMACFTCAKKLKKRNKPCPVCRQPI   55 (64)
T ss_dssp             GGGSCCTTTSSSCSC---EEEEETT-EEEEEECHHHHHHHHHTTCCCTTTCCCC
T ss_pred             CCcCCCCcCCCCCCC---EEEECCC-CCChhhHHHHHHHHHHcCCcCCCcCcch
Confidence            456789999998655   333  48 9999 89999999999999999999975

>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=99.14  E-value=6.1e-12  Score=94.23  Aligned_cols=47  Identities=32%  Similarity=0.780  Sum_probs=40.0

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc-CCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR-HGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~-~~sCPlCR~~v  213 (213)
                      .++..|+||++.|..   +..+| |||.||..||.+|+.. +.+||+||+++
T Consensus        13 ~~~~~C~iC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~   60 (115)
T 3l11_A           13 LSECQCGICMEILVE---PVTLP-CNHTLCKPCFQSTVEKASLCCPFCRRRV   60 (115)
T ss_dssp             HHHHBCTTTCSBCSS---CEECT-TSCEECHHHHCCCCCTTTSBCTTTCCBC
T ss_pred             CCCCCCccCCcccCc---eeEcC-CCCHHhHHHHHHHHhHCcCCCCCCCccc
Confidence            345789999999875   56678 9999999999999976 67899999864

>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=99.14  E-value=2.3e-11  Score=91.23  Aligned_cols=46  Identities=28%  Similarity=0.588  Sum_probs=39.6

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc-CCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR-HGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~-~~sCPlCR~~v  213 (213)
                      ++..|+||++.+.+   +..+| |||.||..||.+|+.. +.+||+||+++
T Consensus        22 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~   68 (116)
T 1rmd_A           22 KSISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPC   68 (116)
T ss_dssp             HHTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBC
T ss_pred             CCCCCCCCCcHhcC---cEEcC-CCCcccHHHHHHHHhHCcCcCCCCCCCC
Confidence            35789999999865   45577 9999999999999997 77999999874

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B*

Probab=99.10  E-value=3.1e-11  Score=81.49  Aligned_cols=49  Identities=20%  Similarity=0.425  Sum_probs=39.4

Q ss_pred             CCCCcccccccccccCceeeecCCCCCc-ccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHT-FHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~-FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      +.+..|+||++...+. .+..+| |||. |+..|+.+|.+++.+||+||+++
T Consensus         5 ~~~~~C~IC~~~~~~~-~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i   54 (63)
T 2vje_B            5 NLLKPCSLCEKRPRDG-NIIHGR-TGHLVTCFHCARRLKKAGASCPICKKEI   54 (63)
T ss_dssp             GGGSBCTTTSSSBSCE-EEEETT-EEEEEECHHHHHHHHHTTCBCTTTCCBC
T ss_pred             CcCCCCcccCCcCCCe-EEEecC-CCCHhHHHHHHHHHHHhCCcCCCcCchh
Confidence            4567899999976541 122348 9999 99999999999889999999975

>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=99.09  E-value=5.3e-11  Score=106.79  Aligned_cols=46  Identities=26%  Similarity=0.712  Sum_probs=40.3

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHh-cCCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLI-RHGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~-~~~sCPlCR~~v  213 (213)
                      ....|+||++.+..   +..+| |||.||..|+.+|+. .+.+||+||+++
T Consensus       331 ~~~~C~ICle~~~~---pv~lp-CGH~FC~~Ci~~wl~~~~~~CP~CR~~i  377 (389)
T 2y1n_A          331 TFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEI  377 (389)
T ss_dssp             SSSBCTTTSSSBCC---EEEET-TCCEECHHHHHHHHHHTCSBCTTTCCBC
T ss_pred             CCCCCCccCcCCCC---eEEeC-CCChhhHHHHHHHHhcCCCCCCCCCCcc
Confidence            34789999998855   67788 999999999999999 688999999875

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

Probab=99.08  E-value=7.6e-11  Score=84.21  Aligned_cols=47  Identities=11%  Similarity=0.071  Sum_probs=42.2

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .++..|+||++-|.+   +..+| |||.|+..||.+|+..+.+||+||.++
T Consensus        12 p~~~~CpI~~~~m~d---PV~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l   58 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTD---PVRLP-SGTVMDRSIILRHLLNSPTDPFNRQML   58 (85)
T ss_dssp             CTTTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBC
T ss_pred             chheECcccCchhcC---CeECC-CCCEECHHHHHHHHhcCCCCCCCcCCC
Confidence            456889999999887   67888 999999999999999999999999864

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

Probab=99.06  E-value=3.5e-11  Score=106.04  Aligned_cols=51  Identities=25%  Similarity=0.744  Sum_probs=40.5

Q ss_pred             CCCCccccccccccc-Cceee---ecCCCCCcccHhhHHHHHhcC-----------CCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIV-GELAR---SLPHCHHTFHLACVDKWLIRH-----------GSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~-ge~v~---~Lp~C~H~FH~~CI~~WL~~~-----------~sCPlCR~~v  213 (213)
                      +...+|+||++.+.+ ++.+.   ..++|+|.||..|+.+||++.           ++||.||+++
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pI  371 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKL  371 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEE
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcC
Confidence            567889999999887 43332   244699999999999999853           4799999874

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

Probab=99.05  E-value=3.8e-11  Score=79.05  Aligned_cols=44  Identities=27%  Similarity=0.616  Sum_probs=37.7

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .+...|+||++.|..   +..+| |+|.||..||.+|   +.+||+||+++
T Consensus         4 ~~~~~C~IC~~~~~~---p~~l~-CgH~fC~~Ci~~~---~~~CP~Cr~~~   47 (56)
T 1bor_A            4 FQFLRCQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPW   47 (56)
T ss_dssp             CCCSSCSSSCSSCBC---CSCST-TSCCSBTTTCSSS---SSSCSSCCSSS
T ss_pred             ccCCCceEeCCccCC---eEEcC-CCCcccHHHHccC---CCCCCcCCcEe
Confidence            456789999999876   57788 9999999999884   67899999874

>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=99.05  E-value=8.5e-11  Score=86.60  Aligned_cols=47  Identities=11%  Similarity=0.088  Sum_probs=42.2

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .+...||||++-|.+   +..+| |||.|+..||.+|+..+.+||+||.++
T Consensus        27 p~~~~CpI~~~~m~d---PV~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l   73 (100)
T 2kre_A           27 PDEFRDPLMDTLMTD---PVRLP-SGTIMDRSIILRHLLNSPTDPFNRQTL   73 (100)
T ss_dssp             STTTBCTTTCSBCSS---EEEET-TTEEEEHHHHHHHTTSCSBCSSSCCBC
T ss_pred             cHhhCCcCccCcccC---CeECC-CCCEEchHHHHHHHHcCCCCCCCCCCC
Confidence            456889999999887   77888 999999999999999999999999874

>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=99.03  E-value=5.3e-11  Score=92.85  Aligned_cols=46  Identities=20%  Similarity=0.449  Sum_probs=39.2

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCC-CCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG-SCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~-sCPlCR~~  212 (213)
                      +++..|+||++.+.+   +..++ |||.||..||.+|+.... +||+||.+
T Consensus        29 ~~~~~C~IC~~~~~~---pv~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~   75 (141)
T 3knv_A           29 EAKYLCSACRNVLRR---PFQAQ-CGHRYCSFCLASILSSGPQNCAACVHE   75 (141)
T ss_dssp             CGGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHGGGSCEECHHHHHT
T ss_pred             CcCcCCCCCChhhcC---cEECC-CCCccCHHHHHHHHhcCCCCCCCCCCc
Confidence            456889999999876   34577 999999999999998765 89999985

>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=99.03  E-value=1.4e-10  Score=85.10  Aligned_cols=47  Identities=15%  Similarity=0.128  Sum_probs=41.8

Q ss_pred             CCCCcccccccccccCceeeecCCCC-CcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCH-HTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~-H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .++..||||++-|++   +..+| || |.|+..||.+|+..+.+||+||.++
T Consensus        20 p~~~~CpI~~~~m~d---PV~~~-cG~htf~r~cI~~~l~~~~~cP~~~~~l   67 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCD---PVVLP-SSRVTVDRSTIARHLLSDQTDPFNRSPL   67 (98)
T ss_dssp             CTTTBCTTTCSBCSS---EEECT-TTCCEEEHHHHHHHTTTSCBCTTTCSBC
T ss_pred             cHhcCCcCccccccC---CeECC-CCCeEECHHHHHHHHHhCCCCCCCCCCC
Confidence            456889999999887   66788 99 9999999999999999999999874

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

Probab=99.00  E-value=1.8e-10  Score=81.12  Aligned_cols=50  Identities=18%  Similarity=0.545  Sum_probs=38.7

Q ss_pred             CCCCcccccccccccCce-eeecCCCCCcccHhhHHHHHhc-CCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGEL-ARSLPHCHHTFHLACVDKWLIR-HGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~-v~~Lp~C~H~FH~~CI~~WL~~-~~sCPlCR~~v  213 (213)
                      +++.+|+||++.+...+. +.-++ |||.||..|+.+|+.. +.+||.||+++
T Consensus         9 ~~~~~CpICle~~~~~d~~~~p~~-CGH~fC~~Cl~~~~~~~~~~CP~CR~~~   60 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPY   60 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTTTCCSST-TSCCCCHHHHHHHTTSSCSBCTTTCCBC
T ss_pred             ccCCcCCccCccCccccccccccC-CCCCcCHHHHHHHHhcCCCCCCCCCCcc
Confidence            456889999998865432 22245 9999999999998753 57899999864

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

Probab=99.00  E-value=5.6e-11  Score=89.41  Aligned_cols=44  Identities=30%  Similarity=0.586  Sum_probs=38.0

Q ss_pred             CCCcccccccccccCceeeec-CCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSL-PHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~L-p~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      +...|+||++.|..   +..+ | |||.||..||.+|+.  .+||+||+++
T Consensus        21 ~~~~C~IC~~~~~~---pv~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~   65 (117)
T 1jm7_B           21 KLLRCSRCTNILRE---PVCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPA   65 (117)
T ss_dssp             HTTSCSSSCSCCSS---CBCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBC
T ss_pred             hCCCCCCCChHhhC---ccEeCC-CCCHHHHHHHHHHhc--CCCcCCCCcC
Confidence            46889999999865   5566 7 999999999999988  8899999864

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

Probab=98.99  E-value=7.6e-11  Score=81.93  Aligned_cols=42  Identities=26%  Similarity=0.691  Sum_probs=36.5

Q ss_pred             CCCcccccccccccCceeeecCCCCCc-ccHhhHHHHHhcCCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHT-FHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~-FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ++..|+||++.+.+   +..+| |||. ||..|+.+|    .+||+||+++
T Consensus        23 ~~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i   65 (74)
T 4ic3_A           23 EEKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEAV----DKCPMCYTVI   65 (74)
T ss_dssp             HHTBCTTTSSSBCC---EEEET-TCCBCCCHHHHTTC----SBCTTTCCBC
T ss_pred             cCCCCCCCCCCCCC---EEEcC-CCChhHHHHhhhcC----ccCCCcCcCc
Confidence            45789999998765   66788 9999 999999999    8899999875

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

Probab=98.90  E-value=8.7e-10  Score=73.88  Aligned_cols=47  Identities=23%  Similarity=0.645  Sum_probs=36.7

Q ss_pred             CCCCcccccccccccCceeeecCCCC--C---cccHhhHHHHHhc--CCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCH--H---TFHLACVDKWLIR--HGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~--H---~FH~~CI~~WL~~--~~sCPlCR~~v  213 (213)
                      ++...|.||+++.  ++.. .+| |.  |   .||..|+++|+..  +.+||+||.+.
T Consensus         4 ~~~~~CrIC~~~~--~~~l-~~P-C~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~   57 (60)
T 1vyx_A            4 EDVPVCWICNEEL--GNER-FRA-CGCTGELENVHRSCLSTWLTISRNTACQICGVVY   57 (60)
T ss_dssp             CSCCEETTTTEEC--SCCC-CCS-CCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBC
T ss_pred             CCCCEeEEeecCC--CCce-ecC-cCCCCchhhhHHHHHHHHHHhCCCCccCCCCCee
Confidence            4567899999973  3333 688 55  4   9999999999975  67899999863

>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=98.88  E-value=6.8e-10  Score=88.44  Aligned_cols=47  Identities=34%  Similarity=0.620  Sum_probs=40.0

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCC-CCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG-SCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~-sCPlCR~~v  213 (213)
                      .+...|+||++.+.+   +..+| |||.||..||.+|+..+. +||+||.++
T Consensus        16 ~~~~~C~IC~~~~~~---pv~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~   63 (170)
T 3hcs_A           16 ESKYECPICLMALRE---AVQTP-CGHRFCKACIIKSIRDAGHKCPVDNEIL   63 (170)
T ss_dssp             CGGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBC
T ss_pred             CCCCCCCCCChhhcC---cEECC-CCCHHHHHHHHHHHHhCCCCCCCCccCc
Confidence            456889999999876   45577 999999999999998654 999999874

>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=98.88  E-value=1e-09  Score=92.78  Aligned_cols=47  Identities=21%  Similarity=0.278  Sum_probs=40.7

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCC-CCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG-SCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~-sCPlCR~~v  213 (213)
                      .....||||++-|.+   +.++| |||+|+..||.+|+..++ +||+||.++
T Consensus       206 ~~~~~c~i~~~~~~d---Pv~~~-~gh~f~~~~i~~~~~~~~~~cP~~~~~~  253 (281)
T 2c2l_A          206 PDYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFNPVTRSPL  253 (281)
T ss_dssp             CSTTBCTTTCSBCSS---EEECS-SCCEEETTHHHHHHHHTCSSCTTTCCCC
T ss_pred             CcccCCcCcCCHhcC---CeECC-CCCEECHHHHHHHHHHCCCCCcCCCCCC
Confidence            467889999999876   67888 999999999999998744 599999875

>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=98.86  E-value=9.8e-10  Score=79.72  Aligned_cols=47  Identities=17%  Similarity=0.427  Sum_probs=38.9

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC------CCCcc--cCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH------GSCPV--CRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~------~sCPl--CR~~  212 (213)
                      ..+..||||++.|.+   +..+|.|||.|+..||.+|+..+      .+||+  |++.
T Consensus         5 ~~~~~CPI~~~~~~d---PV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            5 SSGFTCPITKEEMKK---PVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             SSCCBCTTTCSBCSS---EEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             CcEeECcCcCchhcC---CEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            346789999999876   66675699999999999999864      48999  9854

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

Probab=98.84  E-value=2.3e-09  Score=73.43  Aligned_cols=43  Identities=35%  Similarity=0.742  Sum_probs=36.6

Q ss_pred             CCCCcccccccccccCceeeecCCCCCc-ccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHT-FHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~-FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .++..|.||++....   +..+| |+|. |+..|+..    ..+||+||+++
T Consensus        13 ~~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~----~~~CP~CR~~i   56 (68)
T 2ea5_A           13 ENSKDCVVCQNGTVN---WVLLP-CRHTCLCDGCVKY----FQQCPMCRQFV   56 (68)
T ss_dssp             CCSSCCSSSSSSCCC---CEETT-TTBCCSCTTHHHH----CSSCTTTCCCC
T ss_pred             CCCCCCCCcCcCCCC---EEEEC-CCChhhhHHHHhc----CCCCCCCCcch
Confidence            557889999998654   77899 9999 99999984    68999999875

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

Probab=98.83  E-value=1.2e-09  Score=75.77  Aligned_cols=42  Identities=26%  Similarity=0.695  Sum_probs=35.0

Q ss_pred             CCCcccccccccccCceeeecCCCCCc-ccHhhHHHHHhcCCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHT-FHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~-FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ++..|+||++.+.+   +..+| |+|. ||..|+.+    ...||+||+++
T Consensus        24 ~~~~C~IC~~~~~~---~~~~p-CgH~~~C~~C~~~----~~~CP~Cr~~i   66 (75)
T 2ecg_A           24 EEKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEA----VDKCPMCYTVI   66 (75)
T ss_dssp             HHHSCSSSCSSCCC---BCCSS-SCCCCBCHHHHHH----CSBCTTTCCBC
T ss_pred             CCCCCCcCCCCCCC---EEEec-CCCHHHHHHHhhC----CCCCccCCcee
Confidence            35789999998765   66788 9999 99999964    58899999875

>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=98.74  E-value=4.4e-09  Score=75.94  Aligned_cols=48  Identities=27%  Similarity=0.636  Sum_probs=39.6

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc--------CCCCcc--cCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR--------HGSCPV--CRRD  212 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~--------~~sCPl--CR~~  212 (213)
                      +..+|+||++++...+.+...+ |+|.||..|+.+++..        .-+||.  ||..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~-CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceEcCC-CCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            4578999999998766666566 9999999999999863        237999  9976

>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=98.73  E-value=2e-09  Score=75.76  Aligned_cols=42  Identities=36%  Similarity=0.797  Sum_probs=35.6

Q ss_pred             CCCcccccccccccCceeeecCCCCCc-ccHhhHHHHHhcCCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHT-FHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~-FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ++..|+||++.+..   +..+| |||. |+..|+.+|    ..||+||+++
T Consensus        17 ~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i   59 (79)
T 2yho_A           17 EAMLCMVCCEEEIN---STFCP-CGHTVCCESCAAQL----QSCPVCRSRV   59 (79)
T ss_dssp             HHTBCTTTSSSBCC---EEEET-TCBCCBCHHHHTTC----SBCTTTCCBC
T ss_pred             CCCEeEEeCcccCc---EEEEC-CCCHHHHHHHHHhc----CcCCCCCchh
Confidence            35789999998655   67888 9999 999999987    3999999875

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

Probab=98.70  E-value=8.6e-09  Score=83.46  Aligned_cols=47  Identities=19%  Similarity=0.212  Sum_probs=40.6

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC-CCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH-GSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~-~sCPlCR~~v  213 (213)
                      .+...||||++-|.+   +..+| |||.|+..||.+|+..+ .+||+||.++
T Consensus       104 p~~f~CPI~~elm~D---PV~~~-~Ghtfer~~I~~~l~~~~~tcP~t~~~l  151 (179)
T 2f42_A          104 PDYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFDPVTRSPL  151 (179)
T ss_dssp             CGGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBC
T ss_pred             cHhhcccCccccCCC---CeECC-CCCEECHHHHHHHHHhCCCCCCCCcCCC
Confidence            567889999999886   66778 99999999999999875 4699999874

>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=2.5e-08  Score=66.83  Aligned_cols=45  Identities=13%  Similarity=0.250  Sum_probs=38.8

Q ss_pred             CcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          166 SCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       166 ~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ..|+||++-+.+   +..+|.|||+|...||.+||+++.+||++++++
T Consensus         4 ~~CpIs~~~m~d---PV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L   48 (61)
T 2bay_A            4 MLCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPL   48 (61)
T ss_dssp             CCCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBC
T ss_pred             EEecCCCCCCCC---CEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCC
Confidence            579999999885   456633999999999999999999999999864

>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=98.56  E-value=1.3e-08  Score=90.14  Aligned_cols=43  Identities=23%  Similarity=0.735  Sum_probs=37.2

Q ss_pred             CCCCcccccccccccCceeeecCCCCCc-ccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHT-FHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~-FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .++..|+||++.+..   +..+| |||. ||..|+.+|    ..||+||.++
T Consensus       293 ~~~~~C~IC~~~~~~---~v~lp-CgH~~fC~~C~~~~----~~CP~CR~~i  336 (345)
T 3t6p_A          293 QEERTCKVCMDKEVS---VVFIP-CGHLVVCQECAPSL----RKCPICRGII  336 (345)
T ss_dssp             HTTCBCTTTSSSBCC---EEEET-TCCEEECTTTGGGC----SBCTTTCCBC
T ss_pred             cCCCCCCccCCcCCc---eEEcC-CCChhHhHHHHhcC----CcCCCCCCCc
Confidence            356889999998765   66788 9999 999999988    7899999875

>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=98.38  E-value=1e-07  Score=81.24  Aligned_cols=47  Identities=21%  Similarity=0.406  Sum_probs=37.9

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC--CCCcc--cCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH--GSCPV--CRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~--~sCPl--CR~~  212 (213)
                      ..+..||||++.|.+  .|+... |||.|+..||.+|+..+  .+||+  ||+.
T Consensus       179 ~~el~CPIcl~~f~D--PVts~~-CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~  229 (267)
T 3htk_C          179 KIELTCPITCKPYEA--PLISRK-CNHVFDRDGIQNYLQGYTTRDCPQAACSQV  229 (267)
T ss_dssp             BCCSBCTTTSSBCSS--EEEESS-SCCEEEHHHHHHHSTTCSCEECSGGGCSCE
T ss_pred             ceeeECcCccCcccC--CeeeCC-CCCcccHHHHHHHHHhCCCCCCCcccccCc
Confidence            356779999999865  344445 99999999999999865  47999  9975

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=98.36  E-value=2.6e-07  Score=67.52  Aligned_cols=44  Identities=30%  Similarity=0.619  Sum_probs=36.2

Q ss_pred             cccccccccccCceeeecCCCCCcccHhhHHHHHhc-CCCCcccCCCC
Q 028116          167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR-HGSCPVCRRDV  213 (213)
Q Consensus       167 ~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~-~~sCPlCR~~v  213 (213)
                      -|++|--.+.  ...|..| |+|.|+.+|+..|.++ .++||+||.+|
T Consensus         3 fC~~C~~Pi~--iygRmIP-CkHvFCydCa~~~~~~~~k~Cp~C~~~V   47 (101)
T 3vk6_A            3 FCDKCGLPIK--VYGRMIP-CKHVFCYDCAILHEKKGDKMCPGCSDPV   47 (101)
T ss_dssp             BCTTTCSBCS--EEEEEET-TCCEEEHHHHHHHHHTTCCBCTTTCCBC
T ss_pred             ecCccCCCeE--EEeeecc-ccccHHHHHHHHHHhccCCCCcCcCCee
Confidence            4788855544  4678999 9999999999999865 67899999875

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

Probab=98.07  E-value=2.4e-06  Score=71.93  Aligned_cols=46  Identities=33%  Similarity=0.727  Sum_probs=38.1

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCC--CCcccCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG--SCPVCRRD  212 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~--sCPlCR~~  212 (213)
                      ....|.||.+-...|  . ..|+|+|.||..|+.+|++++.  +||.|+.+
T Consensus       179 ~i~~C~iC~~iv~~g--~-~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~  226 (238)
T 3nw0_A          179 AVKICNICHSLLIQG--Q-SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDY  226 (238)
T ss_dssp             TCCBCTTTCSBCSSC--E-ECSSSCCEECHHHHHHHTTTCSSCBCTTTCCB
T ss_pred             CCCcCcchhhHHhCC--c-ccCccChHHHHHHHHHHHHhCCCCCCCCCCCC
Confidence            468899999988775  3 3445999999999999998755  89999874

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=95.87  E-value=0.0047  Score=41.56  Aligned_cols=46  Identities=24%  Similarity=0.525  Sum_probs=34.6

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCC----CCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG----SCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~----sCPlCR~~  212 (213)
                      .....|.||.+   .++.+.-- .|...||..|++..|....    .||.|+..
T Consensus        10 ~~~~~C~vC~~---~~~ll~Cd-~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~   59 (66)
T 2lri_C           10 APGARCGVCGD---GTDVLRCT-HCAAAFHWRCHFPAGTSRPGTGLRCRSCSGD   59 (66)
T ss_dssp             CTTCCCTTTSC---CTTCEECS-SSCCEECHHHHCTTTCCCCSSSCCCTTTTTC
T ss_pred             CCCCCcCCCCC---CCeEEECC-CCCCceecccCCCccCcCCCCCEECccccCC
Confidence            45678999975   34545444 5999999999998887543    69999763

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=95.39  E-value=0.0082  Score=42.93  Aligned_cols=36  Identities=17%  Similarity=0.434  Sum_probs=26.9

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHH-HH
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDK-WL  200 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~-WL  200 (213)
                      ++..|+||++++...-...-++ |+|.|+..|+.. |-
T Consensus         2 ee~~C~~C~~~~~~~av~~C~~-C~~~~C~~Cl~~~h~   38 (101)
T 2jun_A            2 EKVLCQFCDQDPAQDAVKTCVT-CEVSYCDECLKATHP   38 (101)
T ss_dssp             CCCBCTTCCSSSCCBCCEEETT-TTEEECHHHHHHHSC
T ss_pred             CCCCCcCCCCCCCCCceEECCc-CChHHhHHHCHHHhc
Confidence            3578999998754433334476 999999999998 53

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=95.31  E-value=0.0037  Score=41.44  Aligned_cols=49  Identities=24%  Similarity=0.448  Sum_probs=34.8

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHh-----cCCCCcccCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLI-----RHGSCPVCRR  211 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~-----~~~sCPlCR~  211 (213)
                      ++...|+||.+.+.+++....--.|...||..|+.--..     ..-.||.|+.
T Consensus         4 ~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~   57 (64)
T 1we9_A            4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcC
Confidence            456779999998865544444446999999999864321     3457999975

>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=94.78  E-value=0.026  Score=39.71  Aligned_cols=35  Identities=20%  Similarity=0.502  Sum_probs=26.0

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHH
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKW  199 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~W  199 (213)
                      ..++.|.||-. |..++....- -|+-.||..|+.+-
T Consensus        13 ~~D~~C~VC~~-~t~~~l~pCR-vC~RvfH~~CL~r~   47 (89)
T 1wil_A           13 VNDEMCDVCEV-WTAESLFPCR-VCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTTCC-CCSSCCSSCS-SSSSCCCHHHHHHH
T ss_pred             CCCcccCcccc-ccccceeccc-cccccccHhhcccc
Confidence            56899999953 5555544333 39999999999986

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=93.45  E-value=0.038  Score=36.28  Aligned_cols=46  Identities=28%  Similarity=0.776  Sum_probs=33.6

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC----CCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH----GSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~----~sCPlCR~~  212 (213)
                      ..+..|.||.+.   ++.+.-- .|...||..|++.=+...    =.||.|++.
T Consensus         9 ~~~~~C~vC~~~---g~ll~CD-~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A            9 DHQDYCEVCQQG---GEIILCD-TCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             CCCSSCTTTSCC---SSEEECS-SSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCCccCCCC---CcEEECC-CCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            567889999873   4545444 599999999999765432    269999763

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=91.96  E-value=0.064  Score=33.62  Aligned_cols=45  Identities=27%  Similarity=0.602  Sum_probs=31.2

Q ss_pred             cccccccccccCceeeecCCCCCcccHhhHHHHHhcCC----CCcccCCC
Q 028116          167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG----SCPVCRRD  212 (213)
Q Consensus       167 ~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~----sCPlCR~~  212 (213)
                      .|.||.+.-..++.+.-- .|...||..|+++=|.+.+    .||.|+..
T Consensus         2 ~C~vC~~~~~~~~ll~Cd-~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~~   50 (51)
T 1f62_A            2 RCKVCRKKGEDDKLILCD-ECNKAFHLFCLRPALYEVPDGEWQCPACQPA   50 (51)
T ss_dssp             CCTTTCCSSCCSCCEECT-TTCCEECHHHHCTTCCSCCSSCCSCTTTSCC
T ss_pred             CCCCCCCCCCCCCEEECC-CCChhhCcccCCCCcCCCCCCcEECcCcccc
Confidence            589998764444444444 5999999999976444322    59999863

>2kgg_A Histone demethylase jarid1A; PHD finger, histone modification, leukemia, alternative splicing, chromatin regulator, developmental protein; NMR {Homo sapiens} PDB: 2kgi_A* 3gl6_A*

Probab=91.93  E-value=0.052  Score=34.41  Aligned_cols=45  Identities=18%  Similarity=0.183  Sum_probs=31.7

Q ss_pred             CcccccccccccCceeeecC-CCCCcccHhhHHHH----HhcCCCCcccC
Q 028116          166 SCCSICLQDIIVGELARSLP-HCHHTFHLACVDKW----LIRHGSCPVCR  210 (213)
Q Consensus       166 ~~C~ICle~~~~ge~v~~Lp-~C~H~FH~~CI~~W----L~~~~sCPlCR  210 (213)
                      -.|.+|.+.+.+++....-- .|...||..|+.--    ...+-.||.||
T Consensus         3 c~cc~C~~p~~~~~~mI~Cd~~C~~WfH~~Cvgl~~~~~~~~~~~C~~C~   52 (52)
T 2kgg_A            3 CAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA   52 (52)
T ss_dssp             CSCTTCCCCCCTTCCEEECTTTTCCEEETTTTTCCHHHHHHSCCCCSCC-
T ss_pred             ccCCCCcCccCCCCcEEEeCCCCCccCcccccCCCccccCCCCEECCCCC
Confidence            36899999987665554444 59999999997521    12566899996

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*

Probab=91.79  E-value=0.12  Score=34.51  Aligned_cols=49  Identities=22%  Similarity=0.395  Sum_probs=33.3

Q ss_pred             CCCCcccccccccccCceeeecC-CCCCcccHhhHHHH------Hhc----CCCCcccCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLP-HCHHTFHLACVDKW------LIR----HGSCPVCRR  211 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp-~C~H~FH~~CI~~W------L~~----~~sCPlCR~  211 (213)
                      +....|++|.+.+.+++....-- .|.-.||..|+.-=      |..    +-.||.|++
T Consensus         6 ~~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvglt~~~~~~l~~e~~~~w~C~~C~~   65 (65)
T 2vpb_A            6 DPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTCMA   65 (65)
T ss_dssp             ---CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHTCCHHHHHHHHHCTTEEECCHHHHC
T ss_pred             CCcCcCccCCCccCCCCCeEecccCccccCchhccCCCHHHHHHhhccCCCcEECcCccC
Confidence            45678999999988776665555 69999999997411      111    346998863

>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=91.78  E-value=0.036  Score=36.42  Aligned_cols=46  Identities=26%  Similarity=0.602  Sum_probs=32.9

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCC----CCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG----SCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~----sCPlCR~~  212 (213)
                      .++..|.||.+   .++.+.-- .|...||..|+..=|....    .||.|+..
T Consensus         7 ~~~~~C~vC~~---~g~ll~Cd-~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~   56 (61)
T 1mm2_A            7 HHMEFCRVCKD---GGELLCCD-TCPSSYHIHCLNPPLPEIPNGEWLCPRCTCP   56 (61)
T ss_dssp             SSCSSCTTTCC---CSSCBCCS-SSCCCBCSSSSSSCCSSCCSSCCCCTTTTTT
T ss_pred             CCCCcCCCCCC---CCCEEEcC-CCCHHHcccccCCCcCcCCCCccCChhhcCc
Confidence            56788999986   34444444 5999999999986554322    59999864

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=91.56  E-value=0.028  Score=36.23  Aligned_cols=45  Identities=31%  Similarity=0.728  Sum_probs=33.0

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCC----CCcccCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG----SCPVCRR  211 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~----sCPlCR~  211 (213)
                      .++..|.||.+.   ++.+.-- .|...||..|+++=|...+    .||.|++
T Consensus         7 ~~~~~C~vC~~~---g~ll~Cd-~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            7 GHEDFCSVCRKS---GQLLMCD-TCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SSCCSCSSSCCS---SCCEECS-SSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCccCCCC---CeEEEcC-CCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            567889999874   4545444 5999999999986554432    5999975

>1wep_A PHF8; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: g.50.1.2

Probab=91.10  E-value=0.13  Score=35.37  Aligned_cols=48  Identities=25%  Similarity=0.405  Sum_probs=31.3

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHh-----cCCCCcccCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLI-----RHGSCPVCRRD  212 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~-----~~~sCPlCR~~  212 (213)
                      ....| ||...+..+.....--.|...||..|+.---.     ..-.||.|+..
T Consensus        11 ~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~   63 (79)
T 1wep_A           11 VPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAV   63 (79)
T ss_dssp             CCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTT
T ss_pred             CccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCcccc
Confidence            34445 99998764443434345999999999852111     34579999863

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=90.86  E-value=0.085  Score=35.79  Aligned_cols=48  Identities=23%  Similarity=0.401  Sum_probs=33.3

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc----CCCCcccCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR----HGSCPVCRR  211 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~----~~sCPlCR~  211 (213)
                      .+...|.||.+... ++.+..--.|...||..|+..-+..    .-.||.|+.
T Consensus        16 ~~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~   67 (75)
T 2k16_A           16 NQIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCAN   67 (75)
T ss_dssp             CEEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHH
T ss_pred             CCCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccC
Confidence            44566999988754 4434444469999999999754432    336999975

>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2

Probab=90.40  E-value=0.15  Score=36.34  Aligned_cols=44  Identities=34%  Similarity=0.793  Sum_probs=28.5

Q ss_pred             CCCcccccccccccCceeeecCC--CC-CcccHhhHHHHHhc----CCCCcccCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPH--CH-HTFHLACVDKWLIR----HGSCPVCRRD  212 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~--C~-H~FH~~CI~~WL~~----~~sCPlCR~~  212 (213)
                      +...| ||.+... ++.+. --+  |. ..||..|+.  |..    +-.||.|+..
T Consensus        35 e~~yC-iC~~~~~-g~MI~-CD~~dC~~~WfH~~CVg--l~~~p~g~W~Cp~C~~~   85 (91)
T 1weu_A           35 EPTYC-LCHQVSY-GEMIG-CDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQE   85 (91)
T ss_dssp             CCBCS-TTCCBCC-SCCCC-CSCSSCSCCCCCSTTTT--CSSCCCSSCCCTTTCCC
T ss_pred             CCcEE-ECCCCCC-CCEeE-ecCCCCCCCCEecccCC--cCcCCCCCEECcCccCc
Confidence            34556 9988643 54333 334  55 689999997  443    3369999864

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=89.96  E-value=0.13  Score=36.47  Aligned_cols=46  Identities=28%  Similarity=0.650  Sum_probs=33.7

Q ss_pred             CCCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCC----CCcccCC
Q 028116          162 PTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG----SCPVCRR  211 (213)
Q Consensus       162 ~~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~----sCPlCR~  211 (213)
                      +.++..|.+|.+.   |+.+..- .|.-.||..|+++=|...+    .||.|+.
T Consensus        22 d~n~~~C~vC~~~---g~LL~CD-~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~   71 (88)
T 1fp0_A           22 DDSATICRVCQKP---GDLVMCN-QCEFCFHLDCHLPALQDVPGEEWSCSLCHV   71 (88)
T ss_dssp             SSSSSCCSSSCSS---SCCEECT-TSSCEECTTSSSTTCCCCCSSSCCCCSCCC
T ss_pred             CCCCCcCcCcCCC---CCEEECC-CCCCceecccCCCCCCCCcCCCcCCccccC
Confidence            3667889999864   4544444 5999999999987665432    5999985

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=89.90  E-value=0.26  Score=34.37  Aligned_cols=41  Identities=17%  Similarity=0.446  Sum_probs=33.2

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH  203 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~  203 (213)
                      .....|.+|.+.+++...|..-..=.|.||.+|-...++++
T Consensus        13 ~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~q   53 (93)
T 2cs3_A           13 SGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKAQ   53 (93)
T ss_dssp             CCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHHH
T ss_pred             CCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHhc
Confidence            45678999999999987776544457999999999998753

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=89.71  E-value=0.055  Score=35.26  Aligned_cols=45  Identities=31%  Similarity=0.732  Sum_probs=32.3

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCC----CCcccCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG----SCPVCRR  211 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~----sCPlCR~  211 (213)
                      .++..|.||.+.   ++.+.-- .|...||..|+.+=|...+    .||.|+.
T Consensus         3 ~~~~~C~vC~~~---g~ll~Cd-~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~   51 (60)
T 2puy_A            3 IHEDFCSVCRKS---GQLLMCD-TCSRVYHLDCLDPPLKTIPKGMWICPRCQD   51 (60)
T ss_dssp             CCCSSCTTTCCC---SSCEECS-SSSCEECGGGSSSCCSSCCCSCCCCHHHHH
T ss_pred             CCCCCCcCCCCC---CcEEEcC-CCCcCEECCcCCCCcCCCCCCceEChhccC
Confidence            456889999874   5555444 5999999999986554322    5998864

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=89.59  E-value=0.051  Score=36.17  Aligned_cols=45  Identities=31%  Similarity=0.662  Sum_probs=32.4

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCC----CCcccCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG----SCPVCRR  211 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~----sCPlCR~  211 (213)
                      .++..|.||.+.   ++.+..- .|...||..|+.+=|...+    .||.|+.
T Consensus         6 ~~~~~C~vC~~~---g~ll~CD-~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~   54 (66)
T 1xwh_A            6 KNEDECAVCRDG---GELICCD-GCPRAFHLACLSPPLREIPSGTWRCSSCLQ   54 (66)
T ss_dssp             SCCCSBSSSSCC---SSCEECS-SCCCEECTTTSSSCCSSCCSSCCCCHHHHH
T ss_pred             CCCCCCccCCCC---CCEEEcC-CCChhhcccccCCCcCcCCCCCeECccccC
Confidence            567889999864   4544444 5999999999986554322    5999864

>1wem_A Death associated transcription factor 1; structural genomics, PHD domain, death inducer- obliterator 1(DIO-1); NMR {Mus musculus} SCOP: g.50.1.2

Probab=89.45  E-value=0.14  Score=34.87  Aligned_cols=46  Identities=28%  Similarity=0.417  Sum_probs=31.4

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHH------H---hcCCCCcccCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKW------L---IRHGSCPVCRR  211 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~W------L---~~~~sCPlCR~  211 (213)
                      +...| ||...+..+..+..- .|...||..|+.--      +   ..+-.||.|+.
T Consensus        15 ~~~~C-~C~~~~~~~~MI~Cd-~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~   69 (76)
T 1wem_A           15 NALYC-ICRQPHNNRFMICCD-RCEEWFHGDCVGISEARGRLLERNGEDYICPNCTI   69 (76)
T ss_dssp             TCCCS-TTCCCCCSSCEEECS-SSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHH
T ss_pred             CCCEE-ECCCccCCCCEEEeC-CCCCcEeCeEEccchhhhhhccCCCCeEECcCCcC
Confidence            34556 999887644555554 59999999998421      1   24668999974

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=88.33  E-value=0.19  Score=36.06  Aligned_cols=45  Identities=20%  Similarity=0.288  Sum_probs=31.6

Q ss_pred             CCcccccccccccCceeeecCCCCCcccHhhHHHHHhc---CCCCcccCC
Q 028116          165 SSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR---HGSCPVCRR  211 (213)
Q Consensus       165 ~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~---~~sCPlCR~  211 (213)
                      ...| ||-.....+..+..- .|.-.||..|+..=+..   .-.||.|+.
T Consensus        28 ~vrC-iC~~~~~~~~mi~Cd-~C~~w~H~~C~~~~~~~~p~~w~C~~C~~   75 (98)
T 2lv9_A           28 VTRC-ICGFTHDDGYMICCD-KCSVWQHIDCMGIDRQHIPDTYLCERCQP   75 (98)
T ss_dssp             BCCC-TTSCCSCSSCEEEBT-TTCBEEETTTTTCCTTSCCSSBCCTTTSS
T ss_pred             CEEe-ECCCccCCCcEEEcC-CCCCcCcCcCCCCCccCCCCCEECCCCcC
Confidence            3557 898877666655555 59999999998653222   236999974

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=87.80  E-value=0.6  Score=35.86  Aligned_cols=46  Identities=26%  Similarity=0.551  Sum_probs=33.8

Q ss_pred             CCCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc-----------CCCCcccCC
Q 028116          162 PTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR-----------HGSCPVCRR  211 (213)
Q Consensus       162 ~~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~-----------~~sCPlCR~  211 (213)
                      +..+..|.+|-+.   |+.+-.- .|...||..||++=+..           .=.||+|+.
T Consensus        60 Dg~~d~C~vC~~G---G~LlcCD-~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~  116 (142)
T 2lbm_A           60 DGMDEQCRWCAEG---GNLICCD-FCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHP  116 (142)
T ss_dssp             TSCBCSCSSSCCC---SSEEECS-SSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCC
T ss_pred             CCCCCeecccCCC---CcEEeCC-CCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccC
Confidence            3667889999864   5545444 59999999999977631           226999985

>1wen_A Inhibitor of growth family, member 4; ING1-like protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.50.1.2 PDB: 1wes_A

Probab=87.80  E-value=0.34  Score=32.72  Aligned_cols=44  Identities=34%  Similarity=0.801  Sum_probs=28.6

Q ss_pred             CCCcccccccccccCceeeecCC--CC-CcccHhhHHHHHhc----CCCCcccCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPH--CH-HTFHLACVDKWLIR----HGSCPVCRRD  212 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~--C~-H~FH~~CI~~WL~~----~~sCPlCR~~  212 (213)
                      +...| ||.+.. .++.+ .--.  |. ..||..|+.  |..    +-.||.|+..
T Consensus        15 ~~~~C-~C~~~~-~g~MI-~CD~~~C~~~wfH~~Cvg--l~~~p~g~w~Cp~C~~~   65 (71)
T 1wen_A           15 EPTYC-LCHQVS-YGEMI-GCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQE   65 (71)
T ss_dssp             SCCCS-TTCCCS-CSSEE-CCSCSSCSCCCEETTTTT--CSSCCSSCCCCTTTSSC
T ss_pred             CCCEE-ECCCCC-CCCEe-EeeCCCCCCccEecccCC--cCcCCCCCEECCCCCcc
Confidence            34556 898864 35533 3334  66 699999997  443    2369999864

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=86.62  E-value=0.2  Score=36.47  Aligned_cols=47  Identities=19%  Similarity=0.458  Sum_probs=31.2

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc----CCCCcccC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR----HGSCPVCR  210 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~----~~sCPlCR  210 (213)
                      .++..|.||.+.=+..+.+.- ..|...||..|++..+..    .-.||.|+
T Consensus         5 ~~~~~C~~C~~~g~~~~ll~C-~~C~~~~H~~Cl~~~~~~~~~~~W~C~~C~   55 (111)
T 2ysm_A            5 SSGANCAVCDSPGDLLDQFFC-TTCGQHYHGMCLDIAVTPLKRAGWQCPECK   55 (111)
T ss_dssp             CCCSCBTTTCCCCCTTTSEEC-SSSCCEECTTTTTCCCCTTTSTTCCCTTTC
T ss_pred             CCCCCCcCCCCCCCCcCCeEC-CCCCCCcChHHhCCccccccccCccCCcCC
Confidence            567889999876332233444 459999999999877642    12466553

>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein, signal transduction, transcription, metal BI WNT proteins; 1.90A {Homo sapiens}

Probab=86.49  E-value=0.37  Score=35.02  Aligned_cols=47  Identities=21%  Similarity=0.418  Sum_probs=32.3

Q ss_pred             CCcccccccccccCceeeec-CCCCCcccHhhHHHH------Hh----cCCCCcccCC
Q 028116          165 SSCCSICLQDIIVGELARSL-PHCHHTFHLACVDKW------LI----RHGSCPVCRR  211 (213)
Q Consensus       165 ~~~C~ICle~~~~ge~v~~L-p~C~H~FH~~CI~~W------L~----~~~sCPlCR~  211 (213)
                      ...|.||.+.+.+......- ..|...||..|+.-=      +.    .+-.||.|+.
T Consensus         3 ~~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~   60 (105)
T 2xb1_A            3 VYPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLK   60 (105)
T ss_dssp             CCBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHH
T ss_pred             cCCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccC
Confidence            46799999998665444443 259999999997411      10    3447999975

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=86.38  E-value=0.2  Score=36.72  Aligned_cols=48  Identities=27%  Similarity=0.516  Sum_probs=32.0

Q ss_pred             CCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC----CCCcccCCC
Q 028116          165 SSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH----GSCPVCRRD  212 (213)
Q Consensus       165 ~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~----~sCPlCR~~  212 (213)
                      -..|.||.+.-.+.+.+..-..|...||..|+++=|...    =.||.||..
T Consensus        61 C~~C~vC~~~~~~~~~ll~Cd~C~~~yH~~Cl~p~l~~~P~~~W~C~~C~~k  112 (112)
T 3v43_A           61 CKTCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRPR  112 (112)
T ss_dssp             TCCBTTTCCCCCTTCCCEECTTTCCEECGGGCSSCCSSCCSSCCCCTTTSCC
T ss_pred             CCccccccCcCCCccceEEcCCCCCeeecccCCCCCCCCCCCCeECCCCCCc
Confidence            346889986422323344444599999999998666542    269999863

>1wew_A DNA-binding family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=86.26  E-value=0.19  Score=34.48  Aligned_cols=47  Identities=23%  Similarity=0.452  Sum_probs=31.5

Q ss_pred             CCCcccccccccccCceeeec-CCCCCcccHhhHHHHH---------hcCCCCcccCC
Q 028116          164 QSSCCSICLQDIIVGELARSL-PHCHHTFHLACVDKWL---------IRHGSCPVCRR  211 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~L-p~C~H~FH~~CI~~WL---------~~~~sCPlCR~  211 (213)
                      ....| ||-+....+..+..- +.|...||..|+.---         ..+..||.|+.
T Consensus        15 ~~~~C-iC~~~~~~g~MI~CD~~~C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~   71 (78)
T 1wew_A           15 IKVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRL   71 (78)
T ss_dssp             CCCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHH
T ss_pred             CCEEe-ECCCcCCCCCEEEECCccCCccccCEEEccccccccccccCCCCEECCCCCc
Confidence            34557 898875556555544 1599999999985211         13557999975

>1wee_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=86.08  E-value=0.11  Score=35.15  Aligned_cols=48  Identities=19%  Similarity=0.162  Sum_probs=32.5

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHH----hcCCCCcccCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWL----IRHGSCPVCRR  211 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL----~~~~sCPlCR~  211 (213)
                      .....| ||......++....--.|...||..|+.---    ..+-.||.|+.
T Consensus        14 ~~~~~C-~C~~~~~~g~~mI~Cd~C~~W~H~~Cvg~~~~~~~~~~~~C~~C~~   65 (72)
T 1wee_A           14 NWKVDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIE   65 (72)
T ss_dssp             SSEECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHH
T ss_pred             CcceEe-eCCCccCCCCcEEECCCCCCccCCeeeccCccccCCCcEECCCccC
Confidence            344558 7998876665444444699999999986321    23457999974

>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=85.46  E-value=0.091  Score=37.40  Aligned_cols=48  Identities=23%  Similarity=0.444  Sum_probs=32.8

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCC----CCcccCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG----SCPVCRR  211 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~----sCPlCR~  211 (213)
                      .++..|.||.+.-..++.+ .--.|...||..|+.+=|...+    .||.|+.
T Consensus        14 ~~~~~C~vC~~~~~~~~ll-~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~   65 (92)
T 2e6r_A           14 IDSYICQVCSRGDEDDKLL-FCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCIL   65 (92)
T ss_dssp             CCCCCCSSSCCSGGGGGCE-ECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHH
T ss_pred             cCCCCCccCCCcCCCCCEE-EcCCCCchhccccCCCCcccCCCCCcCCccCcC
Confidence            4567899998875443344 4445999999999985443322    4999864

>3o70_A PHD finger protein 13; PHF13, structural genomics consortium, SGC, structural genom type zinc finger, protein binding, zinc ION binding; 1.85A {Homo sapiens}

Probab=85.22  E-value=0.19  Score=33.70  Aligned_cols=48  Identities=21%  Similarity=0.459  Sum_probs=31.8

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHH---hcCCCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWL---IRHGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL---~~~~sCPlCR~~  212 (213)
                      .+...| ||...+..+..+..- .|...||..|+.---   ...-.||.|+..
T Consensus        17 ~~~~~C-iC~~~~~~~~MIqCd-~C~~WfH~~Cvgi~~~~~~~~~~C~~C~~s   67 (68)
T 3o70_A           17 QGLVTC-FCMKPFAGRPMIECN-ECHTWIHLSCAKIRKSNVPEVFVCQKCRDS   67 (68)
T ss_dssp             TTCCCS-TTCCCCTTCCEEECT-TTCCEEETTTTTCCTTSCCSSCCCHHHHTC
T ss_pred             CCceEe-ECCCcCCCCCEEECC-CCCccccccccCcCcccCCCcEECCCCCCC
Confidence            445667 998876533344444 599999999986321   134479999763

>4gne_A Histone-lysine N-methyltransferase NSD3; zinc finger, transcription, nuclear protein, transf nuclear protein complex; 1.47A {Homo sapiens} PDB: 4gnd_A 4gnf_A 4gng_A*

Probab=85.05  E-value=0.61  Score=34.08  Aligned_cols=44  Identities=27%  Similarity=0.612  Sum_probs=29.7

Q ss_pred             CCCCCcccccccccccCceeeec-CCCCCcccHhhHHHHHhcCC----CCcccC
Q 028116          162 PTQSSCCSICLQDIIVGELARSL-PHCHHTFHLACVDKWLIRHG----SCPVCR  210 (213)
Q Consensus       162 ~~~~~~C~ICle~~~~ge~v~~L-p~C~H~FH~~CI~~WL~~~~----sCPlCR  210 (213)
                      ..++..|.+|.+   .|+.+.-- +.|...||..|+.  |...+    .||-|+
T Consensus        12 ~~~~~~C~~C~~---~G~ll~CD~~~Cp~~fH~~Cl~--L~~~P~g~W~Cp~c~   60 (107)
T 4gne_A           12 QMHEDYCFQCGD---GGELVMCDKKDCPKAYHLLCLN--LTQPPYGKWECPWHQ   60 (107)
T ss_dssp             CSSCSSCTTTCC---CSEEEECCSTTCCCEECTGGGT--CSSCCSSCCCCGGGB
T ss_pred             CCCCCCCCcCCC---CCcEeEECCCCCCcccccccCc--CCcCCCCCEECCCCC
Confidence            366788999984   35544433 1488999999998  55422    488664

>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=84.71  E-value=0.66  Score=45.89  Aligned_cols=47  Identities=11%  Similarity=0.110  Sum_probs=40.0

Q ss_pred             CCCCcccccccccccCceeeecCCCC-CcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCH-HTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~-H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ++.-.|||-++-+.+   +..+| -| ++|-..+|.+||.++++||+=|.++
T Consensus       889 P~~F~cPIs~~lM~D---PVilp-sG~~TydR~~I~~wl~~~~tdP~Tr~~L  936 (968)
T 3m62_A          889 PDEFLDPLMYTIMKD---PVILP-ASKMNIDRSTIKAHLLSDSTDPFNRMPL  936 (968)
T ss_dssp             CGGGBCTTTCSBCSS---EEECT-TTCCEEEHHHHHHHHTTCCBCTTTCCBC
T ss_pred             cHHhCCcchhhHHhC---CeEcC-CCCEEECHHHHHHHHhcCCCCCCCCCCC
Confidence            456779999998876   77888 76 6999999999999999999987764

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=84.28  E-value=0.36  Score=32.59  Aligned_cols=49  Identities=20%  Similarity=0.413  Sum_probs=32.7

Q ss_pred             CCCCccccccccc-ccCceeeecCCCCCcccHhhHHHHHhc--CCCCcccCC
Q 028116          163 TQSSCCSICLQDI-IVGELARSLPHCHHTFHLACVDKWLIR--HGSCPVCRR  211 (213)
Q Consensus       163 ~~~~~C~ICle~~-~~ge~v~~Lp~C~H~FH~~CI~~WL~~--~~sCPlCR~  211 (213)
                      .++..|.||.+.- ..++.+..--.|.-.||..|+..=..-  .=.||.|+.
T Consensus        14 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~   65 (71)
T 2ku3_A           14 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQ   65 (71)
T ss_dssp             CSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcC
Confidence            5678899998763 233344455569999999998743221  125888864

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=84.03  E-value=1.4  Score=32.09  Aligned_cols=33  Identities=27%  Similarity=0.524  Sum_probs=23.2

Q ss_pred             CCCccccccccc------ccCceeeecCCCCCcccHhhHH
Q 028116          164 QSSCCSICLQDI------IVGELARSLPHCHHTFHLACVD  197 (213)
Q Consensus       164 ~~~~C~ICle~~------~~ge~v~~Lp~C~H~FH~~CI~  197 (213)
                      ....|.+|+..=      ..++.+.-. .|+..||..|++
T Consensus         4 p~~~C~~C~~~~~~~~~g~~~~Ll~C~-~C~~~~H~~Cl~   42 (112)
T 3v43_A            4 PIPICSFCLGTKEQNREKKPEELISCA-DCGNSGHPSCLK   42 (112)
T ss_dssp             CCSSBTTTCCCTTCCTTSCCCCCEECT-TTCCEECHHHHT
T ss_pred             cCccccccCCchhhCcCCCchhceEhh-hcCCCCCCchhc
Confidence            457799998752      222444444 599999999995

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=82.50  E-value=0.24  Score=34.06  Aligned_cols=45  Identities=29%  Similarity=0.577  Sum_probs=29.3

Q ss_pred             cccccccccccCceeeecCCCCCcccHhhHHHHHhcC-----CCCcccCCC
Q 028116          167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH-----GSCPVCRRD  212 (213)
Q Consensus       167 ~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~-----~sCPlCR~~  212 (213)
                      .|.||.+.-..++.+ .--.|...||..|+++-|...     =.||.|+.+
T Consensus        28 ~C~vC~~~~d~~~ll-~CD~C~~~yH~~Cl~PpL~~~P~g~~W~C~~C~~d   77 (77)
T 3shb_A           28 ACHLCGGRQDPDKQL-MCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRND   77 (77)
T ss_dssp             SBTTTCCCSCGGGEE-ECTTTCCEEETTTSSSCCSSCCSSSCCCCTTTC--
T ss_pred             cCCccCCCCCCccee-EeCCCCCccCcccCCCcccCCCCCCceECcCcccc
Confidence            577776654443444 334599999999998766532     259999864

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=82.05  E-value=0.35  Score=34.00  Aligned_cols=49  Identities=20%  Similarity=0.413  Sum_probs=32.5

Q ss_pred             CCCCccccccccc-ccCceeeecCCCCCcccHhhHHHHHhc--CCCCcccCC
Q 028116          163 TQSSCCSICLQDI-IVGELARSLPHCHHTFHLACVDKWLIR--HGSCPVCRR  211 (213)
Q Consensus       163 ~~~~~C~ICle~~-~~ge~v~~Lp~C~H~FH~~CI~~WL~~--~~sCPlCR~  211 (213)
                      +++..|.||.+.- ...+.+..-..|.-.||..|+..=+.-  .=.||.|+.
T Consensus        23 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~   74 (88)
T 2l43_A           23 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQ   74 (88)
T ss_dssp             CCCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHH
T ss_pred             CCCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccC
Confidence            4568899998763 223344455569999999999753321  225888864

>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine trimethylation, protein, histone-binding protein, transcription-structural complex; HET: M3L; 0.93A {Homo sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A

Probab=81.97  E-value=1.7  Score=32.77  Aligned_cols=45  Identities=24%  Similarity=0.582  Sum_probs=32.3

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHH-----hc------CCCCcccCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWL-----IR------HGSCPVCRR  211 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL-----~~------~~sCPlCR~  211 (213)
                      ..+..|.||-+.   |+.+ .-..|-..||..||++-+     .+      .=.|++|+.
T Consensus        55 g~~~~C~vC~dG---G~Ll-cCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~  110 (129)
T 3ql9_A           55 GMDEQCRWCAEG---GNLI-CCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHP  110 (129)
T ss_dssp             SCBSSCTTTCCC---SEEE-ECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCC
T ss_pred             CCCCcCeecCCC---CeeE-ecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCC
Confidence            567789999864   4544 334699999999999753     11      126999975

---

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	213
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	7e-17
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	3e-11
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	7e-11
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	3e-09
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	7e-09
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	1e-08
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	3e-08
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	1e-07
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	5e-06
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	6e-06
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	7e-06
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	7e-05
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	2e-04
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	4e-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 = 69.5 bits (170), Expect = 7e-17
 Identities = 24/46 (52%), Positives = 30/46 (65%)

Query: 168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           C++CL ++  GE AR LP C H FH  CVD WL  H +CP+CR  V
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 = 55.0 bits (132), Expect = 3e-11
 Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 3/51 (5%)

Query: 163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           T +  C ICL+D      + +LP C H F   C+ +W+ ++ +CP+C+  V
Sbjct: 3   TVAERCPICLEDP--SNYSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPV 50

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.4 bits (130), Expect = 7e-11
 Identities = 13/60 (21%), Positives = 21/60 (35%), Gaps = 1/60 (1%)

Query: 153 CHVILDEIKPTQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD 212
           C +  + I      C +                 C+H FH  C+ +WL     CP+  R+
Sbjct: 24  CAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNRE 82

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: CBL
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (119), Expect = 3e-09
 Identities = 12/52 (23%), Positives = 21/52 (40%), Gaps = 5/52 (9%)

Query: 163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWL-IRHGSCPVCRRDV 213
           +    C IC ++    +  +  P C H    +C+  W       CP CR ++
Sbjct: 21  STFQLCKICAEND---KDVKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEI 68

>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 = 48.2 bits (114), Expect = 7e-09
 Identities = 9/47 (19%), Positives = 20/47 (42%), Gaps = 1/47 (2%)

Query: 168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWL-IRHGSCPVCRRDV 213
           C +C++ + + ++      C +     C  +     +G CP CR+  
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPY 49

>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 = 47.9 bits (113), Expect = 1e-08
 Identities = 12/48 (25%), Positives = 17/48 (35%), Gaps = 2/48 (4%)

Query: 168 CSICLQDIIVGELARSLP-HCHHTFHLACVDKWL-IRHGSCPVCRRDV 213
           C  C          + +   C HT   +CVD       G+CP C   +
Sbjct: 6   CPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 53

>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 = 48.1 bits (113), Expect = 3e-08
 Identities = 18/86 (20%), Positives = 27/86 (31%), Gaps = 22/86 (25%)

Query: 147 SLKKLPCHVI---LDEIKPTQSSCCSICLQDI--------------IVGELARSLPHCHH 189
                P  VI    +E+K      C IC++ +              +   +   L  C H
Sbjct: 4   GSSGEPEQVIRKYTEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSH 63

Query: 190 TFHLACVDKWLIR-----HGSCPVCR 210
            FHL C+              CP C+
Sbjct: 64  AFHLLCLLAMYCNGNKDGSLQCPSCK 89

>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 = 44.9 bits (106), Expect = 1e-07
 Identities = 12/50 (24%), Positives = 19/50 (38%), Gaps = 7/50 (14%)

Query: 164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
           Q   C  C  +    +  + LP C HT    C++        CP+C+   
Sbjct: 5   QFLRCQQCQAEA---KCPKLLP-CLHTLCSGCLEAS---GMQCPICQAPW 47

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

 Score = 40.6 bits (94), Expect = 5e-06
 Identities = 11/47 (23%), Positives = 19/47 (40%), Gaps = 3/47 (6%)

Query: 167 CCSICLQDI-IVGELARSLPHCHHTFHLACVDKWL--IRHGSCPVCR 210
            C IC +++      A          H +C+  WL   R+ +C +C 
Sbjct: 8   VCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICG 54

>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 = 41.6 bits (97), Expect = 6e-06
 Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 7/49 (14%)

Query: 168 CSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG---SCPVCRRDV 213
           C ICL+ I   +   S   C H F   C+ K L +      CP+C+ D+
Sbjct: 24  CPICLELI---KEPVSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDI 68

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.1 bits (96), Expect = 7e-06
 Identities = 15/49 (30%), Positives = 19/49 (38%), Gaps = 5/49 (10%)

Query: 164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGS-CPVCRR 211
           +S  C IC   +           C H F   C+ + L   GS CP CR 
Sbjct: 22  KSISCQICEHILA----DPVETSCKHLFCRICILRCLKVMGSYCPSCRY 66

>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 = 38.2 bits (88), Expect = 7e-05
 Identities = 13/47 (27%), Positives = 15/47 (31%), Gaps = 5/47 (10%)

Query: 167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
            CS C   +        L  C H F   CV   +     CPVC    
Sbjct: 24  RCSRCTNIL---REPVCLGGCEHIFCSNCVSDCI--GTGCPVCYTPA 65

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.0 bits (85), Expect = 2e-04
 Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 9/56 (16%)

Query: 163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWL---IRHG-----SCPVCR 210
           + SS C +CL +  V ++   +  C   F   C+ +++   I+ G     SCP   
Sbjct: 3   SGSSGCKLCLGEYPVEQMTT-IAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA 57

>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 = 35.1 bits (80), Expect = 4e-04
 Identities = 6/47 (12%), Positives = 17/47 (36%), Gaps = 3/47 (6%)

Query: 167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV 213
            C+I  +           P     F  + +++++   G+ P+    +
Sbjct: 2   LCAISGKVP---RRPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPL 45

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	213
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.79
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.61
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.57
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.56
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.56
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.5
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.5
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.42
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.29
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.29
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.29
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.28
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.13
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.05
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.03
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.92
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.73
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	95.44
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	95.17
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	93.29
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	93.25
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	92.84
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	92.24
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	91.83
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	91.61
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	90.62
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	90.39
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	88.95
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	88.44
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	86.52
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	84.9
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	84.54
d2pnxa1	51	Inhibitor of growth protein 4, Ing4 {Homo sapiens	80.78

>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=99.79  E-value=1.4e-20  Score=123.42  Aligned_cols=51  Identities=47%  Similarity=1.024  Sum_probs=47.1

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      +++.+|+||+++|..++.++.+|.|+|.||..||.+||+++++||+||++|
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i   53 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV   53 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCS
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEe
Confidence            345779999999999999998888999999999999999999999999986

>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=99.61  E-value=1.4e-16  Score=108.12  Aligned_cols=47  Identities=34%  Similarity=0.944  Sum_probs=41.4

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      ..++|+||++.+.+  .++.+| |+|.||.+||.+|++++++||+||+++
T Consensus         4 ~~d~C~IC~~~~~~--~~~~~~-C~H~Fc~~Ci~~w~~~~~~CP~CR~~i   50 (68)
T d1chca_           4 VAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPV   50 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCC
T ss_pred             CCCCCccCCcCccC--CcEEeC-CCCcCcHHHHHHHHHhCCcCCCCCcch
Confidence            45779999999864  456788 999999999999999999999999875

>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=99.57  E-value=5.7e-16  Score=114.82  Aligned_cols=68  Identities=28%  Similarity=0.584  Sum_probs=48.1

Q ss_pred             cCCCCCHHHHhcCCceeeeccCCCCCCCcccccccccccC---------------ceeeecCCCCCcccHhhHHHHHhcC
Q 028116          139 LSRGLTGESLKKLPCHVILDEIKPTQSSCCSICLQDIIVG---------------ELARSLPHCHHTFHLACVDKWLIRH  203 (213)
Q Consensus       139 ~~~gls~~~i~~lp~~~~~~~~~~~~~~~C~ICle~~~~g---------------e~v~~Lp~C~H~FH~~CI~~WL~~~  203 (213)
                      ...+.+++.++++.     +......+..|+||++++...               ..+..+| |+|+||..||++||+.+
T Consensus         4 ~ss~~pe~v~~~~~-----e~~~~~~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~-CgH~FH~~Ci~~Wl~~~   77 (114)
T d1v87a_           4 GSSGEPEQVIRKYT-----EELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNG   77 (114)
T ss_dssp             CSSCCHHHHHHHHE-----EECSSCCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHT
T ss_pred             CCCCCCHHHHHHHH-----HHhcccccccccchhheecccccccccccccccccccceEECC-CCChhhHHHHHHHHHhc
Confidence            44566667766632     222224567899999998542               2345566 99999999999999854


Q ss_pred             -----CCCcccCCC
Q 028116          204 -----GSCPVCRRD  212 (213)
Q Consensus       204 -----~sCPlCR~~  212 (213)
                           .+||+||+.
T Consensus        78 ~~~~~~~CP~CR~~   91 (114)
T d1v87a_          78 NKDGSLQCPSCKTI   91 (114)
T ss_dssp             CCSSCCBCTTTCCB
T ss_pred             CcCCCCccccccch
Confidence                 379999975

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=4e-16  Score=100.56  Aligned_cols=46  Identities=20%  Similarity=0.605  Sum_probs=39.1

Q ss_pred             cccccccccccCcee-eecCCCCCcccHhhHHHHHhc-CCCCcccCCCC
Q 028116          167 CCSICLQDIIVGELA-RSLPHCHHTFHLACVDKWLIR-HGSCPVCRRDV  213 (213)
Q Consensus       167 ~C~ICle~~~~ge~v-~~Lp~C~H~FH~~CI~~WL~~-~~sCPlCR~~v  213 (213)
                      +|+||+++|..++.. ..++ |+|.||..|+++|++. +.+||+||+++
T Consensus         2 eCpICl~~~~~~~~~~~~~~-CgH~~c~~C~~~w~~~~~~~CP~CR~~~   49 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPY   49 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSS-SSCCCCHHHHHHHTTTSCCBCTTTCCBC
T ss_pred             CCcCCChhhhCCCceEEecC-CCCccchHHHHHHHhhcCCCCCccCCcC
Confidence            799999999887654 4456 9999999999999986 45799999975

>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=99.56  E-value=9e-16  Score=109.17  Aligned_cols=49  Identities=29%  Similarity=0.672  Sum_probs=41.2

Q ss_pred             CCCCcccccccccccCc---------------eeeecCCCCCcccHhhHHHHHhcCCCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGE---------------LARSLPHCHHTFHLACVDKWLIRHGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge---------------~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~  212 (213)
                      ..++.|+||++++....               .+..+| |+|.||..||.+||+.+++||+||++
T Consensus        19 ~~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR~~   82 (88)
T d3dplr1          19 IVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNRE   82 (88)
T ss_dssp             SCSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSB
T ss_pred             CCCCcCEEccchhhCccccccccccccccccCCeEEcc-ccCcccHHHHHHHHHHCCcCCCCCCc
Confidence            45677999999886532               355677 99999999999999999999999986

>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=99.50  E-value=6.8e-15  Score=102.61  Aligned_cols=46  Identities=26%  Similarity=0.708  Sum_probs=39.4

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc-CCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR-HGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~-~~sCPlCR~~v  213 (213)
                      ....|+||++.+..   ++.+| |||.||..||.+||.. +++||+||++|
T Consensus        22 ~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i   68 (79)
T d1fbva4          22 TFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEI   68 (79)
T ss_dssp             CTTBCTTTSSSBCC---EECSS-SCCEECHHHHHHHHHTTCCSCTTTCCCC
T ss_pred             CCCCCccCCCcCCC---eEEeC-CCCeeeHHHHHHHHHHCcCcCCCCCcCc
Confidence            34579999998765   77888 9999999999999985 57899999975

>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=99.50  E-value=4.8e-15  Score=99.64  Aligned_cols=49  Identities=27%  Similarity=0.565  Sum_probs=39.1

Q ss_pred             CCCcccccccccccC-c-eeeecCCCCCcccHhhHHHHHhc-CCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVG-E-LARSLPHCHHTFHLACVDKWLIR-HGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~g-e-~v~~Lp~C~H~FH~~CI~~WL~~-~~sCPlCR~~v  213 (213)
                      ++..|+||++++... + .+..+| |+|.||..||.+|+.+ +.+||+||+++
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~~CP~CR~~i   53 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPL   53 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCC
T ss_pred             CCCCCCcCCceeecCCceEEEeCc-cChHhhHHHHHHHhCcCcCCCCCCCcCc
Confidence            468899999986543 3 334556 9999999999999975 56899999875

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.42  E-value=2.3e-14  Score=93.50  Aligned_cols=44  Identities=14%  Similarity=0.266  Sum_probs=39.2

Q ss_pred             cccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       167 ~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .|+||++.+++   ...+|+|||+||..||.+||+++++||+||+++
T Consensus         2 ~C~Ic~~~~~~---Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l   45 (56)
T d2baya1           2 LCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPL   45 (56)
T ss_dssp             CCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBC
T ss_pred             CCccCCchHHh---cCccCCCCCcccHHHHHHHHhhccCCCccCCcC
Confidence            59999998875   556667999999999999999999999999875

>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=99.29  E-value=2.2e-13  Score=88.80  Aligned_cols=43  Identities=28%  Similarity=0.647  Sum_probs=36.9

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      +...|+||++.|.+   ++.+| |+|.||..||++|   +.+||+||+++
T Consensus         5 ~~l~C~IC~~~~~~---p~~lp-CgH~fC~~Ci~~~---~~~CP~Cr~~~   47 (56)
T d1bora_           5 QFLRCQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPW   47 (56)
T ss_dssp             CCSSCSSSCSSCBC---CSCST-TSCCSBTTTCSSS---SSSCSSCCSSS
T ss_pred             CCCCCcccCcccCC---CEEec-CCCHHhHHHHHcC---CCcCcCCCCcc
Confidence            34689999999875   56888 9999999999876   77899999975

>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=99.29  E-value=7.4e-13  Score=93.56  Aligned_cols=45  Identities=29%  Similarity=0.590  Sum_probs=38.7

Q ss_pred             CCcccccccccccCceeeecCCCCCcccHhhHHHHHhc-CCCCcccCCCC
Q 028116          165 SSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR-HGSCPVCRRDV  213 (213)
Q Consensus       165 ~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~-~~sCPlCR~~v  213 (213)
                      ...|+||++.+.+   +..+| |||.||..||.+|++. +.+||+||.++
T Consensus        23 ~l~C~IC~~~~~~---pv~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~   68 (86)
T d1rmda2          23 SISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPC   68 (86)
T ss_dssp             HTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBC
T ss_pred             CcCCccCCcchhc---ceecC-CCChhhHHHHHHHHhhCCCcCcccCCCC
Confidence            4679999998865   67788 9999999999999975 45899999864

>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=99.29  E-value=6.4e-13  Score=96.56  Aligned_cols=45  Identities=36%  Similarity=0.727  Sum_probs=38.4

Q ss_pred             CCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC---CCCcccCCCC
Q 028116          165 SSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH---GSCPVCRRDV  213 (213)
Q Consensus       165 ~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~---~sCPlCR~~v  213 (213)
                      ...|+||++.|.+   +..+| |||.||..||.+|+.++   .+||+||+++
T Consensus        21 ~l~CpIC~~~~~~---pv~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~   68 (103)
T d1jm7a_          21 ILECPICLELIKE---PVSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDI   68 (103)
T ss_dssp             HTSCSSSCCCCSS---CCBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCC
T ss_pred             CcCCCccCchhCC---eEEcC-CCCchhhHHHHHHHHHCCCCCcCcCCCCcC
Confidence            4679999998865   56688 99999999999999765   3899999874

>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=99.28  E-value=7.9e-13  Score=87.03  Aligned_cols=51  Identities=18%  Similarity=0.456  Sum_probs=37.6

Q ss_pred             CCCCcccccccccccCceee-ecCCCCCcccHhhHHHHHhc--CCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELAR-SLPHCHHTFHLACVDKWLIR--HGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~-~Lp~C~H~FH~~CI~~WL~~--~~sCPlCR~~v  213 (213)
                      ++...|+||++++....... ....|+|+||..||.+|+..  +.+||+||++.
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~   57 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVY   57 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCee
Confidence            56788999999886543211 11235699999999999964  56899999863

>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=99.13  E-value=5e-12  Score=90.76  Aligned_cols=45  Identities=29%  Similarity=0.563  Sum_probs=36.0

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      +...|+||++.|..   +..++.|||.||..||.+|+.  ++||.||.++
T Consensus        21 ~~l~C~IC~~~~~~---pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~   65 (97)
T d1jm7b_          21 KLLRCSRCTNILRE---PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPA   65 (97)
T ss_dssp             HTTSCSSSCSCCSS---CBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBC
T ss_pred             hcCCCccCCchhhc---CceeCCCCCchhHHHHHHHHh--ccccccCCcC
Confidence            35789999999875   334434999999999999984  4699999864

>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=99.05  E-value=6e-11  Score=82.04  Aligned_cols=47  Identities=19%  Similarity=0.226  Sum_probs=40.2

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc-CCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR-HGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~-~~sCPlCR~~v  213 (213)
                      .++..|+||++-|.+   +..+| |||.|+..||.+|+.+ +.+||.||.++
T Consensus         5 P~~l~CpIc~~l~~d---Pv~~~-cGhtfc~~ci~~~l~~~~~~cP~c~~~l   52 (80)
T d2c2la2           5 PDYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFNPVTRSPL   52 (80)
T ss_dssp             CSTTBCTTTCSBCSS---EEECS-SCCEEETTHHHHHHHHTCSSCTTTCCCC
T ss_pred             CccccCcCcCchhhh---hcccC-CcCeecHHHHHHHHhcCCccCCCccccc
Confidence            456889999998876   55788 9999999999999976 45799999875

>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=99.03  E-value=7.6e-11  Score=81.10  Aligned_cols=47  Identities=19%  Similarity=0.400  Sum_probs=40.3

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC-CCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH-GSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~-~sCPlCR~~v  213 (213)
                      .++..|+||++-|.+   +..++ |||.|+..||.+|+..+ .+||.||.++
T Consensus         6 P~~l~CpIc~~~m~d---PV~~~-cgh~fc~~ci~~~~~~~~~~cP~~~~~l   53 (78)
T d1t1ha_           6 PEYFRCPISLELMKD---PVIVS-TGQTYERSSIQKWLDAGHKTCPKSQETL   53 (78)
T ss_dssp             SSSSSCTTTSCCCSS---EEEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBC
T ss_pred             CccCCCcCcCchhhC---ceEcc-CCCcchHHHHHHHHHHCCCCCCcccccC
Confidence            457889999999876   56788 99999999999999864 5799999864

>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=98.92  E-value=3.3e-10  Score=81.37  Aligned_cols=48  Identities=15%  Similarity=0.129  Sum_probs=42.0

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccCCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCRRDV  213 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR~~v  213 (213)
                      .++..||||++-|.+   +.++|.|+|.|+..||.+||.++.+||+||+++
T Consensus        20 P~~f~CPI~~~lm~d---PV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l   67 (98)
T d1wgma_          20 CDEFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPL   67 (98)
T ss_dssp             CTTTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBC
T ss_pred             cHHhCCcCchhHHHH---HHhcccccchhhHHHHHHHHHhcCCcccccccc
Confidence            457889999999887   778885567999999999999999999999875

>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=98.73  E-value=2.7e-09  Score=75.38  Aligned_cols=47  Identities=26%  Similarity=0.552  Sum_probs=37.9

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC--------CCCcccC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH--------GSCPVCR  210 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~--------~sCPlCR  210 (213)
                      .....|+||++++...+.+..++ |+|.||.+|+.+|++.+        -+||.|+
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           3 SGSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCCCcCccCCCcccCCceEEECC-CCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            34678999999998877776666 99999999999999631        2599864

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=95.44  E-value=0.0015  Score=41.87  Aligned_cols=50  Identities=24%  Similarity=0.450  Sum_probs=36.4

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHH---HHh--cCCCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDK---WLI--RHGSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~---WL~--~~~sCPlCR~~  212 (213)
                      ..+..|.+|.+.+..++....-..|+..||..|+..   ...  .+-.||.|+..
T Consensus         4 ~~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            456789999998877765555556999999999863   111  23479999763

>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=95.17  E-value=0.0038  Score=37.99  Aligned_cols=44  Identities=27%  Similarity=0.631  Sum_probs=32.1

Q ss_pred             cccccccccccCceeeecCCCCCcccHhhHHHHHhcCC----CCcccCC
Q 028116          167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG----SCPVCRR  211 (213)
Q Consensus       167 ~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~----sCPlCR~  211 (213)
                      .|.||...-..++.+ .-..|...||..|++.-+...+    .||.||.
T Consensus         2 ~C~vC~~~~~~~~~i-~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDKLI-LCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCE-ECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCCEE-EcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            588997765444444 4446999999999998765433    5999985

>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=93.29  E-value=0.0082  Score=37.89  Aligned_cols=46  Identities=26%  Similarity=0.608  Sum_probs=32.9

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcC----CCCcccCCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRH----GSCPVCRRD  212 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~----~sCPlCR~~  212 (213)
                      ..+..|.+|.+   .++.+.- -.|.-.||..|++..+...    -.||.|+.+
T Consensus         7 ~~~~~C~~C~~---~g~lv~C-d~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~   56 (61)
T d1mm2a_           7 HHMEFCRVCKD---GGELLCC-DTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCP   56 (61)
T ss_dssp             SSCSSCTTTCC---CSSCBCC-SSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTT
T ss_pred             CCcCCCcCCCC---CCeEEEe-CCCCccCchhhcCCCcCcCCCCcEECCCCcCc
Confidence            45667999975   3454444 4599999999998766542    269999864

>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=93.25  E-value=0.041  Score=36.83  Aligned_cols=35  Identities=20%  Similarity=0.531  Sum_probs=26.8

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHH
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKW  199 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~W  199 (213)
                      .++..|.|| +-|...+..-.- -|+.+||..|+.+-
T Consensus        13 ~~D~mC~vC-~v~t~~~l~pCR-vCtRv~H~~CL~r~   47 (89)
T d1wila_          13 VNDEMCDVC-EVWTAESLFPCR-VCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTT-CCCCSSCCSSCS-SSSSCCCHHHHHHH
T ss_pred             CcCcccccc-Ccccccceecce-eecchhhHHHHHHh
Confidence            678999999 667665544322 38999999999986

>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=92.84  E-value=0.015  Score=37.72  Aligned_cols=45  Identities=29%  Similarity=0.676  Sum_probs=31.9

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCC----CCcccCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHG----SCPVCRR  211 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~----sCPlCR~  211 (213)
                      .....|.+|.+   .++.+.- -.|...||..|+.+.+...+    .||.|+.
T Consensus         5 d~c~~C~~C~~---~~~ll~C-d~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~   53 (70)
T d1fp0a1           5 DSATICRVCQK---PGDLVMC-NQCEFCFHLDCHLPALQDVPGEEWSCSLCHV   53 (70)
T ss_dssp             SSSSCCSSSCS---SSCCEEC-TTSSCEECTTSSSTTCCCCCSSSCCCCSCCC
T ss_pred             CCCCCCCCCCC---cCEEEEC-CCCChhhccccCCCCcCcCCCCCEECcCCcC
Confidence            34556777754   3554444 45999999999998876543    5999975

>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=92.24  E-value=0.032  Score=35.02  Aligned_cols=45  Identities=20%  Similarity=0.355  Sum_probs=32.4

Q ss_pred             CCCcccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCccc
Q 028116          164 QSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVC  209 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlC  209 (213)
                      ....|.=|+.++.+ ..+..-|+|++.|+.+|=.--=+.-.+||-|
T Consensus        14 ~~~~C~gC~~~l~~-~~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKD-QHVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTT-SEEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCCccCCCCcCCC-CceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            35779999988865 3455677899999999933222234579988

>d1wesa_ g.50.1.2 (A:) PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD Inhibitor of growth protein 2, Ing2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.83  E-value=0.046  Score=35.47  Aligned_cols=46  Identities=33%  Similarity=0.652  Sum_probs=27.5

Q ss_pred             CCCcccccccccccCceeee-cCCCC-CcccHhhHHHHHhc----CCCCcccCCC
Q 028116          164 QSSCCSICLQDIIVGELARS-LPHCH-HTFHLACVDKWLIR----HGSCPVCRRD  212 (213)
Q Consensus       164 ~~~~C~ICle~~~~ge~v~~-Lp~C~-H~FH~~CI~~WL~~----~~sCPlCR~~  212 (213)
                      ++..+.||.+.. .++.+.. -..|. ..||..|+.  |..    +-.||.||..
T Consensus        14 ~e~~~CiC~~~~-~~~~i~c~~~~C~~~wfH~~Cvg--l~~~p~~~w~C~~C~~~   65 (71)
T d1wesa_          14 NEPTYCLCNQVS-YGEMIGCDNEQCPIEWFHFSCVS--LTYKPKGKWYCPKCRGD   65 (71)
T ss_dssp             SSCCCSTTCCCC-CSSEECCSCTTCSCCCEETTTTT--CSSCCSSCCCCTTTSSC
T ss_pred             CCCCEEEeCCCC-CCCEEEEECCCCCCcCccCccCC--CCcCCCCcEECcCCccc
Confidence            334445998764 3344433 22354 479999985  333    2369999863

>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=91.61  E-value=0.11  Score=34.08  Aligned_cols=47  Identities=23%  Similarity=0.374  Sum_probs=32.2

Q ss_pred             CcccccccccccCceeeecCCCCCcccHhhHH--HHHhc---CCCCcccCCC
Q 028116          166 SCCSICLQDIIVGELARSLPHCHHTFHLACVD--KWLIR---HGSCPVCRRD  212 (213)
Q Consensus       166 ~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~--~WL~~---~~sCPlCR~~  212 (213)
                      ..|.||.+.+..++....--.|.-.||..|+.  ..-..   +-.||.||..
T Consensus        12 pv~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~   63 (79)
T d1wepa_          12 PVYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAV   63 (79)
T ss_dssp             CCCSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTT
T ss_pred             CeEeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCC
Confidence            44559998876655444455699999999985  22222   3579999863

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.62  E-value=0.1  Score=33.86  Aligned_cols=40  Identities=18%  Similarity=0.448  Sum_probs=32.3

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHHHHHhc
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIR  202 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~  202 (213)
                      .....|.+|.+.+++...|..-..=+|.||.+|-...+++
T Consensus         6 ~~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~   45 (80)
T d2cs3a1           6 SGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   45 (80)
T ss_dssp             CCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CCceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHh
Confidence            3457899999999988777544445799999999999875

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Death associated transcription factor 1, Datf1 (DIO-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.39  E-value=0.091  Score=33.91  Aligned_cols=47  Identities=28%  Similarity=0.438  Sum_probs=31.1

Q ss_pred             CCCCcccccccccccCceeeecCCCCCcccHhhHH----HH--H---hcCCCCcccCC
Q 028116          163 TQSSCCSICLQDIIVGELARSLPHCHHTFHLACVD----KW--L---IRHGSCPVCRR  211 (213)
Q Consensus       163 ~~~~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~----~W--L---~~~~sCPlCR~  211 (213)
                      ++...| ||.+....++.+.-- +|.-.||..|+.    ..  .   ...-.||.|+.
T Consensus        14 ~~~~~C-iC~~~~~~~~mi~Cd-~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~   69 (76)
T d1wema_          14 PNALYC-ICRQPHNNRFMICCD-RCEEWFHGDCVGISEARGRLLERNGEDYICPNCTI   69 (76)
T ss_dssp             TTCCCS-TTCCCCCSSCEEECS-SSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHH
T ss_pred             CCcCEE-ECCCccCCCeEEEEC-CCCCcCCccccCCCcccccccCCCCCcEECCCCcC
Confidence            344557 898876655555444 599999999982    11  1   12458999964

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=88.95  E-value=0.096  Score=28.47  Aligned_cols=28  Identities=36%  Similarity=0.672  Sum_probs=24.6

Q ss_pred             CcccccccccccCceeeecCCCCCcccHhh
Q 028116          166 SCCSICLQDIIVGELARSLPHCHHTFHLAC  195 (213)
Q Consensus       166 ~~C~ICle~~~~ge~v~~Lp~C~H~FH~~C  195 (213)
                      ..|+-|.+.+...|.|++-.  +++||..|
T Consensus         3 g~Ca~C~~~I~~~e~VmRA~--~~VyHl~C   30 (31)
T d1rutx3           3 GACSACGQSIPASELVMRAQ--GNVYHLKC   30 (31)
T ss_dssp             EECTTTCCEECTTSEEEEET--TEEECGGG
T ss_pred             cccccccCcCChhHhheecc--cceeeecc
Confidence            56999999999999888763  79999999

>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At1g33420
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=88.44  E-value=0.027  Score=36.42  Aligned_cols=45  Identities=20%  Similarity=0.202  Sum_probs=31.2

Q ss_pred             CcccccccccccCceeeecCCCCCcccHhhHHHHHh----cCCCCcccCC
Q 028116          166 SCCSICLQDIIVGELARSLPHCHHTFHLACVDKWLI----RHGSCPVCRR  211 (213)
Q Consensus       166 ~~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~----~~~sCPlCR~  211 (213)
                      ..| ||......++.+..-..|...||..|+..=..    ..-.||.|+.
T Consensus        17 ~~C-~C~~~~~~~~~mv~Cd~C~~w~H~~C~g~~~~~~~~~~~~C~~C~~   65 (72)
T d1weea_          17 VDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIE   65 (72)
T ss_dssp             ECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHH
T ss_pred             EEe-eCCCCcCCCCeEEEeCCCCCcCchhhcCCccccCCCCcEECcCCcC
Confidence            446 89877767665555557999999999754211    2346999974

>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=86.52  E-value=0.043  Score=36.70  Aligned_cols=48  Identities=23%  Similarity=0.537  Sum_probs=31.7

Q ss_pred             CCCccccccccccc-CceeeecCCCCCcccHhhHHHHHh----c----CCCCcccCC
Q 028116          164 QSSCCSICLQDIIV-GELARSLPHCHHTFHLACVDKWLI----R----HGSCPVCRR  211 (213)
Q Consensus       164 ~~~~C~ICle~~~~-ge~v~~Lp~C~H~FH~~CI~~WL~----~----~~sCPlCR~  211 (213)
                      ....|.||.+.... ...+..--.|...||..|+...+.    .    .-.||.|+.
T Consensus        15 ~~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~   71 (88)
T d1weva_          15 MGLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTR   71 (88)
T ss_dssp             HCCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHH
T ss_pred             CcCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCc
Confidence            34679999875443 234444456999999999875432    1    235999964

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=84.90  E-value=0.4  Score=31.05  Aligned_cols=46  Identities=24%  Similarity=0.491  Sum_probs=30.7

Q ss_pred             CCcccccccccccCceeeec-CCCCCcccHhhHHH----HHh-----cCCCCcccCC
Q 028116          165 SSCCSICLQDIIVGELARSL-PHCHHTFHLACVDK----WLI-----RHGSCPVCRR  211 (213)
Q Consensus       165 ~~~C~ICle~~~~ge~v~~L-p~C~H~FH~~CI~~----WL~-----~~~sCPlCR~  211 (213)
                      ...| ||.+....+..+..- .+|...||..|+.-    .-.     .+-.||.|+.
T Consensus        16 ~~~C-~C~~~~~~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~   71 (78)
T d1wewa_          16 KVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRL   71 (78)
T ss_dssp             CCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHH
T ss_pred             ccEe-ECCCccCCCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcC
Confidence            3457 999887766555443 25999999999841    111     1357999974

>d1y02a2 g.50.1.1 (A:20-70) Rififylin (FYVE-RING finger protein Sakura) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Rififylin (FYVE-RING finger protein Sakura)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.54  E-value=0.064  Score=32.55  Aligned_cols=44  Identities=16%  Similarity=0.417  Sum_probs=30.3

Q ss_pred             cccccccccccCceeeecCCCCCcccHhhHHHHHhcCCCCcccC
Q 028116          167 CCSICLQDIIVGELARSLPHCHHTFHLACVDKWLIRHGSCPVCR  210 (213)
Q Consensus       167 ~C~ICle~~~~ge~v~~Lp~C~H~FH~~CI~~WL~~~~sCPlCR  210 (213)
                      .|.+|...|.....-..-..||++|+..|..+.-..+..|..|.
T Consensus         2 ~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~RvC~~C~   45 (51)
T d1y02a2           2 SCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQ   45 (51)
T ss_dssp             CCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHH
T ss_pred             CccccCCcccCCccCcccccCCcccCccccCCCCCCCeECHhHh
Confidence            58899999876554445556999999999765544555677764

>d2pnxa1 g.50.1.2 (A:195-245) Inhibitor of growth protein 4, Ing4 {Homo sapiens [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Inhibitor of growth protein 4, Ing4
species: Homo sapiens [TaxId: 9606]

Probab=80.78  E-value=0.15  Score=30.68  Aligned_cols=42  Identities=38%  Similarity=0.839  Sum_probs=25.1

Q ss_pred             cccccccccccCceeeec-CCCC-CcccHhhHHHHHhc----CCCCcccCCC
Q 028116          167 CCSICLQDIIVGELARSL-PHCH-HTFHLACVDKWLIR----HGSCPVCRRD  212 (213)
Q Consensus       167 ~C~ICle~~~~ge~v~~L-p~C~-H~FH~~CI~~WL~~----~~sCPlCR~~  212 (213)
                      -| ||.+.. .++.+..- .+|. -.||..|+.  |..    +-.||.|+++
T Consensus         4 yC-~C~~~~-~~~mi~Cd~~~C~~~WfH~~Cvg--l~~~p~~~w~C~~C~~k   51 (51)
T d2pnxa1           4 YC-LCHQVS-YGEMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQE   51 (51)
T ss_dssp             ET-TTTEEC-CSEEEECSCTTCSSCEEEGGGGT--CSSCCSSCCCCHHHHCC
T ss_pred             EE-EcCCCC-CCCEEEEecCCCCCCCEeCCccC--CCcCCCCcEECcCCCCc
Confidence            46 887764 33433321 1244 479999986  332    2259999864