Citrus Sinensis ID: 043988

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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-
Protein Sequence
RSSNAETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPWHSEFDCSQFQKL
Secondary Structure (PSIPRED)
cccccccccccccEEcccccccccccccEEEcccccccHHHHHHHHHHHHHHccccccccccccccccccHHHHHccccHHHHHHHHHHHHHHHHccccEEcccccccccEEEcccccccEEEccccccHHcccccccccccccHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccEEEccccHHHcccccccccHHHHHHHHHHEEEEEEcccEccccccccccccccHHHHHHHccHHHHHHHHHHHHHHHccccccEEcccccccEEEEccccccccccccccccEEEEEccccccccccHHHHHcc
Coil and Loop (DISEMBL)
rssnaetddgtpsFVCEICVesrslydsfdvkgcshfncTSCIVRYIASKlegnitniscpqlgcearlefedcrlilpddVFARWGLALCESALVghkkfycpykdcssmlidegeairksncphcrrlfcvqckvpwhsefdcsqfqkl
Flexible Loop (DISEMBL)
rssnaetddgtpsfVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPWHSEFDCSQFQKL
Low Complexity Region (SEG)
RSSNAETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPWHSEFDCSQFQKL
Disordered region (IsUnstruct)
************SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPWHSEFDC******
Disordered Region (DISOPRED)
****************EICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPWHSEFDCSQFQKL
Disordered Region (DISEMBL)
***********PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPWHSEF********
Disordered Region (DISPRO)
************SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPWHSEFDCSQF*KL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
RSSNAETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPWHSEFDCSQFQKL
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	151	2.2.26 [Sep-21-2011]
P50636	840	E3 ubiquitin-protein liga	yes	no	0.913	0.164	0.298	2e-07
Q9NV58	838	E3 ubiquitin-protein liga	yes	no	0.913	0.164	0.298	3e-07
Q2VJ60	838	E3 ubiquitin-protein liga	no	no	0.913	0.164	0.291	9e-07
Q7Z419	303	E3 ubiquitin-protein liga	no	no	0.927	0.462	0.261	1e-06
Q4KLT0	282	Probable E3 ubiquitin-pro	N/A	no	0.854	0.457	0.248	4e-06
A5PK27	304	E3 ubiquitin-protein liga	no	no	0.913	0.453	0.265	4e-06
Q8BKD6	301	E3 ubiquitin-protein liga	no	no	0.913	0.458	0.265	2e-05
Q5RFV4	293	Probable E3 ubiquitin-pro	no	no	0.900	0.464	0.251	2e-05
P50876	292	Probable E3 ubiquitin-pro	no	no	0.900	0.465	0.251	8e-05
Q1L8L6	701	E3 ubiquitin-protein liga	no	no	0.834	0.179	0.265	8e-05

>sp|P50636|RN19A_MOUSE E3 ubiquitin-protein ligase RNF19A OS=Mus musculus GN=Rnf19a PE=1 SV=2

 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 48/161 (29%), Positives = 68/161 (42%), Gaps = 23/161 (14%)

Query: 2   SSNAETDDGTPSFV--------CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEG 53
           S+N  +D+G  S          C +C+   S     D+  C H +C  C+ +Y+  ++  
Sbjct: 110 STNTSSDNGLTSISKQIGDFIECPLCLLRHSKDRFPDIMTCHHRSCVDCLRQYLRIEISE 169

Query: 54  NITNISCPQLGCEARLEFEDCRLILPDDVFA-RWGLALCESALVGHKK-FYCPYKDCSSM 111
           +  NISCP+  C  R    D RLIL DDV   ++   +    LV      +CP  DC   
Sbjct: 170 SRVNISCPE--CTERFNPHDIRLILSDDVLMEKYEEFMLRRWLVADPDCRWCPAPDCGYA 227

Query: 112 LIDEGEAIRKSNCPH-------CRRLFCVQCKVPWHSEFDC 145
           +I  G A    +CP        C   FC  CK  WH    C
Sbjct: 228 VIAFGCA----SCPKLTCGREGCGTEFCYHCKQIWHPNQTC 264

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates, such as SNCAIP or CASR.
Mus musculus (taxid: 10090)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|Q9NV58|RN19A_HUMAN E3 ubiquitin-protein ligase RNF19A OS=Homo sapiens GN=RNF19A PE=1 SV=3

 Score = 54.3 bits (129), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 48/161 (29%), Positives = 68/161 (42%), Gaps = 23/161 (14%)

Query: 2   SSNAETDDGTPSFV--------CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEG 53
           S+N  +D+G  S          C +C+   S     D+  C H +C  C+ +Y+  ++  
Sbjct: 110 STNTSSDNGLTSISKQIGDFIECPLCLLRHSKDRFPDIMTCHHRSCVDCLRQYLRIEISE 169

Query: 54  NITNISCPQLGCEARLEFEDCRLILPDDVFA-RWGLALCESALVGHKK-FYCPYKDCSSM 111
           +  NISCP+  C  R    D RLIL DDV   ++   +    LV      +CP  DC   
Sbjct: 170 SRVNISCPE--CTERFNPHDIRLILSDDVLMEKYEEFMLRRWLVADPDCRWCPAPDCGYA 227

Query: 112 LIDEGEAIRKSNCPH-------CRRLFCVQCKVPWHSEFDC 145
           +I  G A    +CP        C   FC  CK  WH    C
Sbjct: 228 VIAFGCA----SCPKLTCGREGCGTEFCYHCKQIWHPNQTC 264

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates, such as SNCAIP or CASR. Specifically ubiquitinates pathogenic SOD1 variants, which leads to their proteasomal degradation and to neuronal protection.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q2VJ60|RN19A_PIG E3 ubiquitin-protein ligase RNF19A OS=Sus scrofa GN=RNF19A PE=2 SV=1

 Score = 52.8 bits (125), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 47/161 (29%), Positives = 68/161 (42%), Gaps = 23/161 (14%)

Query: 2   SSNAETDDGTPSFV--------CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEG 53
           S+N  +D+G  S          C +C+   S     ++  C H +C  C+ +Y+  ++  
Sbjct: 110 STNTSSDNGLTSISKQIGDFIECPLCLLRHSKDRFPEIMTCHHRSCVDCLRQYLRIEISE 169

Query: 54  NITNISCPQLGCEARLEFEDCRLILPDDVFA-RWGLALCESALVGHKK-FYCPYKDCSSM 111
           +  NISCP+  C  R    D RLIL DDV   ++   +    LV      +CP  DC   
Sbjct: 170 SRVNISCPE--CTERFNPHDIRLILSDDVLMEKYEEFMLRRWLVADPDCRWCPAPDCGYA 227

Query: 112 LIDEGEAIRKSNCPH-------CRRLFCVQCKVPWHSEFDC 145
           +I  G A    +CP        C   FC  CK  WH    C
Sbjct: 228 VIAFGCA----SCPKLTCGREGCGTEFCYHCKQIWHPNQTC 264

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates, such as SNCAIP or CASR.

Sus scrofa (taxid: 9823)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q7Z419|R144B_HUMAN E3 ubiquitin-protein ligase RNF144B OS=Homo sapiens GN=RNF144B PE=1 SV=1

 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 39/149 (26%), Positives = 67/149 (44%), Gaps = 9/149 (6%)

Query: 11  TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKL-EGNITNISCPQLGC--EA 67
            P   C++C+  +SL     ++ C    CT+C+ +Y+   + EG  + I+CP + C    
Sbjct: 25  APLITCKLCLCEQSLDKMTTLQECQCIFCTACLKQYMQLAIREGCGSPITCPDMVCLNHG 84

Query: 68  RLEFEDCRLILPDDVFARWG-LALCESALVGHKKFYCPYKDCSSMLI----DEGEAIRKS 122
            L+  +   ++P D F  +  L       +   + +CP  DC ++      D G+ +   
Sbjct: 85  TLQEAEIACLVPVDQFQLYQRLKFEREVHLDPYRTWCPVADCQTVCPVASSDPGQPVL-V 143

Query: 123 NCPHCRRLFCVQCKVPWHSEFDCSQFQKL 151
            CP C   FC  CK  WH+E  C   Q +
Sbjct: 144 ECPSCHLKFCSCCKDAWHAEVSCRDSQPI 172

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates such as LCMT2, thereby promoting their degradation. Induces apoptosis via a p53/TP53-dependent but caspase-independent mechanism. However, its overexpression also produces a decrease of the ubiquitin-dependent stability of BAX, a pro-apoptotic protein, ultimately leading to protection of cell death; But, it is not an anti-apoptotic protein per se.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q4KLT0|RN217_XENLA Probable E3 ubiquitin-protein ligase RNF217 OS=Xenopus laevis GN=rnf217 PE=2 SV=1

 Score = 50.4 bits (119), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 36/145 (24%), Positives = 59/145 (40%), Gaps = 16/145 (11%)

Query: 16  CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR 75
           C +C+E RS+     +  C    C  C+ RY++S+++     I CP   C   L+     
Sbjct: 3   CRVCLEDRSIKP---LPCCKKPVCDECLKRYLSSQVQLGQAEIQCPITECNKHLDESTIL 59

Query: 76  LILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLI----------DEGEAIRKSNCP 125
             LP D   ++   L  S +    K   P   C                + E   K  CP
Sbjct: 60  YSLPHDDIIKYKYFLELSRMDSSTK---PCPQCKHFTTFKRKTHIPNPTKSENKLKIQCP 116

Query: 126 HCRRLFCVQCKVPWHSEFDCSQFQK 150
            C+ ++C +C  PWH   +C +++K
Sbjct: 117 SCQFIWCFRCHAPWHEGVNCREYKK 141

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

Xenopus laevis (taxid: 8355)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|A5PK27|R144B_BOVIN E3 ubiquitin-protein ligase RNF144B OS=Bos taurus GN=RNF144B PE=2 SV=1

 Score = 50.4 bits (119), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 39/147 (26%), Positives = 66/147 (44%), Gaps = 9/147 (6%)

Query: 11  TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKL-EGNITNISCPQLGC--EA 67
            P   C++C+  +SL     ++ C    CT+C+ +Y+   + EG  + I+CP + C    
Sbjct: 26  VPLVTCKLCLCEQSLDKMTTLQECRCIFCTACLKQYMQLAIREGCGSPITCPDMVCLNHG 85

Query: 68  RLEFEDCRLILPDDVFARWG-LALCESALVGHKKFYCPYKDCSSM----LIDEGEAIRKS 122
            L+  +   ++P D F  +  L       +   + +CP  DC ++      D G+ +   
Sbjct: 86  TLQEAEIACLVPVDQFQLYQRLKFEREVHLDPCRTWCPVADCQTVCPVATSDPGQPVL-V 144

Query: 123 NCPHCRRLFCVQCKVPWHSEFDCSQFQ 149
            CP C   FC  CK  WH+E  C   Q
Sbjct: 145 ECPSCHLKFCSCCKDAWHAEVSCRDSQ 171

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates such as LCMT2, thereby promoting their degradation. Induces apoptosis via a p53/TP53-dependent but caspase-independent mechanism. However, its overexpression also produces a decrease of the ubiquitin-dependent stability of BAX, a pro-apoptotic protein, ultimately leading to protection of cell death; But, it is not an anti-apoptotic protein per se.

Bos taurus (taxid: 9913)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q8BKD6|R144B_MOUSE E3 ubiquitin-protein ligase RNF144B OS=Mus musculus GN=Rnf144b PE=2 SV=2

 Score = 48.5 bits (114), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 39/147 (26%), Positives = 64/147 (43%), Gaps = 9/147 (6%)

Query: 11  TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKL-EGNITNISCPQLGC--EA 67
            P   C++C+  +SL     ++ C    CT C+ +Y+   + EG  + I+CP + C    
Sbjct: 25  APLVTCKLCLCEQSLDKMTMLQECQCIFCTPCLKQYMVLSIREGCGSPITCPDMVCLNHG 84

Query: 68  RLEFEDCRLILPDDVFARWG-LALCESALVGHKKFYCPYKDCSSM----LIDEGEAIRKS 122
            L+  +   ++P D F  +  L       +   + +CP  DC ++      D G+ +   
Sbjct: 85  TLQETEIACLVPLDEFQLYQRLKFEREVHMDPLRTWCPVADCQTVCHISAGDPGQPVL-V 143

Query: 123 NCPHCRRLFCVQCKVPWHSEFDCSQFQ 149
            CP C   FC  CK  WH E  C   Q
Sbjct: 144 ECPSCHLKFCSCCKDAWHEESSCRDSQ 170

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates such as LCMT2, thereby promoting their degradation. Induces apoptosis via a p53/TP53-dependent but caspase-independent mechanism. However, its overexpression also produces a decrease of the ubiquitin-dependent stability of BAX, a pro-apoptotic protein, ultimately leading to protection of cell death; But, it is not an anti-apoptotic protein per se.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q5RFV4|R1441_DANRE Probable E3 ubiquitin-protein ligase RNF144A-A OS=Danio rerio GN=rnf144aa PE=3 SV=1

 Score = 48.1 bits (113), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 36/143 (25%), Positives = 63/143 (44%), Gaps = 7/143 (4%)

Query: 12  PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKL-EGNITNISCPQLGCEAR-- 68
           P   C++C+    L     +  C    CT C+ +Y+   + EG  T ISCP   C  R  
Sbjct: 16  PLVSCKLCLGEFPLEQMTTITQCQCVFCTMCLKQYVELLIKEGFETAISCPDSACPKRGH 75

Query: 69  LEFEDCRLILPDDVFARW-GLALCESALVGHKKFYCPYKDCSSM-LIDEGEAI--RKSNC 124
           L+  +   ++  ++  R+  L   +  L+   + +CP   C ++  + E + +  +   C
Sbjct: 76  LQENEIECMVATEIMQRYRKLQFEKEVLLDPSRTWCPSSTCQAVCQLKESDTVLPQLVRC 135

Query: 125 PHCRRLFCVQCKVPWHSEFDCSQ 147
             C   FC  CK  WH + DC +
Sbjct: 136 SVCTLEFCSACKASWHPDQDCQE 158

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes ube2l3 and ube2l6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

Danio rerio (taxid: 7955)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|P50876|R144A_HUMAN Probable E3 ubiquitin-protein ligase RNF144A OS=Homo sapiens GN=RNF144A PE=1 SV=2

 Score = 46.2 bits (108), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 36/143 (25%), Positives = 60/143 (41%), Gaps = 7/143 (4%)

Query: 12  PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKL-EGNITNISCPQLGC--EAR 68
           P   C++C+    +     +  C    CT C+ +Y+   + EG  T ISCP   C  +  
Sbjct: 16  PLVSCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGH 75

Query: 69  LEFEDCRLILPDDVFARWG-LALCESALVGHKKFYCPYKDCSSM--LIDEG-EAIRKSNC 124
           L+  +   ++  ++  R+  L      L    + +CP   C ++  L D G +  +   C
Sbjct: 76  LQENEIECMVAAEIMQRYKKLQFEREVLFDPCRTWCPASTCQAVCQLQDVGLQTPQPVQC 135

Query: 125 PHCRRLFCVQCKVPWHSEFDCSQ 147
             CR  FC  CK  WH    C +
Sbjct: 136 KACRMEFCSTCKASWHPGQGCPE 158

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q1L8L6|RN19B_DANRE E3 ubiquitin-protein ligase RNF19B OS=Danio rerio GN=rnf19b PE=3 SV=2

 Score = 46.2 bits (108), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 39/147 (26%), Positives = 62/147 (42%), Gaps = 21/147 (14%)

Query: 16  CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR 75
           C +C+  +      +++GCSH +C  C+ +Y+  ++  +   +SCP+  C  RL      
Sbjct: 107 CPLCLVRQPAEQLPELQGCSHRSCLCCLRQYLRIEITESRVQLSCPE--CAERLAPWQVA 164

Query: 76  LILPD-DVFARWGLALCESALVGHKK-FYCPYKDCSSMLIDEGEAIRKSNCPHCRRL--- 130
           LIL D ++  ++   L    L       +CP  DC       G A+  S C  C RL   
Sbjct: 165 LILDDPNLMEKYEEFLLRRCLASDPDCRWCPAPDC-------GFAVIASGCASCPRLVCR 217

Query: 131 -------FCVQCKVPWHSEFDCSQFQK 150
                  FC  CK  WH    C   ++
Sbjct: 218 REGCGAEFCYHCKQAWHPNQTCDSARQ 244

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

Danio rerio (taxid: 7955)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	151
297738503	329	unnamed protein product [Vitis vinifera]	0.993	0.455	0.565	9e-46
225444595	358	PREDICTED: probable E3 ubiquitin-protein	0.993	0.418	0.565	1e-45
255550303	400	zinc finger protein, putative [Ricinus c	0.927	0.35	0.609	2e-45
224142755	307	predicted protein [Populus trichocarpa]	0.980	0.482	0.559	1e-44
255550305	264	zinc finger protein, putative [Ricinus c	0.953	0.545	0.579	7e-44
297820104	322	zinc finger family protein [Arabidopsis	0.940	0.440	0.538	7e-41
15231861	320	RING/U-box domain-containing protein [Ar	1.0	0.471	0.509	1e-39
356530471	333	PREDICTED: putative uncharacterized prot	0.940	0.426	0.541	1e-39
356558463	685	PREDICTED: uncharacterized protein LOC10	0.940	0.207	0.520	8e-38
326518170	445	predicted protein [Hordeum vulgare subsp	0.907	0.307	0.503	2e-33

>gi|297738503|emb|CBI27748.3| unnamed protein product [Vitis vinifera]

 Score =  187 bits (476), Expect = 9e-46,   Method: Compositional matrix adjust.
 Identities = 86/152 (56%), Positives = 113/152 (74%), Gaps = 2/152 (1%)

Query: 1   RSSNAETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISC 60
           + SN++ D   P+FVCEIC++ + L  SF +KGC H  C+ C+ +Y+ASKL+ N++ ISC
Sbjct: 111 QPSNSKPDP-PPTFVCEICIDPKPLNHSFSIKGCPHSYCSDCMTKYVASKLQDNVSRISC 169

Query: 61  PQLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLI-DEGEAI 119
           P   C   LE + CR ILP  VF RWG ALCE+ ++G +KFYCPYKDCS++LI DEGE I
Sbjct: 170 PAPNCTGVLEPQQCRPILPSHVFDRWGNALCEALILGSQKFYCPYKDCSALLIRDEGEVI 229

Query: 120 RKSNCPHCRRLFCVQCKVPWHSEFDCSQFQKL 151
           ++S CP+CRRLFC QC+VPWHS  DC +FQKL
Sbjct: 230 KESECPNCRRLFCAQCEVPWHSGIDCGEFQKL 261

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225444595|ref|XP_002277363.1| PREDICTED: probable E3 ubiquitin-protein ligase RNF144A-B-like [Vitis vinifera]

 Score =  187 bits (476), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 86/152 (56%), Positives = 113/152 (74%), Gaps = 2/152 (1%)

Query: 1   RSSNAETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISC 60
           + SN++ D   P+FVCEIC++ + L  SF +KGC H  C+ C+ +Y+ASKL+ N++ ISC
Sbjct: 111 QPSNSKPDP-PPTFVCEICIDPKPLNHSFSIKGCPHSYCSDCMTKYVASKLQDNVSRISC 169

Query: 61  PQLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLI-DEGEAI 119
           P   C   LE + CR ILP  VF RWG ALCE+ ++G +KFYCPYKDCS++LI DEGE I
Sbjct: 170 PAPNCTGVLEPQQCRPILPSHVFDRWGNALCEALILGSQKFYCPYKDCSALLIRDEGEVI 229

Query: 120 RKSNCPHCRRLFCVQCKVPWHSEFDCSQFQKL 151
           ++S CP+CRRLFC QC+VPWHS  DC +FQKL
Sbjct: 230 KESECPNCRRLFCAQCEVPWHSGIDCGEFQKL 261

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255550303|ref|XP_002516202.1| zinc finger protein, putative [Ricinus communis] gi|223544688|gb|EEF46204.1| zinc finger protein, putative [Ricinus communis]

 Score =  186 bits (472), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 86/141 (60%), Positives = 106/141 (75%), Gaps = 1/141 (0%)

Query: 12  PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF 71
           P FVCEICVES++  +S  ++GC+H  CT C+ +Y+ASK++ NIT I CP  GC   LE 
Sbjct: 203 PQFVCEICVESKTADESLAIRGCTHAYCTDCMAKYVASKIQENITGIYCPVSGCGGLLEP 262

Query: 72  EDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLI-DEGEAIRKSNCPHCRRL 130
           E CR ILP +VF RWG ALCE+  +G +KFYCP+KDCS+MLI D GE IR+S CPHCRRL
Sbjct: 263 EYCRSILPQEVFDRWGNALCEALNLGSQKFYCPFKDCSAMLINDGGEVIRESECPHCRRL 322

Query: 131 FCVQCKVPWHSEFDCSQFQKL 151
           FC  CKVPWHS  DC++FQ L
Sbjct: 323 FCAHCKVPWHSGIDCNKFQTL 343

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224142755|ref|XP_002324718.1| predicted protein [Populus trichocarpa] gi|222866152|gb|EEF03283.1| predicted protein [Populus trichocarpa]

 Score =  184 bits (467), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 85/152 (55%), Positives = 116/152 (76%), Gaps = 4/152 (2%)

Query: 1   RSSNAETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISC 60
           +SSN++ D   P FVC+ICVE   L +SF +KGC+H  CT C+V+Y++SKL+ NIT I C
Sbjct: 88  QSSNSQID---PDFVCQICVEPTILKNSFLIKGCTHAYCTECMVKYVSSKLQENITKICC 144

Query: 61  PQLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEG-EAI 119
           P   C+  LE EDCR +LP++VF RWG ALCE+ ++G +KFYCP+KDCS+MLID+G E +
Sbjct: 145 PVPDCKGALEPEDCRSVLPENVFDRWGNALCEAVILGSQKFYCPFKDCSAMLIDDGEEVV 204

Query: 120 RKSNCPHCRRLFCVQCKVPWHSEFDCSQFQKL 151
           R+S CP+C R+FC QCKVPWHS+  C +++ L
Sbjct: 205 RESECPNCWRMFCAQCKVPWHSQISCEEYKML 236

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255550305|ref|XP_002516203.1| zinc finger protein, putative [Ricinus communis] gi|223544689|gb|EEF46205.1| zinc finger protein, putative [Ricinus communis]

 Score =  181 bits (460), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 84/145 (57%), Positives = 107/145 (73%), Gaps = 1/145 (0%)

Query: 2   SSNAETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCP 61
           S     ++ +P+F+C+ICVE ++L DSF++KGC+HF C  C VRY+ SKL+ N+ +ISCP
Sbjct: 57  SDEEHQENNSPTFICDICVEEKALNDSFNLKGCTHFYCIDCTVRYVTSKLDDNLISISCP 116

Query: 62  QLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDE-GEAIR 120
              CE  LE E CR ILP DVF RWG+ALCES + G +KFYCP+KDCS +LID+ G  I 
Sbjct: 117 GSDCEGMLEPEYCRQILPQDVFDRWGIALCESLIDGSQKFYCPFKDCSGLLIDDTGMEIE 176

Query: 121 KSNCPHCRRLFCVQCKVPWHSEFDC 145
           KS CP C+R FCV+CKVPWHSE  C
Sbjct: 177 KSECPFCKRSFCVKCKVPWHSELSC 201

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297820104|ref|XP_002877935.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata] gi|297323773|gb|EFH54194.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  171 bits (434), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 77/143 (53%), Positives = 103/143 (72%), Gaps = 1/143 (0%)

Query: 10  GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARL 69
            T +F CEICVE++S+ ++F + GCSHF C  C+ +YIA+KL+ NI +I CP  GC  RL
Sbjct: 112 ATVTFDCEICVETKSIIETFRIGGCSHFYCNDCVSKYIAAKLQDNILSIECPVSGCSGRL 171

Query: 70  EFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSML-IDEGEAIRKSNCPHCR 128
           E + CR ILP +VF RWG ALCE+ ++  K+FYCPYKDCS++L +DE E ++ S CPHC 
Sbjct: 172 EPDQCRQILPREVFDRWGDALCEAVVMRSKRFYCPYKDCSALLFMDESEVMKDSECPHCH 231

Query: 129 RLFCVQCKVPWHSEFDCSQFQKL 151
           R+ CV+C   WH E  C +FQKL
Sbjct: 232 RMVCVECGTKWHPEMTCEEFQKL 254

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15231861|ref|NP_190937.1| RING/U-box domain-containing protein [Arabidopsis thaliana] gi|6729520|emb|CAB67676.1| putative protein [Arabidopsis thaliana] gi|21536688|gb|AAM61020.1| unknown [Arabidopsis thaliana] gi|332645607|gb|AEE79128.1| RING/U-box domain-containing protein [Arabidopsis thaliana]

 Score =  167 bits (424), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 78/153 (50%), Positives = 105/153 (68%), Gaps = 2/153 (1%)

Query: 1   RSSNAETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISC 60
           R     +   T +F CEICV+S+S+ +SF + GCSHF C  C+ +YIA+KL+ NI +I C
Sbjct: 100 REKGQSSSSKTATFDCEICVDSKSIIESFRIGGCSHFYCNDCVSKYIAAKLQDNILSIEC 159

Query: 61  PQLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSML-IDEGEA- 118
           P  GC  RLE + CR ILP +VF RWG ALCE+ ++  KKFYCPYKDCS+++ ++E E  
Sbjct: 160 PVSGCSGRLEPDQCRQILPKEVFDRWGDALCEAVVMRSKKFYCPYKDCSALVFLEESEVK 219

Query: 119 IRKSNCPHCRRLFCVQCKVPWHSEFDCSQFQKL 151
           ++ S CPHC R+ CV+C   WH E  C +FQKL
Sbjct: 220 MKDSECPHCHRMVCVECGTQWHPEMTCEEFQKL 252

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530471|ref|XP_003533804.1| PREDICTED: putative uncharacterized protein At4g01020, chloroplastic-like [Glycine max]

 Score =  167 bits (423), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 78/144 (54%), Positives = 96/144 (66%), Gaps = 2/144 (1%)

Query: 10  GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARL 69
            + SFVCEIC E+++  DSF + GC H  C SC+ +Y+ SKLE NI +I CP  GC   L
Sbjct: 122 NSASFVCEICTETKTARDSFSIIGCHHVYCNSCVAQYVESKLEENIVSIPCPVPGCRGLL 181

Query: 70  EFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLID--EGEAIRKSNCPHC 127
           E +DCR IL   VF RWG ALCE+ +   +KFYCP+ DCS MLI   E   IR++ CP+C
Sbjct: 182 EADDCREILAPRVFDRWGKALCEAVIAAEEKFYCPFADCSVMLIRGIEENNIREAECPNC 241

Query: 128 RRLFCVQCKVPWHSEFDCSQFQKL 151
           RRLFC QC+VPWH    C  FQKL
Sbjct: 242 RRLFCAQCRVPWHDNMPCEDFQKL 265

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356558463|ref|XP_003547526.1| PREDICTED: uncharacterized protein LOC100803898 [Glycine max]

 Score =  161 bits (408), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 75/144 (52%), Positives = 94/144 (65%), Gaps = 2/144 (1%)

Query: 10  GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARL 69
            T  F+CEIC E+++  DSF + GC H  C SC+ +Y+ SKLE N+ NI CP  GC   L
Sbjct: 122 STAPFLCEICTETKTDRDSFSITGCRHVYCNSCVAQYVESKLEDNVVNIPCPVPGCRGLL 181

Query: 70  EFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLI--DEGEAIRKSNCPHC 127
           E + CR IL   VF RWG ALCE+ +   +KFYCP+ DCS+MLI   E   IR+  CP+C
Sbjct: 182 EADYCREILSPRVFDRWGNALCEAVIDAEEKFYCPFADCSAMLIRASEDADIRECECPNC 241

Query: 128 RRLFCVQCKVPWHSEFDCSQFQKL 151
           RRLFC  C+VPWH    C +FQKL
Sbjct: 242 RRLFCALCRVPWHENIPCEEFQKL 265

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|326518170|dbj|BAK07337.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 72/143 (50%), Positives = 96/143 (67%), Gaps = 6/143 (4%)

Query: 14  FVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGC-EARLEFE 72
           F C IC+E     + F V GC+H  C SC+ +YIA+K+E N+  I CP  GC +  L+ E
Sbjct: 234 FYCTICMEEVPAIECFPVDGCTHAFCVSCVRQYIAAKVEENVVPIRCPDPGCKDGMLQPE 293

Query: 73  DCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLID---EGEA-IRKSNCPHCR 128
            CR ++P  +F RWG ALC+ AL G  KFYCP+KDCS++L+D   +G+A I    CPHC 
Sbjct: 294 ACRDVIPTPLFQRWGAALCDMALEG-LKFYCPFKDCSALLVDDHQDGDAVITDVECPHCS 352

Query: 129 RLFCVQCKVPWHSEFDCSQFQKL 151
           R+FC QCKVPWH   DC++FQ+L
Sbjct: 353 RMFCAQCKVPWHGGVDCAEFQRL 375

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

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	151
TAIR|locus:2084116	320	AT3G53690 [Arabidopsis thalian	1.0	0.471	0.509	8.1e-44
TAIR|locus:2091030	303	AT3G14250 [Arabidopsis thalian	0.966	0.481	0.430	5.2e-33
TAIR|locus:2085622	222	AT3G45470 [Arabidopsis thalian	0.887	0.603	0.347	4e-19
TAIR|locus:2151689	444	AT5G37560 [Arabidopsis thalian	0.887	0.301	0.323	4.5e-19
TAIR|locus:1006230127	384	AT2G26135 [Arabidopsis thalian	0.913	0.359	0.317	2.5e-18
TAIR|locus:2040065	373	AT2G25360 [Arabidopsis thalian	0.933	0.378	0.3	2.8e-18
TAIR|locus:2133935	532	AT4G19670 [Arabidopsis thalian	0.953	0.270	0.331	7.2e-18
TAIR|locus:2085657	312	AT3G45570 [Arabidopsis thalian	0.887	0.429	0.298	1.3e-16
TAIR|locus:2143995	655	AT5G60250 [Arabidopsis thalian	0.894	0.206	0.324	1.3e-16
TAIR|locus:2050100	468	AT2G21420 [Arabidopsis thalian	0.887	0.286	0.338	1.8e-16

TAIR|locus:2084116 AT3G53690 [Arabidopsis thaliana (taxid:3702)]

 Score = 462 (167.7 bits), Expect = 8.1e-44, P = 8.1e-44
 Identities = 78/153 (50%), Positives = 105/153 (68%)

Query:     1 RSSNAETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISC 60
             R     +   T +F CEICV+S+S+ +SF + GCSHF C  C+ +YIA+KL+ NI +I C
Sbjct:   100 REKGQSSSSKTATFDCEICVDSKSIIESFRIGGCSHFYCNDCVSKYIAAKLQDNILSIEC 159

Query:    61 PQLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSML-IDEGEA- 118
             P  GC  RLE + CR ILP +VF RWG ALCE+ ++  KKFYCPYKDCS+++ ++E E  
Sbjct:   160 PVSGCSGRLEPDQCRQILPKEVFDRWGDALCEAVVMRSKKFYCPYKDCSALVFLEESEVK 219

Query:   119 IRKSNCPHCRRLFCVQCKVPWHSEFDCSQFQKL 151
             ++ S CPHC R+ CV+C   WH E  C +FQKL
Sbjct:   220 MKDSECPHCHRMVCVECGTQWHPEMTCEEFQKL 252

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2091030 AT3G14250 [Arabidopsis thaliana (taxid:3702)]

 Score = 360 (131.8 bits), Expect = 5.2e-33, P = 5.2e-33
 Identities = 65/151 (43%), Positives = 93/151 (61%)

Query:     5 AETDDGTPSF-VCEICVESRSLYDSF-DVKGCSHFNCTSCIVRYIASKLEGNITNISCPQ 62
             AE +   PS  +C IC++ +   D F     C+H  CT C VRY+A+K++ N + I CP 
Sbjct:    83 AENEPMEPSRRLCMICMDEKPSSDIFRGTTNCTHAYCTDCTVRYVATKIKENASRIKCPD 142

Query:    63 LGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLI--DEGEA-I 119
             + C   +E   CR ++P DVF RW   LCES +    KFYCP+KDCS+M++  + G+A +
Sbjct:   143 VECTRLIEPYTCRDLIPKDVFDRWEKILCESLISSWDKFYCPFKDCSAMMVNNENGDANV 202

Query:   120 RKSNCPHCRRLFCVQCKVPWHSEFDCSQFQK 150
              ++ C  C RLFCVQCKV WH+   C +FQ+
Sbjct:   203 TQTECRSCHRLFCVQCKVTWHAGIGCDEFQR 233

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2085622 AT3G45470 [Arabidopsis thaliana (taxid:3702)]

 Score = 229 (85.7 bits), Expect = 4.0e-19, P = 4.0e-19
 Identities = 49/141 (34%), Positives = 74/141 (52%)

Query:    16 CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR 75
             C IC+E       F +  C H +C  C+ + +  KL  N T  +C    C+ +L  E+C 
Sbjct:     6 CVICLEETKADRMFVMDKCLHRHCYPCVNQLVEVKLR-NGTVPTCLDYECKLKLSLENCF 64

Query:    76 LILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEGEAIR--KSN---CPHCRRL 130
              +L   V   W   + E ++   K+ YCPY +CS+ L+ + E  R  KSN   C  C  L
Sbjct:    65 KVLKPKVIELWKHMMKEESIPLAKRIYCPYINCST-LMSKTEISRSNKSNDRACIKCSGL 123

Query:   131 FCVQCKVPWHSEFDCSQFQKL 151
              C+ CKVPWHS+  C++++KL
Sbjct:   124 VCIDCKVPWHSDLSCAEYKKL 144

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2151689 AT5G37560 [Arabidopsis thaliana (taxid:3702)]

 Score = 234 (87.4 bits), Expect = 4.5e-19, P = 4.5e-19
 Identities = 46/142 (32%), Positives = 71/142 (50%)

Query:    16 CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR 75
             C IC +            C H +C SC+ + +  KL   I    C + GC++ L  E C 
Sbjct:   181 CSICSDKTDAEHMLLNDKCLHRHCFSCVKQQVKVKLRSGIVP-PCLEDGCKSELTLESCS 239

Query:    76 LILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEGEAIRK---SN---CPHCRR 129
             ++L   +   W   + E  +   +K YCPY+ CS ML+ + E  R+   SN   C  C  
Sbjct:   240 MVLTPKLIEMWKRKMEEDLIPDAEKIYCPYRSCS-MLMSKTELSREAEQSNVRACIKCSE 298

Query:   130 LFCVQCKVPWHSEFDCSQFQKL 151
             LFC+ CKVPWHS+  C+ ++++
Sbjct:   299 LFCIDCKVPWHSDLSCADYKRI 320

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:1006230127 AT2G26135 [Arabidopsis thaliana (taxid:3702)]

 Score = 225 (84.3 bits), Expect = 2.5e-18, P = 2.5e-18
 Identities = 46/145 (31%), Positives = 74/145 (51%)

Query:    12 PSFVCEICVESRSLYDS-FDVKGCSHFNCTSCIVRYI-ASKLEGNITNISCPQLGCEARL 69
             P   C IC +     D  F +  C H  C+ C+ R+I  S L+G++  I+CP   C+++L
Sbjct:   149 PKKTCTICFDDDINADMMFYIDQCGHMFCSECVKRHIEVSLLQGSL--ITCPSYRCKSKL 206

Query:    70 EFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSML-IDEGEAIRKSN--CPH 126
              +  C  IL   V   W   + E ++    + YCP   CS+++ + E + +  S   C  
Sbjct:   207 TYGSCVNILTPKVKEMWIQRMGEDSIPVTDRVYCPNPTCSALMSVTELDQLTGSKRCCVK 266

Query:   127 CRRLFCVQCKVPWHSEFDCSQFQKL 151
             C   FC++CKVPWH    C +++KL
Sbjct:   267 CGESFCIKCKVPWHDNLSCKRYKKL 291

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016020 "membrane" evidence=ISS

TAIR|locus:2040065 AT2G25360 [Arabidopsis thaliana (taxid:3702)]

 Score = 224 (83.9 bits), Expect = 2.8e-18, P = 2.8e-18
 Identities = 45/150 (30%), Positives = 75/150 (50%)

Query:     9 DGTPSFVCEICVE-SRSLYDSFDVKGCSHFNCTSCIVRYIASKL-EGNITNISCPQLGCE 66
             D   + +C IC E +      F  + C H +C  C+ +Y+  KL  G +   +C   GC+
Sbjct:    83 DDVKAEICSICFEETEGERMFFTTEKCVHRHCFPCVKQYVEVKLLSGTVP--TCLDDGCK 140

Query:    67 ARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSM-----LIDEGEAIRK 121
              +L  E C  +L  ++   W   + E ++   ++ YCPY +CS +     L  E +    
Sbjct:   141 FKLTLESCSKVLTLELIEMWKQKMKEDSIPAAERIYCPYPNCSMLMSKTELSSESDLSND 200

Query:   122 SNCPHCRRLFCVQCKVPWHSEFDCSQFQKL 151
              +C  C  LFC+ CKVP HS+  C++++KL
Sbjct:   201 RSCVKCCGLFCIDCKVPSHSDLSCAEYKKL 230

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2133935 AT4G19670 [Arabidopsis thaliana (taxid:3702)]

 Score = 225 (84.3 bits), Expect = 7.2e-18, P = 7.2e-18
 Identities = 55/166 (33%), Positives = 77/166 (46%)

Query:     2 SSNAETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCP 61
             SSN + D   P   C IC E R       +K C+H  C+ C+  Y+  K++ +   I CP
Sbjct:   195 SSNLDGDK--PIENCSICCEDRQSEMMLSLK-CTHKFCSHCMKTYVEGKVKTSEVPIRCP 251

Query:    62 QLGCEARLEFEDCRLILPDDVFARWGLA-LCESALVGHKKFYCPYKDCSSML-----IDE 115
             Q+ C+  L   +C+  LP   F  +  A +C      + K YCPY +CS +L     +  
Sbjct:   252 QVQCKHYLSAAECKSFLPVTTFKSFEEANVCSK---NNGKIYCPYPNCSFLLDPQECLSS 308

Query:   116 GEAIRKSN----------CPHCRRLFCVQCKVPWHSEFDCSQFQKL 151
             G A   S+          CP C R  CV C VPWH+   C +FQ L
Sbjct:   309 GRASSSSSTQSENSCCVECPVCERFVCVDCGVPWHASMSCEEFQIL 354

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2085657 AT3G45570 [Arabidopsis thaliana (taxid:3702)]

 Score = 189 (71.6 bits), Expect = 1.3e-16, Sum P(2) = 1.3e-16
 Identities = 43/144 (29%), Positives = 64/144 (44%)

Query:    16 CEICV-ESRSLYDSFDVKGCSHFNCTSCIVRYIASKL-EGNITNISCPQLGCEARLEFED 73
             C IC  ++      F V  C H  C  C+ ++I  KL  G +    C    CE+ L    
Sbjct:   163 CSICSGDNIEPEQIFSVALCGHEFCMECVKQHIEVKLLSGGVPR--CLHYQCESNLTLGS 220

Query:    74 CRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLI------DEGEAIRKSNCPHC 127
             C  IL   + A W L + E ++   ++ YCP   CSS++          E +    C  C
Sbjct:   221 CGNILTSKLKAMWELRIEEESIPVAERVYCPNPLCSSLMSVTKLSNSTREDVTMRTCVKC 280

Query:   128 RRLFCVQCKVPWHSEFDCSQFQKL 151
                FC+ CK+PWHS   C+ ++ L
Sbjct:   281 GEPFCINCKLPWHSNLSCNDYKSL 304

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2143995 AT5G60250 [Arabidopsis thaliana (taxid:3702)]

 Score = 215 (80.7 bits), Expect = 1.3e-16, P = 1.3e-16
 Identities = 48/148 (32%), Positives = 69/148 (46%)

Query:    16 CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR 75
             C IC         F V  C H  C  C+ +++  KL   +    CP  GC++ L  + C 
Sbjct:   301 CAICFNDIVAEGMFSVDKCRHRFCFQCVKQHVEVKLLHGMAP-KCPHDGCKSELVIDACG 359

Query:    76 LILPDDVFARWGLALCESALVGHKKFYCPYKDCSSML----IDEG-----EAIRKSN--- 123
              +L   +   W   L E+A+   ++ YCPY  CS+++    I E          KS    
Sbjct:   360 KLLTPKLSKLWQQRLQENAIPVTERVYCPYPRCSALMSKTKISESAKSLLSLYPKSGVRR 419

Query:   124 CPHCRRLFCVQCKVPWHSEFDCSQFQKL 151
             C  CR LFCV CKVPWH    C++++KL
Sbjct:   420 CVECRGLFCVDCKVPWHGNLSCTEYKKL 447

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2050100 AT2G21420 [Arabidopsis thaliana (taxid:3702)]

 Score = 211 (79.3 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 48/142 (33%), Positives = 69/142 (48%)

Query:    16 CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR 75
             C IC E+      F  + C H  C SC+ R++   L   I+  +C    C + L FE C 
Sbjct:   187 CCICRENTDADRMFFTENCFHRQCFSCVNRHVQRMLLCGISP-TCLHFPCNSELTFESCS 245

Query:    76 LILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEGEAIRK---SN---CPHCRR 129
              +L  ++   W   + E  +    K YCPY+ CS ML+ +    R+   SN   C  C R
Sbjct:   246 KVLTPNLIEFWKRKIEEDLVPAADKIYCPYRRCS-MLMSKTALSRETDQSNVRACIKCCR 304

Query:   130 LFCVQCKVPWHSEFDCSQFQKL 151
             LFC+ CKVP H+   C  ++KL
Sbjct:   305 LFCIDCKVPSHAGLSCVDYKKL 326

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	151
smart00647	64	smart00647, IBR, In Between Ring fingers	1e-08
pfam01485	63	pfam01485, IBR, IBR domain	7e-06

>gnl|CDD|214763 smart00647, IBR, In Between Ring fingers

 Score = 48.6 bits (116), Expect = 1e-08
 Identities = 23/64 (35%), Positives = 32/64 (50%), Gaps = 2/64 (3%)

Query: 84  ARWGLALCESALVGHKKF-YCPYKDCSSMLIDEGEAI-RKSNCPHCRRLFCVQCKVPWHS 141
            ++   L ES +  +    +CP  DCS+ +I   E    +  CP C   FC +CKVPWHS
Sbjct: 1   EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHS 60

Query: 142 EFDC 145
              C
Sbjct: 61  PVSC 64

the domains occurs between pairs og RING fingers. Length = 64

>gnl|CDD|216524 pfam01485, IBR, IBR domain

 Score = 41.0 bits (96), Expect = 7e-06
 Identities = 14/44 (31%), Positives = 19/44 (43%)

Query: 102 YCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPWHSEFDC 145
           +CP  DC +++       +   C  C   FC  CK PWH    C
Sbjct: 20  WCPTPDCGNIIEKTDGGSQNVTCSKCGTEFCFSCKEPWHEGLTC 63

The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (pfam00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain. Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organisms. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. The ubiquitin ligase Parkin is an RBR family protein whose mutations are involved in forms of familial Parkinson's disease. Length = 63

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	151
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	99.93
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	99.92
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	99.82
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	99.67
smart00647	64	IBR In Between Ring fingers. the domains occurs be	99.57
PF01485	64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	99.51
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.9
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.88
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.85
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	98.82
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.8
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.79
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	98.71
PF14634	44	zf-RING_5: zinc-RING finger domain	98.68
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.55
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.42
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.28
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.24
PHA02929	238	N1R/p28-like protein; Provisional	98.23
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.22
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.2
PHA02926	242	zinc finger-like protein; Provisional	98.16
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.13
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.11
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.11
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	97.98
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	97.88
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.82
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.71
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	97.63
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	97.43
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.38
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	97.31
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	97.28
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	97.27
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	97.26
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.25
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.21
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	97.18
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	96.97
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	96.92
KOG2660	331	consensus Locus-specific chromosome binding protei	96.73
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	96.1
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	96.06
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	96.02
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	95.87
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	95.62
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	95.58
COG5152	259	Uncharacterized conserved protein, contains RING a	95.43
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	95.42
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	95.4
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	95.39
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	95.28
KOG4445	368	consensus Uncharacterized conserved protein, conta	95.2
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	95.12
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	95.05
KOG4739	233	consensus Uncharacterized protein involved in syna	94.97
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	94.96
PF04641	260	Rtf2: Rtf2 RING-finger	94.95
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	94.94
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	94.93
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	94.92
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	94.39
KOG0297	391	consensus TNF receptor-associated factor [Signal t	94.35
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	94.21
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	94.11
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	94.07
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	93.7
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	93.67
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	93.29
KOG3002	299	consensus Zn finger protein [General function pred	93.27
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	93.08
KOG3039	303	consensus Uncharacterized conserved protein [Funct	92.87
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	92.67
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	92.59
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	92.24
smart00661	52	RPOL9 RNA polymerase subunit 9.	92.0
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	91.88
COG5222	427	Uncharacterized conserved protein, contains RING Z	91.49
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	91.47
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	90.92
COG5175	480	MOT2 Transcriptional repressor [Transcription]	90.82
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	90.71
PHA03096	284	p28-like protein; Provisional	90.43
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	90.01
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	89.76
PF12773	50	DZR: Double zinc ribbon	89.55
KOG1001	674	consensus Helicase-like transcription factor HLTF/	88.1
KOG3579	352	consensus Predicted E3 ubiquitin ligase [Posttrans	87.82
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	87.47
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	87.25
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	87.17
PF14353	128	CpXC: CpXC protein	87.03
PRK06266	178	transcription initiation factor E subunit alpha; V	86.82
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	86.56
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	86.45
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	86.28
smart00531	147	TFIIE Transcription initiation factor IIE.	86.19
COG5236	493	Uncharacterized conserved protein, contains RING Z	86.14
PF13248	26	zf-ribbon_3: zinc-ribbon domain	85.58
COG5109	396	Uncharacterized conserved protein, contains RING Z	85.28
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	85.22
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	84.79
PF14369	35	zf-RING_3: zinc-finger	83.91
KOG2807	378	consensus RNA polymerase II transcription initiati	83.13
KOG2906	105	consensus RNA polymerase III subunit C11 [Transcri	83.12
cd00021	39	BBOX B-Box-type zinc finger; zinc binding domain (	81.79
COG5151	421	SSL1 RNA polymerase II transcription initiation/nu	81.65
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	81.58
PF06844	68	DUF1244: Protein of unknown function (DUF1244); In	80.89
KOG1940	276	consensus Zn-finger protein [General function pred	80.86
KOG0825	1134	consensus PHD Zn-finger protein [General function	80.78
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	80.62
TIGR00622	112	ssl1 transcription factor ssl1. This family is bas	80.34
PLN00209	86	ribosomal protein S27; Provisional	80.2

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

Probab=99.93  E-value=3.9e-26  Score=173.51  Aligned_cols=140  Identities=36%  Similarity=0.808  Sum_probs=122.7

Q ss_pred             CCeeecccccccCC-CCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcCCHHHHHHHHHH
Q 043988           11 TPSFVCEICVESRS-LYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARWGLA   89 (151)
Q Consensus        11 ~~~~~C~iC~~~~~-~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~~   89 (151)
                      .+..+|.||+.+.+ ..+++....|+|.||.+|+++|+..+ ......+.||..+|...++.+....+|++.+.+.|+..
T Consensus       144 ~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~-~~~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~  222 (384)
T KOG1812|consen  144 LPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK-LLSGTVIRCPHDGCESRLTLESCRKLLTPKLREMWEQR  222 (384)
T ss_pred             cccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh-hccCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHHHH
Confidence            45779999995444 44677777899999999999999999 44455799999999999999999999999999999999


Q ss_pred             HHhhhhcCCCeeecCcccCCccccccc----cccCcccCcccchhhhhcCCCCCCCCCCchhhhhC
Q 043988           90 LCESALVGHKKFYCPYKDCSSMLIDEG----EAIRKSNCPHCRRLFCVQCKVPWHSEFDCSQFQKL  151 (151)
Q Consensus        90 ~~~~~~~~~~~~~Cp~~~C~~~~~~~~----~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~  151 (151)
                      +.+.++...+.+|||+|+|...+....    .......|+.|+..||..|+.+||.+++|++|++|
T Consensus       223 ~~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~  288 (384)
T KOG1812|consen  223 LKEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKL  288 (384)
T ss_pred             HHHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHh
Confidence            999998887777999999998887663    44566789999999999999999999999999997

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

Probab=99.92  E-value=1.4e-25  Score=166.53  Aligned_cols=136  Identities=25%  Similarity=0.575  Sum_probs=122.6

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCc-cccCCCCCCCCCccChhHHhhcCCHHHHHHHHHH
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNI-TNISCPQLGCEARLEFEDCRLILPDDVFARWGLA   89 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~-~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~~   89 (151)
                      ...+.|.|||++..+..-+.+++|+|.||++|++.|+...|++|. ..++||.++|++..+...++.+|+.++++||+.+
T Consensus       182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~l  261 (445)
T KOG1814|consen  182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARYEKL  261 (445)
T ss_pred             hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHHHHH
Confidence            456899999999988777788899999999999999999999874 5799999999999999999999999999999999


Q ss_pred             HHhhhhcC-CCeeecCcccCCccccccccccCcccCcccchhhhhcCCCCCCCCCCchh
Q 043988           90 LCESALVG-HKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPWHSEFDCSQ  147 (151)
Q Consensus        90 ~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~  147 (151)
                      ++++.+.. .+.+|||++.|+.++-. +.+...+.|.+|+..||..|+..||++..|.-
T Consensus       262 ~lqk~l~~msdv~yCPr~~Cq~p~~~-d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~  319 (445)
T KOG1814|consen  262 MLQKTLELMSDVVYCPRACCQLPVKQ-DPGRALAICSKCNFAFCTLCKLTWHGVSPCKV  319 (445)
T ss_pred             HHHHHHHhhcccccCChhhccCcccc-CchhhhhhhccCccHHHHHHHHhhcCCCcccC
Confidence            99988886 67789999999999844 45677899999999999999999999988863

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

Probab=99.82  E-value=1.2e-20  Score=146.75  Aligned_cols=138  Identities=24%  Similarity=0.491  Sum_probs=119.3

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCcc-ccCCCCCCCCCccChhHHhhcCCH-HHHHHHHH
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNIT-NISCPQLGCEARLEFEDCRLILPD-DVFARWGL   88 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~-~i~CP~~~C~~~~~~~~i~~~l~~-~~~~~~~~   88 (151)
                      ....+|.||++..+. .++ .+.|+|.||..|+..|+..+|.++.. .|+||..+|...+....|..++++ ++.++|.+
T Consensus        68 ~~~~~c~ic~~~~~~-~~~-~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~  145 (444)
T KOG1815|consen   68 KGDVQCGICVESYDG-EII-GLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQR  145 (444)
T ss_pred             CccccCCcccCCCcc-hhh-hcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHHH
Confidence            345899999998866 444 45899999999999999999987532 399999999999999999999988 49999999


Q ss_pred             HHHhhhhcCC-CeeecCcccCCccccccccccCcccCcccchhhhhcCCCCCCCCCCchhhhhC
Q 043988           89 ALCESALVGH-KKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPWHSEFDCSQFQKL  151 (151)
Q Consensus        89 ~~~~~~~~~~-~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~  151 (151)
                      .+.++++... ...|||+|+|+..+.........+.| .|++.||+.|+.+||.|.+|..+.+|
T Consensus       146 ~i~~syve~~~~lkwCP~~~C~~av~~~~~~~~~v~C-~~g~~FC~~C~~~~H~p~~C~~~~~w  208 (444)
T KOG1815|consen  146 YILRSYVEDNVPLKWCPAPGCGLAVKFGSLESVEVDC-GCGHEFCFACGEESHSPVSCPGAKKW  208 (444)
T ss_pred             HHHHHHHhcCCccccCCCCCCCceeeccCCCccceeC-CCCchhHhhccccccCCCcccchHHH
Confidence            9999999875 45699999999988864445788999 58889999999999999999999887

>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]

Probab=99.67  E-value=1.1e-16  Score=116.06  Aligned_cols=133  Identities=26%  Similarity=0.570  Sum_probs=110.7

Q ss_pred             CCCCCeeecccccccCCCCCceecCCCC--CccchHHHHHHHHHHHhCC--------ccccCCCCCCCCCccChhHH-hh
Q 043988            8 DDGTPSFVCEICVESRSLYDSFDVKGCS--HFNCTSCIVRYIASKLEGN--------ITNISCPQLGCEARLEFEDC-RL   76 (151)
Q Consensus         8 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~--------~~~i~CP~~~C~~~~~~~~i-~~   76 (151)
                      ..+.++.+|..|.+..   +.+...+|.  |..|.+|++.|..+.+.+.        .+.+.||. +|...+-.+.. -.
T Consensus       216 ~~N~~ni~C~~Ctdv~---~~vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~  291 (446)
T KOG0006|consen  216 ATNSRNITCITCTDVR---SPVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFR  291 (446)
T ss_pred             hcccccceeEEecCCc---cceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhhe
Confidence            3567889999997543   445555787  9999999999999998653        24688987 88876654443 67


Q ss_pred             cCCHHHHHHHHHHHHhhhhcCCCeeecCcccCCccccccccccCcccCcc-cchhhhhcCCCCCCCCCCch
Q 043988           77 ILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEGEAIRKSNCPH-CRRLFCVQCKVPWHSEFDCS  146 (151)
Q Consensus        77 ~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~C~~-C~~~~C~~C~~~~H~~~~C~  146 (151)
                      ||+.+.|.+|+++..+..+.....+.||+|+|+..+..+. +.++++|+. |++.||+.|++.+|.| .|.
T Consensus       292 ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EP-D~rkvtC~~gCgf~FCR~C~e~yh~g-eC~  360 (446)
T KOG0006|consen  292 ILGEEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEP-DQRKVTCEGGCGFAFCRECKEAYHEG-ECS  360 (446)
T ss_pred             ecchhHHHHHHHhhhhhheeecCCEecCCCCCCcccccCC-CCCcccCCCCchhHhHHHHHhhhccc-cce
Confidence            8999999999999999999888899999999999888865 689999986 9999999999999987 554

>smart00647 IBR In Between Ring fingers

Probab=99.57  E-value=1.7e-15  Score=87.80  Aligned_cols=62  Identities=37%  Similarity=0.835  Sum_probs=54.7

Q ss_pred             HHHHHHHHhhhhcC-CCeeecCcccCCcccccc-ccccCcccCcccchhhhhcCCCCCCCCCCc
Q 043988           84 ARWGLALCESALVG-HKKFYCPYKDCSSMLIDE-GEAIRKSNCPHCRRLFCVQCKVPWHSEFDC  145 (151)
Q Consensus        84 ~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~-~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C  145 (151)
                      ++|++++.+.++.. .+.+|||+++|+.++... +.....+.|+.|+..||+.|+.+||.|++|
T Consensus         1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~~C   64 (64)
T smart00647        1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPVSC   64 (64)
T ss_pred             ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence            47889999998887 466799999999999887 346788999999999999999999999987

the domains occurs between pairs og RING fingers

>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.51  E-value=1.9e-15  Score=87.48  Aligned_cols=62  Identities=26%  Similarity=0.702  Sum_probs=42.1

Q ss_pred             HHHHHHHHhhhhcCC-CeeecCcccCCccccccccccC-cccCcccchhhhhcCCCCCCCCCCc
Q 043988           84 ARWGLALCESALVGH-KKFYCPYKDCSSMLIDEGEAIR-KSNCPHCRRLFCVQCKVPWHSEFDC  145 (151)
Q Consensus        84 ~~~~~~~~~~~~~~~-~~~~Cp~~~C~~~~~~~~~~~~-~~~C~~C~~~~C~~C~~~~H~~~~C  145 (151)
                      ++|++++++.++..+ +.+|||+++|+.++..+..... .+.|+.|++.||+.|+.+||.|.+|
T Consensus         1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~~C   64 (64)
T PF01485_consen    1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGVTC   64 (64)
T ss_dssp             HCHHHCCCHS---S---CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred             ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCCCC
Confidence            578888888888654 4579999999999998855333 3999999999999999999999987

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 a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.

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

Probab=98.90  E-value=4.5e-10  Score=59.28  Aligned_cols=40  Identities=33%  Similarity=0.726  Sum_probs=27.2

Q ss_pred             cccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCC
Q 043988           16 CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCP   61 (151)
Q Consensus        16 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP   61 (151)
                      |+||++.+  .+++++ +|||.||.+|+..+++..-   ...+.||
T Consensus         1 CpiC~~~~--~~Pv~l-~CGH~FC~~Cl~~~~~~~~---~~~~~CP   40 (42)
T PF15227_consen    1 CPICLDLF--KDPVSL-PCGHSFCRSCLERLWKEPS---GSGFSCP   40 (42)
T ss_dssp             ETTTTSB---SSEEE--SSSSEEEHHHHHHHHCCSS---SST---S
T ss_pred             CCccchhh--CCcccc-CCcCHHHHHHHHHHHHccC---CcCCCCc
Confidence            89999877  566665 8999999999999876532   1227888

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

Probab=98.88  E-value=1.6e-09  Score=73.12  Aligned_cols=57  Identities=23%  Similarity=0.609  Sum_probs=44.7

Q ss_pred             CCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHh
Q 043988            9 DGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR   75 (151)
Q Consensus         9 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~   75 (151)
                      ..+..+.||||++++....++.. .|||.||..|++.-++..       -+||  -|...|+..++-
T Consensus       127 ~~~~~~~CPiCl~~~sek~~vsT-kCGHvFC~~Cik~alk~~-------~~CP--~C~kkIt~k~~~  183 (187)
T KOG0320|consen  127 RKEGTYKCPICLDSVSEKVPVST-KCGHVFCSQCIKDALKNT-------NKCP--TCRKKITHKQFH  183 (187)
T ss_pred             ccccccCCCceecchhhcccccc-ccchhHHHHHHHHHHHhC-------CCCC--Ccccccchhhhe
Confidence            34566899999999876666654 899999999999877664       5899  577778777653

>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=98.85  E-value=3.8e-09  Score=55.47  Aligned_cols=39  Identities=26%  Similarity=0.744  Sum_probs=31.0

Q ss_pred             cccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCC
Q 043988           16 CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCP   61 (151)
Q Consensus        16 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP   61 (151)
                      |+||++.+..  ...+++|||.||..|+..+++.     ...++||
T Consensus         1 C~iC~~~~~~--~~~~~~C~H~fC~~C~~~~~~~-----~~~~~CP   39 (41)
T PF00097_consen    1 CPICLEPFED--PVILLPCGHSFCRDCLRKWLEN-----SGSVKCP   39 (41)
T ss_dssp             ETTTSSBCSS--EEEETTTSEEEEHHHHHHHHHH-----TSSSBTT
T ss_pred             CCcCCccccC--CCEEecCCCcchHHHHHHHHHh-----cCCccCC
Confidence            7999987743  4446699999999999999987     2246788

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 ....

>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=98.82  E-value=1.1e-09  Score=58.52  Aligned_cols=41  Identities=29%  Similarity=0.551  Sum_probs=32.5

Q ss_pred             ecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCC
Q 043988           15 VCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQ   62 (151)
Q Consensus        15 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   62 (151)
                      +|+||++++...+.+..++|+|.|+.+|+..|++..       .+||.
T Consensus         2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~-------~~CP~   42 (44)
T PF13639_consen    2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN-------NSCPV   42 (44)
T ss_dssp             CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS-------SB-TT
T ss_pred             CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC-------CcCCc
Confidence            699999999765555556899999999999999773       38883

...

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

Probab=98.80  E-value=4.6e-09  Score=55.47  Aligned_cols=42  Identities=29%  Similarity=0.576  Sum_probs=23.0

Q ss_pred             cccccccCC-CCCceecCCCCCccchHHHHHHHHHHHhCCccccCCC
Q 043988           16 CEICVESRS-LYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCP   61 (151)
Q Consensus        16 C~iC~~~~~-~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP   61 (151)
                      |+||.+ +. ......++.|||+||++|+.++++...   ...|+||
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~---~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSD---RNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S----S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCC---CCeeeCc
Confidence            899998 53 344555668999999999999988543   2357887

>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=98.79  E-value=3.1e-09  Score=55.24  Aligned_cols=38  Identities=34%  Similarity=0.860  Sum_probs=28.8

Q ss_pred             cccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCC
Q 043988           16 CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQ   62 (151)
Q Consensus        16 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   62 (151)
                      |+||++..  .+++.++.|||.||.+|+.+|++..       .+||.
T Consensus         1 C~iC~~~~--~~~~~~~~CGH~fC~~C~~~~~~~~-------~~CP~   38 (39)
T PF13923_consen    1 CPICLDEL--RDPVVVTPCGHSFCKECIEKYLEKN-------PKCPV   38 (39)
T ss_dssp             ETTTTSB---SSEEEECTTSEEEEHHHHHHHHHCT-------SB-TT
T ss_pred             CCCCCCcc--cCcCEECCCCCchhHHHHHHHHHCc-------CCCcC
Confidence            89999877  4465667999999999999997662       57773

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=98.71  E-value=1.8e-08  Score=69.60  Aligned_cols=65  Identities=22%  Similarity=0.451  Sum_probs=48.4

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHh---------CCccccCCCCCCCCCccChhHHhhcCCH
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLE---------GNITNISCPQLGCEARLEFEDCRLILPD   80 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~---------~~~~~i~CP~~~C~~~~~~~~i~~~l~~   80 (151)
                      ...++|+||++..  .+++. ..|||.||..|+..|+...-.         .......||  -|+..++...+..+.+.
T Consensus        16 ~~~~~CpICld~~--~dPVv-T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CP--vCR~~Is~~~LvPiygr   89 (193)
T PLN03208         16 GGDFDCNICLDQV--RDPVV-TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCP--VCKSDVSEATLVPIYGR   89 (193)
T ss_pred             CCccCCccCCCcC--CCcEE-cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCC--CCCCcCChhcEEEeecc
Confidence            4568999999876  45554 489999999999999864321         122357999  69999998888766553

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.68  E-value=1.9e-08  Score=53.66  Aligned_cols=41  Identities=27%  Similarity=0.648  Sum_probs=33.2

Q ss_pred             ecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCC
Q 043988           15 VCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQ   62 (151)
Q Consensus        15 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   62 (151)
                      .|++|++.+...+.+.+++|||.||..|+....       ...+.||.
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-------~~~~~CP~   41 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-------GKSVKCPI   41 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-------CCCCCCcC
Confidence            489999999655567777999999999999876       23578984

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

Probab=98.55  E-value=1e-07  Score=50.43  Aligned_cols=44  Identities=32%  Similarity=0.763  Sum_probs=33.5

Q ss_pred             ecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCc
Q 043988           15 VCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEAR   68 (151)
Q Consensus        15 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~   68 (151)
                      +|+||++.+  .+.+.+..|+|.||.+|+..+++.      ....||  .|+..
T Consensus         1 ~C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~------~~~~Cp--~C~~~   44 (45)
T cd00162           1 ECPICLEEF--REPVVLLPCGHVFCRSCIDKWLKS------GKNTCP--LCRTP   44 (45)
T ss_pred             CCCcCchhh--hCceEecCCCChhcHHHHHHHHHh------CcCCCC--CCCCc
Confidence            589999877  345555569999999999999876      246788  57643

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

Probab=98.42  E-value=1.1e-07  Score=70.26  Aligned_cols=112  Identities=22%  Similarity=0.359  Sum_probs=67.4

Q ss_pred             cCCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcCCHHHHHHH
Q 043988            7 TDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARW   86 (151)
Q Consensus         7 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~   86 (151)
                      .........|+||++.+..+   .+++|+|.||+.|+...+.       ..+.||  .|.. ...    .+...-.....
T Consensus         7 ~~~~~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~-------~~~~Cp--~cr~-~~~----~~~~n~~l~~~   69 (386)
T KOG2177|consen    7 LEVLQEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE-------GPLSCP--VCRP-PSR----NLRPNVLLANL   69 (386)
T ss_pred             hhhccccccChhhHHHhhcC---ccccccchHhHHHHHHhcC-------CCcCCc--ccCC-chh----ccCccHHHHHH
Confidence            34456778999999998655   5568999999999999887       358999  6773 222    22222122222


Q ss_pred             HHHHHhhhhcCC-C--eeecCcccCCccccccccccCcccCcccchhhhhcCC-CCCCCCCCc
Q 043988           87 GLALCESALVGH-K--KFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCK-VPWHSEFDC  145 (151)
Q Consensus        87 ~~~~~~~~~~~~-~--~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C~-~~~H~~~~C  145 (151)
                      ............ .  ...|+.          ......+.|..|....|..|. ...|.++.-
T Consensus        70 ~~~~~~~~~~~~~~~~~~~c~~----------~~~~~~~~c~~~~~~~c~~c~~~~~h~~h~~  122 (386)
T KOG2177|consen   70 VERLRQLRLSRPLGSKEELCEK----------HGEELKLFCEEDEKLLCVLCRESGEHRGHPV  122 (386)
T ss_pred             HHHHHhcCCcccccccchhhhh----------cCCcceEEecccccccCCCCCCcccccCCcc
Confidence            222222111110 0  112331          122267889899999999998 666776653

>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=98.28  E-value=9.2e-07  Score=48.35  Aligned_cols=46  Identities=30%  Similarity=0.709  Sum_probs=33.7

Q ss_pred             eeecccccccCCCCCceecCCCCCc-cchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           13 SFVCEICVESRSLYDSFDVKGCSHF-NCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      ...|.||++..  .+ +.+.+|||. ||.+|+..+++       ...+||  -|...+.
T Consensus         2 ~~~C~iC~~~~--~~-~~~~pCgH~~~C~~C~~~~~~-------~~~~CP--~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENP--RD-VVLLPCGHLCFCEECAERLLK-------RKKKCP--ICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSB--SS-EEEETTCEEEEEHHHHHHHHH-------TTSBBT--TTTBB-S
T ss_pred             cCCCccCCccC--Cc-eEEeCCCChHHHHHHhHHhcc-------cCCCCC--cCChhhc
Confidence            35899999865  33 444589999 99999999987       246899  5877654

...

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.24  E-value=1.2e-06  Score=67.26  Aligned_cols=70  Identities=23%  Similarity=0.432  Sum_probs=47.1

Q ss_pred             ccCCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH-hhcCCHHHHH
Q 043988            6 ETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC-RLILPDDVFA   84 (151)
Q Consensus         6 ~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i-~~~l~~~~~~   84 (151)
                      ..+..+..+.|+||++.+.  +++ +..|||.||..|+..++..       ...||  .|...+....+ .+.+=.++++
T Consensus        19 ~l~~Le~~l~C~IC~d~~~--~Pv-itpCgH~FCs~CI~~~l~~-------~~~CP--~Cr~~~~~~~Lr~N~~L~~iVe   86 (397)
T TIGR00599        19 SLYPLDTSLRCHICKDFFD--VPV-LTSCSHTFCSLCIRRCLSN-------QPKCP--LCRAEDQESKLRSNWLVSEIVE   86 (397)
T ss_pred             cccccccccCCCcCchhhh--Ccc-CCCCCCchhHHHHHHHHhC-------CCCCC--CCCCccccccCccchHHHHHHH
Confidence            3455567789999998774  334 4589999999999998754       13799  68877765544 2222234445


Q ss_pred             HHH
Q 043988           85 RWG   87 (151)
Q Consensus        85 ~~~   87 (151)
                      .|.
T Consensus        87 ~~~   89 (397)
T TIGR00599        87 SFK   89 (397)
T ss_pred             HHH
Confidence            543

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

>PHA02929 N1R/p28-like protein; Provisional

Probab=98.23  E-value=1e-06  Score=63.29  Aligned_cols=51  Identities=24%  Similarity=0.500  Sum_probs=36.9

Q ss_pred             CCeeecccccccCCCCC-----ceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           11 TPSFVCEICVESRSLYD-----SFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~-----~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      .+..+|+||++.+....     ...+.+|+|.||.+|+..|++.       ..+||  -|...+.
T Consensus       172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-------~~tCP--lCR~~~~  227 (238)
T PHA02929        172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-------KNTCP--VCRTPFI  227 (238)
T ss_pred             CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc-------CCCCC--CCCCEee
Confidence            34579999999865432     2345589999999999999764       24899  5776543

>smart00184 RING Ring finger

Probab=98.22  E-value=1.5e-06  Score=44.22  Aligned_cols=30  Identities=40%  Similarity=0.825  Sum_probs=23.9

Q ss_pred             cccccccCCCCCceecCCCCCccchHHHHHHHH
Q 043988           16 CEICVESRSLYDSFDVKGCSHFNCTSCIVRYIA   48 (151)
Q Consensus        16 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~   48 (151)
                      |+||++..  .. ...+.|+|.||..|+..++.
T Consensus         1 C~iC~~~~--~~-~~~~~C~H~~c~~C~~~~~~   30 (39)
T smart00184        1 CPICLEEL--KD-PVVLPCGHTFCRSCIRKWLK   30 (39)
T ss_pred             CCcCccCC--CC-cEEecCCChHHHHHHHHHHH
Confidence            78998773  33 44458999999999999987

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)

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

Probab=98.20  E-value=1.1e-06  Score=62.07  Aligned_cols=61  Identities=21%  Similarity=0.582  Sum_probs=47.2

Q ss_pred             CCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcCC
Q 043988           10 GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILP   79 (151)
Q Consensus        10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~   79 (151)
                      ....++|.||++..  .+++.. .|||.||=.||-+|+.....    .-.||  -|+..++.+.|--|.+
T Consensus        44 ~~~~FdCNICLd~a--kdPVvT-lCGHLFCWpClyqWl~~~~~----~~~cP--VCK~~Vs~~~vvPlYG  104 (230)
T KOG0823|consen   44 DGGFFDCNICLDLA--KDPVVT-LCGHLFCWPCLYQWLQTRPN----SKECP--VCKAEVSIDTVVPLYG  104 (230)
T ss_pred             CCCceeeeeecccc--CCCEEe-ecccceehHHHHHHHhhcCC----CeeCC--ccccccccceEEeeec
Confidence            46789999999866  455554 69999999999999987643    24678  6998888888766654

>PHA02926 zinc finger-like protein; Provisional

Probab=98.16  E-value=1.9e-06  Score=60.53  Aligned_cols=57  Identities=25%  Similarity=0.476  Sum_probs=39.2

Q ss_pred             CCeeecccccccCCC-----C-CceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           11 TPSFVCEICVESRSL-----Y-DSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~-----~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      .+..+|+||++....     . .+-.+.+|+|.||..|+..|.+..-..+ ..-.||  -|...+.
T Consensus       168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~-~~rsCP--iCR~~f~  230 (242)
T PHA02926        168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETG-ASDNCP--ICRTRFR  230 (242)
T ss_pred             cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccC-cCCcCC--CCcceee
Confidence            345799999987522     1 2334568999999999999998653223 245799  5775443

>smart00504 Ubox Modified RING finger domain

Probab=98.13  E-value=4.9e-06  Score=47.51  Aligned_cols=50  Identities=22%  Similarity=0.251  Sum_probs=38.4

Q ss_pred             eecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHh
Q 043988           14 FVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR   75 (151)
Q Consensus        14 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~   75 (151)
                      +.|+||.+.+.  +++. ..|||.||++|+..|++.       ..+||  -|+..++.+++.
T Consensus         2 ~~Cpi~~~~~~--~Pv~-~~~G~v~~~~~i~~~~~~-------~~~cP--~~~~~~~~~~l~   51 (63)
T smart00504        2 FLCPISLEVMK--DPVI-LPSGQTYERRAIEKWLLS-------HGTDP--VTGQPLTHEDLI   51 (63)
T ss_pred             cCCcCCCCcCC--CCEE-CCCCCEEeHHHHHHHHHH-------CCCCC--CCcCCCChhhce
Confidence            57999998774  4554 489999999999999976       24788  577777766653

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

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

Probab=98.11  E-value=1.4e-06  Score=67.82  Aligned_cols=59  Identities=27%  Similarity=0.616  Sum_probs=44.8

Q ss_pred             eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcC
Q 043988           13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLIL   78 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l   78 (151)
                      ...||||+++.+..   .+..|||.||-.|+.+|+......  ....||  -|...|...++..+.
T Consensus       186 ~~~CPICL~~~~~p---~~t~CGHiFC~~CiLqy~~~s~~~--~~~~CP--iC~s~I~~kdl~pv~  244 (513)
T KOG2164|consen  186 DMQCPICLEPPSVP---VRTNCGHIFCGPCILQYWNYSAIK--GPCSCP--ICRSTITLKDLLPVF  244 (513)
T ss_pred             CCcCCcccCCCCcc---cccccCceeeHHHHHHHHhhhccc--CCccCC--chhhhccccceeeee
Confidence            67899999877543   334699999999999999987222  256888  488888887776554

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.11  E-value=5.3e-06  Score=61.46  Aligned_cols=54  Identities=24%  Similarity=0.447  Sum_probs=38.2

Q ss_pred             eecccccccCC-CCCceecC-CCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHh
Q 043988           14 FVCEICVESRS-LYDSFDVK-GCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR   75 (151)
Q Consensus        14 ~~C~iC~~~~~-~~~~~~~~-~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~   75 (151)
                      ..||+|..+.. .+++..+. .|||.||.+|+...+..    +  +..||  .|...+....++
T Consensus         4 ~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~----~--~~~CP--~C~~~lrk~~fr   59 (309)
T TIGR00570         4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR----G--SGSCP--ECDTPLRKNNFR   59 (309)
T ss_pred             CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcC----C--CCCCC--CCCCccchhhcc
Confidence            57999998644 34432221 69999999999998632    2  35899  798888777653

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

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

Probab=97.98  E-value=3.6e-06  Score=61.19  Aligned_cols=52  Identities=29%  Similarity=0.695  Sum_probs=41.0

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      .....|.+|++....   ++..+|||.||-+|+..|...+-       .||  -|...+...++
T Consensus       237 ~a~~kC~LCLe~~~~---pSaTpCGHiFCWsCI~~w~~ek~-------eCP--lCR~~~~pskv  288 (293)
T KOG0317|consen  237 EATRKCSLCLENRSN---PSATPCGHIFCWSCILEWCSEKA-------ECP--LCREKFQPSKV  288 (293)
T ss_pred             CCCCceEEEecCCCC---CCcCcCcchHHHHHHHHHHcccc-------CCC--cccccCCCcce
Confidence            445789999987743   34568999999999999988763       499  69888877665

>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]

Probab=97.88  E-value=7e-06  Score=60.54  Aligned_cols=95  Identities=23%  Similarity=0.526  Sum_probs=62.0

Q ss_pred             CCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcCCHHHHHHHHHHHHhhhhcCCCeeecCcccCCccc
Q 043988           33 GCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARWGLALCESALVGHKKFYCPYKDCSSML  112 (151)
Q Consensus        33 ~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~  112 (151)
                      +||-.||++|+..|....-..+. .-. -...|...++....       ..++|..+..+.  .+.....||  .|....
T Consensus       341 gCgf~FCR~C~e~yh~geC~~~~-~as-~t~tc~y~vde~~a-------~~arwd~as~~T--Ik~tTkpCP--kChvpt  407 (446)
T KOG0006|consen  341 GCGFAFCRECKEAYHEGECSAVF-EAS-GTTTCAYRVDERAA-------EQARWDAASKET--IKKTTKPCP--KCHVPT  407 (446)
T ss_pred             CchhHhHHHHHhhhccccceeee-ccc-cccceeeecChhhh-------hhhhhhhhhhhh--hhhccCCCC--CccCcc
Confidence            49999999999998654332110 000 01145555555432       335666543332  233455788  999999


Q ss_pred             cccccccCcccCcc--cchhhhhcCCCCCCC
Q 043988          113 IDEGEAIRKSNCPH--CRRLFCVQCKVPWHS  141 (151)
Q Consensus       113 ~~~~~~~~~~~C~~--C~~~~C~~C~~~~H~  141 (151)
                      .+++ ...+|.|+.  |+.+|||.|+-+|..
T Consensus       408 ErnG-GCmHm~Ct~~~Cg~eWCw~C~tEW~r  437 (446)
T KOG0006|consen  408 ERNG-GCMHMKCTQPQCGLEWCWNCGTEWNR  437 (446)
T ss_pred             ccCC-ceEEeecCCCCCCceeEeccCChhhh
Confidence            9875 488999965  999999999999954

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

Probab=97.82  E-value=1.7e-05  Score=44.52  Aligned_cols=52  Identities=31%  Similarity=0.578  Sum_probs=33.4

Q ss_pred             CCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCC
Q 043988            8 DDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCE   66 (151)
Q Consensus         8 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~   66 (151)
                      ++....+.|||-...+  .+++.-..|+|.|-++-+.+|+     ++...+.||..+|.
T Consensus         6 ~~~~~~~~CPiT~~~~--~~PV~s~~C~H~fek~aI~~~i-----~~~~~~~CPv~GC~   57 (57)
T PF11789_consen    6 EGGTISLKCPITLQPF--EDPVKSKKCGHTFEKEAILQYI-----QRNGSKRCPVAGCN   57 (57)
T ss_dssp             -SSB--SB-TTTSSB---SSEEEESSS--EEEHHHHHHHC-----TTTS-EE-SCCC-S
T ss_pred             eccEeccCCCCcCChh--hCCcCcCCCCCeecHHHHHHHH-----HhcCCCCCCCCCCC
Confidence            3456678999999776  6777766899999999999999     23346899998884

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

Probab=97.71  E-value=2.5e-05  Score=61.33  Aligned_cols=58  Identities=31%  Similarity=0.755  Sum_probs=44.3

Q ss_pred             CCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChh
Q 043988            8 DDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFE   72 (151)
Q Consensus         8 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~   72 (151)
                      +++....+|.+|-++.  .+.+. ..|.|.||+-|++.|+.....+.  .++||  .|...++.+
T Consensus       531 ~enk~~~~C~lc~d~a--ed~i~-s~ChH~FCrlCi~eyv~~f~~~~--nvtCP--~C~i~LsiD  588 (791)
T KOG1002|consen  531 DENKGEVECGLCHDPA--EDYIE-SSCHHKFCRLCIKEYVESFMENN--NVTCP--VCHIGLSID  588 (791)
T ss_pred             ccccCceeecccCChh--hhhHh-hhhhHHHHHHHHHHHHHhhhccc--CCCCc--ccccccccc
Confidence            3456678999998765  45554 48999999999999998887654  38999  687665544

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

Probab=97.63  E-value=4.5e-05  Score=56.03  Aligned_cols=54  Identities=20%  Similarity=0.490  Sum_probs=43.4

Q ss_pred             CCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988           10 GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus        10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      .+...+|.||++++-..+-+..++|.|.|-..|+.+|+..-      ..+||  .|...+++
T Consensus       320 a~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y------~~~CP--vCrt~iPP  373 (374)
T COG5540         320 ADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGY------SNKCP--VCRTAIPP  373 (374)
T ss_pred             cCCCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhh------cccCC--ccCCCCCC
Confidence            34568999999988766667777999999999999998643      46899  68877654

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

Probab=97.43  E-value=8.5e-05  Score=55.41  Aligned_cols=63  Identities=27%  Similarity=0.568  Sum_probs=45.0

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhh-cCCHHHHHHH
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRL-ILPDDVFARW   86 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~-~l~~~~~~~~   86 (151)
                      ...-|.||++-+..+-   +.+|+|+||.=|++.|+..+       ..||  .|...+...+++. .+-++.++-|
T Consensus        22 ~lLRC~IC~eyf~ip~---itpCsHtfCSlCIR~~L~~~-------p~CP--~C~~~~~Es~Lr~n~il~Eiv~S~   85 (442)
T KOG0287|consen   22 DLLRCGICFEYFNIPM---ITPCSHTFCSLCIRKFLSYK-------PQCP--TCCVTVTESDLRNNRILDEIVKSL   85 (442)
T ss_pred             HHHHHhHHHHHhcCce---eccccchHHHHHHHHHhccC-------CCCC--ceecccchhhhhhhhHHHHHHHHH
Confidence            3467999998875432   34799999999999998764       5788  6888888888742 2333444444

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

Probab=97.38  E-value=8e-05  Score=60.69  Aligned_cols=55  Identities=25%  Similarity=0.652  Sum_probs=42.2

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhc
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLI   77 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~   77 (151)
                      ....|++|.. .+ .+.+ +..|+|.||.+|++..+...      .=+||  .|...|...+|..|
T Consensus       642 ~~LkCs~Cn~-R~-Kd~v-I~kC~H~FC~~Cvq~r~etR------qRKCP--~Cn~aFganDv~~I  696 (698)
T KOG0978|consen  642 ELLKCSVCNT-RW-KDAV-ITKCGHVFCEECVQTRYETR------QRKCP--KCNAAFGANDVHRI  696 (698)
T ss_pred             hceeCCCccC-ch-hhHH-HHhcchHHHHHHHHHHHHHh------cCCCC--CCCCCCCccccccc
Confidence            4579999983 22 3333 34799999999999988776      35999  89999998887543

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

Probab=97.31  E-value=0.00015  Score=55.98  Aligned_cols=39  Identities=26%  Similarity=0.663  Sum_probs=33.5

Q ss_pred             eeecCcccCCccccccccccCcccCcccchhhhhcCCCCCCCC
Q 043988          100 KFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPWHSE  142 (151)
Q Consensus       100 ~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~  142 (151)
                      .+.||  .|.+.+...++ .++|+|. |++.||+.|+.+|+.+
T Consensus       306 wr~Cp--kC~~~ie~~~G-Cnhm~Cr-C~~~fcy~C~~~~~~~  344 (384)
T KOG1812|consen  306 WRQCP--KCKFMIELSEG-CNHMTCR-CGHQFCYMCGGDWKTH  344 (384)
T ss_pred             cCcCc--ccceeeeecCC-cceEEee-ccccchhhcCcchhhC
Confidence            45799  99998888765 9999998 9999999999999543

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

Probab=97.28  E-value=0.00013  Score=55.71  Aligned_cols=111  Identities=20%  Similarity=0.435  Sum_probs=66.6

Q ss_pred             Ceeeccc--ccccC---CCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcC-----CH-
Q 043988           12 PSFVCEI--CVESR---SLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLIL-----PD-   80 (151)
Q Consensus        12 ~~~~C~i--C~~~~---~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l-----~~-   80 (151)
                      ....||-  |--+.   +...+.....|.-.||.-|...|.-      +.       .|+.... +.++..+     |. 
T Consensus       272 dv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG------~s-------~Ck~~~~-~~~~l~~~~~~~d~a  337 (445)
T KOG1814|consen  272 DVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHG------VS-------PCKVKAE-KLIELYLEYLEADEA  337 (445)
T ss_pred             ccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcC------CC-------cccCchH-HHHHHHHHHhhcCHH
Confidence            3456766  43221   1233445557899999999877642      21       2554332 2221111     11 


Q ss_pred             ---HHHHHHHHHHHhhhh----c----CCCeeecCcccCCccccccccccCcccCcccchhhhhcCCCCC
Q 043988           81 ---DVFARWGLALCESAL----V----GHKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPW  139 (151)
Q Consensus        81 ---~~~~~~~~~~~~~~~----~----~~~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~  139 (151)
                         ++.+||.+++.+..+    +    ..+...||  .|...+.+.+ +.++|.|..|++.|||.|....
T Consensus       338 ~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP--~C~v~IEr~e-GCnKM~C~~c~~~fc~~c~~~l  404 (445)
T KOG1814|consen  338 RKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCP--KCKVVIERSE-GCNKMHCTKCGTYFCWICAELL  404 (445)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCC--cccceeecCC-Cccceeeccccccceeehhhhc
Confidence               344566644333322    2    12445799  9999998865 5899999999999999998843

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

Probab=97.27  E-value=0.0002  Score=51.65  Aligned_cols=52  Identities=25%  Similarity=0.636  Sum_probs=38.5

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHH-HHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVR-YIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~-~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      ..+.|.||++....   +...+|||.||-.|+.. +-+.+      .-.||  -|...+.+.++
T Consensus       214 ~d~kC~lC~e~~~~---ps~t~CgHlFC~~Cl~~~~t~~k------~~~Cp--lCRak~~pk~v  266 (271)
T COG5574         214 ADYKCFLCLEEPEV---PSCTPCGHLFCLSCLLISWTKKK------YEFCP--LCRAKVYPKKV  266 (271)
T ss_pred             cccceeeeecccCC---cccccccchhhHHHHHHHHHhhc------cccCc--hhhhhccchhh
Confidence            46789999976633   45568999999999998 43333      34688  68888777766

>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=97.26  E-value=0.00013  Score=43.06  Aligned_cols=42  Identities=24%  Similarity=0.441  Sum_probs=29.9

Q ss_pred             eecccccccCCC----------CCceecCCCCCccchHHHHHHHHHHHhCCccccCCCC
Q 043988           14 FVCEICVESRSL----------YDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQ   62 (151)
Q Consensus        14 ~~C~iC~~~~~~----------~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   62 (151)
                      -.|.||++++..          .-.+....|||.|...||.++++..       -+||.
T Consensus        20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~-------~~CP~   71 (73)
T PF12678_consen   20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN-------NTCPL   71 (73)
T ss_dssp             SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS-------SB-TT
T ss_pred             CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC-------CcCCC
Confidence            359999998832          1234445799999999999998553       28884

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 ....

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

Probab=97.25  E-value=0.00047  Score=50.09  Aligned_cols=51  Identities=25%  Similarity=0.542  Sum_probs=37.1

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      +...+|++|-++-  .-++....|+|+||..|+..-+....     .++||  .|++...
T Consensus       237 t~~~~C~~Cg~~P--tiP~~~~~C~HiyCY~Ci~ts~~~~a-----sf~Cp--~Cg~~~~  287 (298)
T KOG2879|consen  237 TSDTECPVCGEPP--TIPHVIGKCGHIYCYYCIATSRLWDA-----SFTCP--LCGENVE  287 (298)
T ss_pred             cCCceeeccCCCC--CCCeeeccccceeehhhhhhhhcchh-----hcccC--ccCCCCc
Confidence            4467999998643  34555656999999999887655442     48999  6886654

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

Probab=97.21  E-value=4.3e-05  Score=43.37  Aligned_cols=50  Identities=30%  Similarity=0.702  Sum_probs=22.1

Q ss_pred             eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHh
Q 043988           13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR   75 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~   75 (151)
                      ..-|++|.+-+  .+++.+..|.|.||..|+...+.         -.||  -|..+.-..+++
T Consensus         7 lLrCs~C~~~l--~~pv~l~~CeH~fCs~Ci~~~~~---------~~CP--vC~~Paw~qD~~   56 (65)
T PF14835_consen    7 LLRCSICFDIL--KEPVCLGGCEHIFCSSCIRDCIG---------SECP--VCHTPAWIQDIQ   56 (65)
T ss_dssp             TTS-SSS-S----SS-B---SSS--B-TTTGGGGTT---------TB-S--SS--B-S-SS--
T ss_pred             hcCCcHHHHHh--cCCceeccCccHHHHHHhHHhcC---------CCCC--CcCChHHHHHHH
Confidence            45699999876  45556668999999999866321         2488  687666555553

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

Probab=97.18  E-value=0.00029  Score=53.22  Aligned_cols=46  Identities=28%  Similarity=0.621  Sum_probs=38.9

Q ss_pred             eecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCC
Q 043988           14 FVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEA   67 (151)
Q Consensus        14 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~   67 (151)
                      .+|-||+|++...+-+..++|.|.|-..|+..|+...      .-.||.  |+.
T Consensus       230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~------r~~CPv--CK~  275 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT------RTFCPV--CKR  275 (348)
T ss_pred             ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc------CccCCC--CCC
Confidence            7999999999988888888999999999999998775      236885  553

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

Probab=96.97  E-value=0.00063  Score=39.77  Aligned_cols=58  Identities=19%  Similarity=0.348  Sum_probs=27.0

Q ss_pred             eeecccccccCC-CCCcee--c--CCCCCccchHHHHHHHHHHHhCCc-c---ccCCCCCCCCCccChh
Q 043988           13 SFVCEICVESRS-LYDSFD--V--KGCSHFNCTSCIVRYIASKLEGNI-T---NISCPQLGCEARLEFE   72 (151)
Q Consensus        13 ~~~C~iC~~~~~-~~~~~~--~--~~C~H~fC~~Cl~~~~~~~i~~~~-~---~i~CP~~~C~~~~~~~   72 (151)
                      ..+|+||+.... ..+...  .  ..|+..|-..||.+|+...-.... +   .=+||  .|...|...
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP--~C~~~i~~~   68 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECP--YCSSPISWS   68 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-T--TT-SEEEGG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCc--CCCCeeeEe
Confidence            468999998765 222211  1  368899999999999987765432 2   22699  688877543

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

Probab=96.92  E-value=0.00085  Score=39.53  Aligned_cols=51  Identities=24%  Similarity=0.235  Sum_probs=35.2

Q ss_pred             eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988           13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      .+.|+|+.+.+  .+++.+ ++||+|.++++..|+..      ....||  -++..++..++
T Consensus         4 ~f~CpIt~~lM--~dPVi~-~~G~tyer~~I~~~l~~------~~~~~P--~t~~~l~~~~l   54 (73)
T PF04564_consen    4 EFLCPITGELM--RDPVIL-PSGHTYERSAIERWLEQ------NGGTDP--FTRQPLSESDL   54 (73)
T ss_dssp             GGB-TTTSSB---SSEEEE-TTSEEEEHHHHHHHHCT------TSSB-T--TT-SB-SGGGS
T ss_pred             ccCCcCcCcHh--hCceeC-CcCCEEcHHHHHHHHHc------CCCCCC--CCCCcCCcccc
Confidence            47899999877  566665 79999999999999877      135788  45677776554

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 ....

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

Probab=96.73  E-value=0.00086  Score=49.94  Aligned_cols=49  Identities=31%  Similarity=0.764  Sum_probs=37.2

Q ss_pred             CCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCcc
Q 043988           10 GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARL   69 (151)
Q Consensus        10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~   69 (151)
                      ..+-.+|.+|-.-+  .+......|-|+||++|+..|+...       ..||  .|...+
T Consensus        12 ~n~~itC~LC~GYl--iDATTI~eCLHTFCkSCivk~l~~~-------~~CP--~C~i~i   60 (331)
T KOG2660|consen   12 LNPHITCRLCGGYL--IDATTITECLHTFCKSCIVKYLEES-------KYCP--TCDIVI   60 (331)
T ss_pred             cccceehhhcccee--ecchhHHHHHHHHHHHHHHHHHHHh-------ccCC--ccceec
Confidence            35668999997655  4555566899999999999999883       5899  465433

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

Probab=96.10  E-value=0.0034  Score=46.19  Aligned_cols=52  Identities=25%  Similarity=0.450  Sum_probs=35.9

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      +...-|-||-+-+..   .....|||.||.=|++.|+..+       ..||  -|........+
T Consensus        23 Ds~lrC~IC~~~i~i---p~~TtCgHtFCslCIR~hL~~q-------p~CP--~Cr~~~~esrl   74 (391)
T COG5432          23 DSMLRCRICDCRISI---PCETTCGHTFCSLCIRRHLGTQ-------PFCP--VCREDPCESRL   74 (391)
T ss_pred             hhHHHhhhhhheeec---ceecccccchhHHHHHHHhcCC-------CCCc--cccccHHhhhc
Confidence            445679999776643   3335899999999999998664       4788  46654443333

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

Probab=96.06  E-value=0.0052  Score=46.67  Aligned_cols=54  Identities=26%  Similarity=0.477  Sum_probs=37.4

Q ss_pred             CCeeecccccccCCCCC-----ceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCC
Q 043988           11 TPSFVCEICVESRSLYD-----SFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCE   66 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~-----~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~   66 (151)
                      .+..+|.||++.....-     +-.+++|.|.||..|++.|-...-.+....-.||  -|.
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP--~CR  217 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCP--FCR  217 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCC--ccc
Confidence            34679999998765433     3334689999999999998744433333456888  465

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

Probab=96.02  E-value=0.00064  Score=51.07  Aligned_cols=47  Identities=30%  Similarity=0.692  Sum_probs=32.6

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCc
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEAR   68 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~   68 (151)
                      ..+.|+||++-+..  ......|.|+||.+|+..-++..      .-.||  .|...
T Consensus        42 ~~v~c~icl~llk~--tmttkeClhrfc~~ci~~a~r~g------n~ecp--tcRk~   88 (381)
T KOG0311|consen   42 IQVICPICLSLLKK--TMTTKECLHRFCFDCIWKALRSG------NNECP--TCRKK   88 (381)
T ss_pred             hhhccHHHHHHHHh--hcccHHHHHHHHHHHHHHHHHhc------CCCCc--hHHhh
Confidence            45789999987643  33345899999999987755443      23788  56643

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

Probab=95.87  E-value=0.0059  Score=36.83  Aligned_cols=51  Identities=25%  Similarity=0.502  Sum_probs=33.5

Q ss_pred             eeecccccccCCC---------CC-ceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCcc
Q 043988           13 SFVCEICVESRSL---------YD-SFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARL   69 (151)
Q Consensus        13 ~~~C~iC~~~~~~---------~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~   69 (151)
                      .-.|+||...++.         .+ ++..-.|+|.|-..|+.+++.++-.    .-.||+  |...+
T Consensus        21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~----~~~CPm--CR~~w   81 (85)
T PF12861_consen   21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSS----KGQCPM--CRQPW   81 (85)
T ss_pred             CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccC----CCCCCC--cCCee
Confidence            3467777665541         12 2334479999999999999987521    248995  66544

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

Probab=95.62  E-value=0.035  Score=41.43  Aligned_cols=117  Identities=19%  Similarity=0.341  Sum_probs=63.0

Q ss_pred             eeecccccccCCCC---CceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCc--cChhHHhhcCCH-HHHHHH
Q 043988           13 SFVCEICVESRSLY---DSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEAR--LEFEDCRLILPD-DVFARW   86 (151)
Q Consensus        13 ~~~C~iC~~~~~~~---~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~--~~~~~i~~~l~~-~~~~~~   86 (151)
                      ...|.||-++++..   ..+..+.|||.+|..|+...+...      .+.||  -|...  +...+++.+-.. ..++..
T Consensus         3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~------~i~cp--fcR~~~~~~~~~~~~l~kNf~ll~~~   74 (296)
T KOG4185|consen    3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNS------RILCP--FCRETTEIPDGDVKSLQKNFALLQAI   74 (296)
T ss_pred             CCceeecCccccccCcccCCcccccCceehHhHHHHHhcCc------eeecc--CCCCcccCCchhHhhhhhhHHHHHHH
Confidence            46899999888743   345566899999999998876543      46777  67765  555555544321 222222


Q ss_pred             HHHHHhhhhcCCCeeecCcccCCcccccc-ccccCcccCcccchhhhhcCCCCC
Q 043988           87 GLALCESALVGHKKFYCPYKDCSSMLIDE-GEAIRKSNCPHCRRLFCVQCKVPW  139 (151)
Q Consensus        87 ~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~-~~~~~~~~C~~C~~~~C~~C~~~~  139 (151)
                      +.. ....+.......+|. .|....... ......-.|+.-...+|..|...-
T Consensus        75 ~~~-~~~~~~~~~~~~~~~-~c~~~~~nl~~~vc~~~~~~~~~~~~c~t~~~~~  126 (296)
T KOG4185|consen   75 EHM-KKTTVEEKGEADSPP-KCKEHPYNLAEFVCVEPDCSSKDKLMCRTCEEFG  126 (296)
T ss_pred             HHH-hcccccccCcccCCc-ccccCcccccceeecCCCcchhhhhhhhhccchh
Confidence            222 111111111222331 244322221 111222246666777888887744

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

Probab=95.58  E-value=0.013  Score=31.41  Aligned_cols=44  Identities=25%  Similarity=0.640  Sum_probs=20.3

Q ss_pred             cccccccCCCCC--ceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCc
Q 043988           16 CEICVESRSLYD--SFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEAR   68 (151)
Q Consensus        16 C~iC~~~~~~~~--~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~   68 (151)
                      ||+|.++++..+  +..- .|++.+|+.|+..-++    ++  .=.||  +|++.
T Consensus         1 cp~C~e~~d~~d~~~~PC-~Cgf~IC~~C~~~i~~----~~--~g~CP--gCr~~   46 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPC-ECGFQICRFCYHDILE----NE--GGRCP--GCREP   46 (48)
T ss_dssp             -TTTS-B--CCCTT--SS-TTS----HHHHHHHTT----SS---SB-T--TT--B
T ss_pred             CCCcccccccCCCccccC-cCCCcHHHHHHHHHHh----cc--CCCCC--CCCCC
Confidence            789998886543  3333 7999999999887544    11  23788  67754

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

Probab=95.43  E-value=0.0077  Score=41.94  Aligned_cols=32  Identities=28%  Similarity=0.730  Sum_probs=24.8

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHH
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVR   45 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~   45 (151)
                      .-++.|.||-.++.  .++. ..|||.||..|...
T Consensus       194 ~IPF~C~iCKkdy~--spvv-t~CGH~FC~~Cai~  225 (259)
T COG5152         194 KIPFLCGICKKDYE--SPVV-TECGHSFCSLCAIR  225 (259)
T ss_pred             CCceeehhchhhcc--chhh-hhcchhHHHHHHHH
Confidence            34689999998884  3333 48999999999665

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

Probab=95.42  E-value=0.011  Score=47.79  Aligned_cols=44  Identities=23%  Similarity=0.504  Sum_probs=34.2

Q ss_pred             CeeecccccccCCCCCc--eecCCCCCccchHHHHHHHHHHHhCCccccCCCC
Q 043988           12 PSFVCEICVESRSLYDS--FDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQ   62 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   62 (151)
                      ....|+||.++.....-  ...+.|+|.|+..|++.|++.+       -+||.
T Consensus       290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~-------qtCP~  335 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ-------QTCPT  335 (543)
T ss_pred             cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHh-------CcCCc
Confidence            35689999998864321  3456899999999999999984       47884

>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]

Probab=95.40  E-value=0.0036  Score=44.78  Aligned_cols=52  Identities=29%  Similarity=0.501  Sum_probs=37.4

Q ss_pred             eecccccccCC-CCCcee--cCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988           14 FVCEICVESRS-LYDSFD--VKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus        14 ~~C~iC~~~~~-~~~~~~--~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      .-||||-.+.. .+++..  -+.|-|++|.+|+-..+...      +-.||.++|..++-.
T Consensus        11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~G------pAqCP~~gC~kILRK   65 (314)
T COG5220          11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRG------PAQCPYKGCGKILRK   65 (314)
T ss_pred             ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCC------CCCCCCccHHHHHHH
Confidence            46999977654 455433  23599999999998866442      678999999866543

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

Probab=95.39  E-value=0.018  Score=44.71  Aligned_cols=48  Identities=27%  Similarity=0.683  Sum_probs=34.4

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      ...++|.||+..+  ..++.. +|||.||..|+.+-+.       ....||  .|...+.
T Consensus        82 ~sef~c~vc~~~l--~~pv~t-pcghs~c~~Cl~r~ld-------~~~~cp--~Cr~~l~  129 (398)
T KOG4159|consen   82 RSEFECCVCSRAL--YPPVVT-PCGHSFCLECLDRSLD-------QETECP--LCRDELV  129 (398)
T ss_pred             cchhhhhhhHhhc--CCCccc-cccccccHHHHHHHhc-------cCCCCc--ccccccc
Confidence            5678999998776  445554 9999999999777322       135777  5776555

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

Probab=95.28  E-value=0.03  Score=49.78  Aligned_cols=70  Identities=21%  Similarity=0.343  Sum_probs=54.1

Q ss_pred             CCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCc---cccCCCCCCCCCccChhHHhhcCCH
Q 043988            9 DGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNI---TNISCPQLGCEARLEFEDCRLILPD   80 (151)
Q Consensus         9 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~---~~i~CP~~~C~~~~~~~~i~~~l~~   80 (151)
                      .++..-.|-|||.+....-+-..+.|+|.|-..|.+..++..-.+..   ..|.||  -|..++.-..++++|++
T Consensus      3482 kQD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCP--iC~n~InH~~LkDLldP 3554 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCP--ICKNKINHIVLKDLLDP 3554 (3738)
T ss_pred             hcccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecc--cccchhhhHHHHHHHHH
Confidence            34455689999987765555444699999999999998877655432   258999  69999999999999986

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

Probab=95.20  E-value=0.0093  Score=44.11  Aligned_cols=47  Identities=26%  Similarity=0.576  Sum_probs=39.3

Q ss_pred             CcccCCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHH
Q 043988            4 NAETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASK   50 (151)
Q Consensus         4 ~a~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~   50 (151)
                      +..++++.+...|.||+.-+-..+.|....|-|.|-..||.+|+...
T Consensus       106 e~LT~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~  152 (368)
T KOG4445|consen  106 EFLTENNHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTEC  152 (368)
T ss_pred             HHcccCCCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHH
Confidence            45678888999999998877776767777999999999999998744

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

Probab=95.12  E-value=0.028  Score=42.91  Aligned_cols=49  Identities=18%  Similarity=0.466  Sum_probs=36.1

Q ss_pred             CCeeecccccccCCCC----------CceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCc
Q 043988           11 TPSFVCEICVESRSLY----------DSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEAR   68 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~----------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~   68 (151)
                      .....|.||+|+.-.+          ..++.++|||.+--+|++.|++.+       -+||  -|+.+
T Consensus       285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq-------QTCP--ICr~p  343 (491)
T COG5243         285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ-------QTCP--ICRRP  343 (491)
T ss_pred             CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc-------cCCC--cccCc
Confidence            3456899999983321          123556999999999999999875       4888  46654

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=95.05  E-value=0.014  Score=29.61  Aligned_cols=29  Identities=31%  Similarity=0.816  Sum_probs=22.3

Q ss_pred             eecCcccCCccccccc----cccCcccCcccchhh
Q 043988          101 FYCPYKDCSSMLIDEG----EAIRKSNCPHCRRLF  131 (151)
Q Consensus       101 ~~Cp~~~C~~~~~~~~----~~~~~~~C~~C~~~~  131 (151)
                      +.||  .|+..+...+    .....+.|+.|++.|
T Consensus         3 i~CP--~C~~~f~v~~~~l~~~~~~vrC~~C~~~f   35 (37)
T PF13719_consen    3 ITCP--NCQTRFRVPDDKLPAGGRKVRCPKCGHVF   35 (37)
T ss_pred             EECC--CCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence            5788  8998887763    346689999998865

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

Probab=94.97  E-value=0.0097  Score=42.66  Aligned_cols=47  Identities=26%  Similarity=0.593  Sum_probs=33.2

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      ..+.|..|+.--+ .+.+.+..|+|.||..|...-..         -.||  -|+..+.
T Consensus         2 ~~VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~~---------~~C~--lCkk~ir   48 (233)
T KOG4739|consen    2 DFVHCNKCFRFPS-QDPFFLTACRHVFCEPCLKASSP---------DVCP--LCKKSIR   48 (233)
T ss_pred             ceEEeccccccCC-CCceeeeechhhhhhhhcccCCc---------cccc--cccceee
Confidence            3578999987555 56677779999999999654211         1787  5775543

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

Probab=94.96  E-value=0.015  Score=42.99  Aligned_cols=53  Identities=21%  Similarity=0.342  Sum_probs=37.1

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      ....+|+||+.+-..+  +. +.|+|.||.-|++......      ...|+  -|...|+...+
T Consensus         5 ~~~~eC~IC~nt~n~P--v~-l~C~HkFCyiCiKGsy~nd------k~~Ca--vCR~pids~i~   57 (324)
T KOG0824|consen    5 TKKKECLICYNTGNCP--VN-LYCFHKFCYICIKGSYKND------KKTCA--VCRFPIDSTID   57 (324)
T ss_pred             ccCCcceeeeccCCcC--cc-ccccchhhhhhhcchhhcC------CCCCc--eecCCCCcchh
Confidence            4556899999877543  33 5899999999988754432      34688  47766665543

>PF04641 Rtf2: Rtf2 RING-finger

Probab=94.95  E-value=0.063  Score=39.43  Aligned_cols=73  Identities=14%  Similarity=0.273  Sum_probs=52.0

Q ss_pred             CCCCCeeecccccccCCC-CCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcCCH-HHHHH
Q 043988            8 DDGTPSFVCEICVESRSL-YDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPD-DVFAR   85 (151)
Q Consensus         8 ~~~~~~~~C~iC~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~~-~~~~~   85 (151)
                      +.....|.|||...++.. ..++.+.+|||.|....+...-    .    .-.||  .|+..+...+|-.|.+. ++++.
T Consensus       108 ~~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k----~----~~~Cp--~c~~~f~~~DiI~Lnp~~ee~~~  177 (260)
T PF04641_consen  108 DNSEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK----K----SKKCP--VCGKPFTEEDIIPLNPPEEELEK  177 (260)
T ss_pred             ccCCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc----c----ccccc--ccCCccccCCEEEecCCccHHHH
Confidence            345778999999988864 3456667999999999998871    1    13588  69999998887666553 34444


Q ss_pred             HHHHH
Q 043988           86 WGLAL   90 (151)
Q Consensus        86 ~~~~~   90 (151)
                      +.+.+
T Consensus       178 l~~~~  182 (260)
T PF04641_consen  178 LRERM  182 (260)
T ss_pred             HHHHH
Confidence            44443

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

Probab=94.94  E-value=0.015  Score=46.02  Aligned_cols=38  Identities=26%  Similarity=0.735  Sum_probs=30.8

Q ss_pred             eecCcccCCccccccccccCcccCcc--cchhhhhcCCCCC--CC
Q 043988          101 FYCPYKDCSSMLIDEGEAIRKSNCPH--CRRLFCVQCKVPW--HS  141 (151)
Q Consensus       101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~--H~  141 (151)
                      ..||  .|...+..++ ..+++.|..  |++.|||.|.+.|  |.
T Consensus       227 k~CP--~c~~~iek~~-gc~~~~~~~~~c~~~FCw~Cl~~~~~h~  268 (444)
T KOG1815|consen  227 KECP--KCKVPIEKDG-GCNHMTCKSASCKHEFCWVCLASLSDHG  268 (444)
T ss_pred             ccCC--CcccchhccC-CccccccccCCcCCeeceeeeccccccc
Confidence            3488  9998888865 477888865  9999999998887  64

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

Probab=94.93  E-value=0.031  Score=42.89  Aligned_cols=59  Identities=19%  Similarity=0.319  Sum_probs=45.3

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhh
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRL   76 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~   76 (151)
                      ..+.|||=-+.....+++..+.|||.++++=+.+..+    +|...++||  -|+.....++.+.
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~----ng~~sfKCP--YCP~e~~~~~~kq  391 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSK----NGSQSFKCP--YCPVEQLASDTKQ  391 (394)
T ss_pred             ceeecccchhhccCCCCCeeeeccceecHHHHHHHhh----CCCeeeeCC--CCCcccCHHhccc
Confidence            3579999888777777877889999999998887643    354579999  6987766665543

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=94.92  E-value=0.016  Score=29.15  Aligned_cols=29  Identities=28%  Similarity=0.716  Sum_probs=21.9

Q ss_pred             eecCcccCCccccccc----cccCcccCcccchhh
Q 043988          101 FYCPYKDCSSMLIDEG----EAIRKSNCPHCRRLF  131 (151)
Q Consensus       101 ~~Cp~~~C~~~~~~~~----~~~~~~~C~~C~~~~  131 (151)
                      +.||  .|+..+..++    .....+.|+.|++.|
T Consensus         3 i~Cp--~C~~~y~i~d~~ip~~g~~v~C~~C~~~f   35 (36)
T PF13717_consen    3 ITCP--NCQAKYEIDDEKIPPKGRKVRCSKCGHVF   35 (36)
T ss_pred             EECC--CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence            5788  8988777662    345689999998865

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

Probab=94.39  E-value=0.032  Score=43.04  Aligned_cols=54  Identities=22%  Similarity=0.575  Sum_probs=38.8

Q ss_pred             eeecccccccCCCC---CceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988           13 SFVCEICVESRSLY---DSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus        13 ~~~C~iC~~~~~~~---~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      ..+||||++++...   .+++ +.|||.|=.+|++.|+-     .+....||  -|..+-....|
T Consensus         4 g~tcpiclds~~~~g~hr~vs-l~cghlFgs~cie~wl~-----k~~~~~cp--~c~~katkr~i   60 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVS-LQCGHLFGSQCIEKWLG-----KKTKMQCP--LCSGKATKRQI   60 (463)
T ss_pred             cccCceeeeeeeecCceEEee-ecccccccHHHHHHHHh-----hhhhhhCc--ccCChhHHHHH
Confidence            35899999987632   2344 58999999999999993     23457899  57765555444

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

Probab=94.35  E-value=0.032  Score=43.43  Aligned_cols=38  Identities=21%  Similarity=0.629  Sum_probs=29.6

Q ss_pred             CCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHH
Q 043988           10 GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIAS   49 (151)
Q Consensus        10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~   49 (151)
                      .+....|++|....  .+++....|||.||..|+..+...
T Consensus        18 ~~~~l~C~~C~~vl--~~p~~~~~cgh~fC~~C~~~~~~~   55 (391)
T KOG0297|consen   18 LDENLLCPICMSVL--RDPVQTTTCGHRFCAGCLLESLSN   55 (391)
T ss_pred             CcccccCccccccc--cCCCCCCCCCCcccccccchhhcc
Confidence            35678999998766  455553489999999999988765

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

Probab=94.21  E-value=0.017  Score=42.10  Aligned_cols=62  Identities=16%  Similarity=0.443  Sum_probs=44.6

Q ss_pred             CCCCeeecccccccCCCC--------CceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH-hhcC
Q 043988            9 DGTPSFVCEICVESRSLY--------DSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC-RLIL   78 (151)
Q Consensus         9 ~~~~~~~C~iC~~~~~~~--------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i-~~~l   78 (151)
                      +....-.|.||-..+..+        +.++ ++|+|.|-..|++.|....    + .-+||  -|++.++...+ ++..
T Consensus       220 khl~d~vCaVCg~~~~~s~~eegvienty~-LsCnHvFHEfCIrGWcivG----K-kqtCP--YCKekVdl~rmfsnpW  290 (328)
T KOG1734|consen  220 KHLSDSVCAVCGQQIDVSVDEEGVIENTYK-LSCNHVFHEFCIRGWCIVG----K-KQTCP--YCKEKVDLKRMFSNPW  290 (328)
T ss_pred             CCCCcchhHhhcchheeecchhhhhhhhee-eecccchHHHhhhhheeec----C-CCCCc--hHHHHhhHhhhccCcc
Confidence            334556899998766543        3444 4899999999999997542    2 35899  79999988876 4433

>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=94.11  E-value=0.025  Score=26.33  Aligned_cols=23  Identities=35%  Similarity=0.956  Sum_probs=16.0

Q ss_pred             ecCcccCCccccccccccCcccCcccchhh
Q 043988          102 YCPYKDCSSMLIDEGEAIRKSNCPHCRRLF  131 (151)
Q Consensus       102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~  131 (151)
                      .||  +|+..+..     ....||.||+.|
T Consensus         2 ~CP--~C~~~V~~-----~~~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCP--ECGAEVPE-----SAKFCPHCGYDF   24 (26)
T ss_pred             cCC--CCcCCchh-----hcCcCCCCCCCC
Confidence            477  88876643     235788888876

Several members are annotated as putative helicases.

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

Probab=94.07  E-value=0.036  Score=43.76  Aligned_cols=52  Identities=21%  Similarity=0.584  Sum_probs=37.1

Q ss_pred             CCeeecccccccCCCC-----Cc---------eecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           11 TPSFVCEICVESRSLY-----DS---------FDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~-----~~---------~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      +...+|+||+.+.+..     .+         +-+.+|.|.|-++|+..|+..-      .+.||.  |..+++
T Consensus       569 ~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~y------kl~CPv--CR~pLP  634 (636)
T KOG0828|consen  569 RRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTY------KLICPV--CRCPLP  634 (636)
T ss_pred             hccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhh------cccCCc--cCCCCC
Confidence            3456899999887631     11         2245899999999999998753      478994  655554

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

Probab=93.70  E-value=0.076  Score=40.27  Aligned_cols=49  Identities=24%  Similarity=0.579  Sum_probs=34.3

Q ss_pred             CCCCeeecccccccCCCCCceecCCCCCc-cchHHHHHHHHHHHhCCccccCCCCCCCCCcc
Q 043988            9 DGTPSFVCEICVESRSLYDSFDVKGCSHF-NCTSCIVRYIASKLEGNITNISCPQLGCEARL   69 (151)
Q Consensus         9 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~   69 (151)
                      +++...+|.||+.+.  .+ +.+++|.|. .|.+|.....-+   .    =.||.  |...+
T Consensus       286 ~~~~gkeCVIClse~--rd-t~vLPCRHLCLCs~Ca~~Lr~q---~----n~CPI--CRqpi  335 (349)
T KOG4265|consen  286 ESESGKECVICLSES--RD-TVVLPCRHLCLCSGCAKSLRYQ---T----NNCPI--CRQPI  335 (349)
T ss_pred             cccCCCeeEEEecCC--cc-eEEecchhhehhHhHHHHHHHh---h----cCCCc--cccch
Confidence            346678999999655  34 455699999 999998876522   1    26884  77554

>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=93.67  E-value=0.034  Score=36.48  Aligned_cols=36  Identities=19%  Similarity=0.368  Sum_probs=27.5

Q ss_pred             CeeecccccccCCC-CCceecCCCC------CccchHHHHHHHH
Q 043988           12 PSFVCEICVESRSL-YDSFDVKGCS------HFNCTSCIVRYIA   48 (151)
Q Consensus        12 ~~~~C~iC~~~~~~-~~~~~~~~C~------H~fC~~Cl~~~~~   48 (151)
                      ...+|.||++.+.. ...+.+ .++      |.||.+|+.+|-.
T Consensus        25 ~~~EC~IC~~~I~~~~GvV~v-t~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   25 CTVECQICFDRIDNNDGVVYV-TDGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             cCeeehhhhhhhhcCCCEEEE-ecCCeehHHHHHHHHHHHHHHh
Confidence            36899999999877 333443 676      7799999999943

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.

>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2

Probab=93.29  E-value=0.025  Score=28.27  Aligned_cols=28  Identities=21%  Similarity=0.740  Sum_probs=19.6

Q ss_pred             eecCcccCCccccccccccCcccCcccchh
Q 043988          101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRRL  130 (151)
Q Consensus       101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~  130 (151)
                      .+||  .|+..+....+....+.|+.|++.
T Consensus         2 ~FCp--~C~nlL~p~~~~~~~~~C~~C~Y~   29 (35)
T PF02150_consen    2 RFCP--ECGNLLYPKEDKEKRVACRTCGYE   29 (35)
T ss_dssp             -BET--TTTSBEEEEEETTTTEEESSSS-E
T ss_pred             eeCC--CCCccceEcCCCccCcCCCCCCCc
Confidence            4789  999999887554444478888764

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....

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

Probab=93.27  E-value=0.077  Score=39.76  Aligned_cols=44  Identities=25%  Similarity=0.647  Sum_probs=31.7

Q ss_pred             CCeeecccccccCCCCCceecCCC--CCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGC--SHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C--~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      ...++||||++.+..+.   + +|  ||..|.+|-...          .-+||  .|...++
T Consensus        46 ~~lleCPvC~~~l~~Pi---~-QC~nGHlaCssC~~~~----------~~~CP--~Cr~~~g   91 (299)
T KOG3002|consen   46 LDLLDCPVCFNPLSPPI---F-QCDNGHLACSSCRTKV----------SNKCP--TCRLPIG   91 (299)
T ss_pred             hhhccCchhhccCcccc---e-ecCCCcEehhhhhhhh----------cccCC--ccccccc
Confidence            45679999999886533   2 45  899999997521          35788  5877666

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=93.08  E-value=0.058  Score=27.29  Aligned_cols=29  Identities=21%  Similarity=0.586  Sum_probs=20.1

Q ss_pred             eecCcccCCccccccc----cccCcccCcccchhh
Q 043988          101 FYCPYKDCSSMLIDEG----EAIRKSNCPHCRRLF  131 (151)
Q Consensus       101 ~~Cp~~~C~~~~~~~~----~~~~~~~C~~C~~~~  131 (151)
                      +.||  .|+..+....    .....+.||.|+..|
T Consensus         3 ~~CP--~C~~~~~v~~~~~~~~~~~v~C~~C~~~~   35 (38)
T TIGR02098         3 IQCP--NCKTSFRVVDSQLGANGGKVRCGKCGHVW   35 (38)
T ss_pred             EECC--CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence            4688  8988766652    223478999998764

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.87  E-value=0.083  Score=38.18  Aligned_cols=57  Identities=12%  Similarity=0.248  Sum_probs=42.1

Q ss_pred             CCeeecccccccCCCCCc-eecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhh
Q 043988           11 TPSFVCEICVESRSLYDS-FDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRL   76 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~   76 (151)
                      ...+.||||-+.+...-. ..+-+|||.++.+|+..+|...       +.+|  -+..++...+|-.
T Consensus       219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D-------~v~p--v~d~plkdrdiI~  276 (303)
T KOG3039|consen  219 SKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKD-------MVDP--VTDKPLKDRDIIG  276 (303)
T ss_pred             ccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcccc-------cccc--CCCCcCcccceEe
Confidence            367999999998865433 3455899999999999988764       4567  4677777776643

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

Probab=92.67  E-value=0.049  Score=42.02  Aligned_cols=46  Identities=33%  Similarity=0.809  Sum_probs=32.3

Q ss_pred             eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCC
Q 043988           13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCE   66 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~   66 (151)
                      ...|.||-+..   +.+...+|||..|..|+..|-.+.  +|   -.||-+.|.
T Consensus       369 FeLCKICaend---KdvkIEPCGHLlCt~CLa~WQ~sd--~g---q~CPFCRcE  414 (563)
T KOG1785|consen  369 FELCKICAEND---KDVKIEPCGHLLCTSCLAAWQDSD--EG---QTCPFCRCE  414 (563)
T ss_pred             HHHHHHhhccC---CCcccccccchHHHHHHHhhcccC--CC---CCCCceeeE
Confidence            34699998644   335667999999999999984332  22   378866664

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

Probab=92.59  E-value=0.1  Score=39.71  Aligned_cols=35  Identities=29%  Similarity=0.703  Sum_probs=25.4

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHH
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIAS   49 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~   49 (151)
                      +.-.|+||+. .++.-++  .+|+|+-|..|+.+|+-.
T Consensus       421 Ed~lCpICyA-~pi~Avf--~PC~H~SC~~CI~qHlmN  455 (489)
T KOG4692|consen  421 EDNLCPICYA-GPINAVF--APCSHRSCYGCITQHLMN  455 (489)
T ss_pred             ccccCcceec-ccchhhc--cCCCCchHHHHHHHHHhc
Confidence            3458999984 2333333  489999999999998744

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

Probab=92.24  E-value=0.19  Score=27.03  Aligned_cols=41  Identities=24%  Similarity=0.614  Sum_probs=28.5

Q ss_pred             ecccccccCCCCCceecCCCC-----CccchHHHHHHHHHHHhCCccccCCC
Q 043988           15 VCEICVESRSLYDSFDVKGCS-----HFNCTSCIVRYIASKLEGNITNISCP   61 (151)
Q Consensus        15 ~C~iC~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~i~CP   61 (151)
                      .|-||++.....+.+. .+|.     |.+-.+||..|+..+.     ..+||
T Consensus         1 ~CrIC~~~~~~~~~l~-~PC~C~G~~~~vH~~Cl~~W~~~~~-----~~~C~   46 (49)
T smart00744        1 ICRICHDEGDEGDPLV-SPCRCKGSLKYVHQECLERWINESG-----NKTCE   46 (49)
T ss_pred             CccCCCCCCCCCCeeE-eccccCCchhHHHHHHHHHHHHHcC-----CCcCC
Confidence            3789998433444444 3675     7899999999998763     23777

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

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=92.00  E-value=0.081  Score=28.62  Aligned_cols=27  Identities=33%  Similarity=0.803  Sum_probs=19.4

Q ss_pred             ecCcccCCcccccccccc-CcccCcccchh
Q 043988          102 YCPYKDCSSMLIDEGEAI-RKSNCPHCRRL  130 (151)
Q Consensus       102 ~Cp~~~C~~~~~~~~~~~-~~~~C~~C~~~  130 (151)
                      +||  .|+..+....... ..+.|+.|++.
T Consensus         2 FCp--~Cg~~l~~~~~~~~~~~vC~~Cg~~   29 (52)
T smart00661        2 FCP--KCGNMLIPKEGKEKRRFVCRKCGYE   29 (52)
T ss_pred             CCC--CCCCccccccCCCCCEEECCcCCCe
Confidence            688  8998887764332 47789888864

>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=91.88  E-value=0.032  Score=30.37  Aligned_cols=36  Identities=28%  Similarity=0.747  Sum_probs=19.7

Q ss_pred             cCCccccccc---cccCcccCcccchhhhhcCCCCCCCC
Q 043988          107 DCSSMLIDEG---EAIRKSNCPHCRRLFCVQCKVPWHSE  142 (151)
Q Consensus       107 ~C~~~~~~~~---~~~~~~~C~~C~~~~C~~C~~~~H~~  142 (151)
                      +|...+....   .....+.||.|+..||..|-...|+-
T Consensus         4 gC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~   42 (51)
T PF07975_consen    4 GCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHET   42 (51)
T ss_dssp             TTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTT
T ss_pred             cCCCCCCCcccccccCCeEECCCCCCccccCcChhhhcc
Confidence            4555444431   12467999999999999999988874

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.

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

Probab=91.49  E-value=0.24  Score=36.93  Aligned_cols=43  Identities=23%  Similarity=0.678  Sum_probs=31.6

Q ss_pred             eecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCC
Q 043988           14 FVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCE   66 (151)
Q Consensus        14 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~   66 (151)
                      +.|+.|-..+  .+......|+|.||.+|+..-+...      .+.||  .|.
T Consensus       275 LkCplc~~Ll--rnp~kT~cC~~~fc~eci~~al~ds------Df~Cp--nC~  317 (427)
T COG5222         275 LKCPLCHCLL--RNPMKTPCCGHTFCDECIGTALLDS------DFKCP--NCS  317 (427)
T ss_pred             ccCcchhhhh--hCcccCccccchHHHHHHhhhhhhc------cccCC--Ccc
Confidence            6899997654  4555556799999999988654432      58999  465

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

Probab=91.47  E-value=0.27  Score=36.35  Aligned_cols=52  Identities=27%  Similarity=0.514  Sum_probs=34.3

Q ss_pred             ecccccccCC-CCCceec-CCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988           15 VCEICVESRS-LYDSFDV-KGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus        15 ~C~iC~~~~~-~~~~~~~-~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      .||+|-.+.. .++++.+ ..|+|+.|.+|+-..+...      +-.||  +|..++-...+
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g------~~~Cp--eC~~iLRk~nf   55 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLG------PAQCP--ECMVILRKNNF   55 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcC------CCCCC--cccchhhhccc
Confidence            4888865443 3343322 3799999999998766442      35788  89877665544

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

Probab=90.92  E-value=0.29  Score=41.28  Aligned_cols=54  Identities=24%  Similarity=0.558  Sum_probs=42.6

Q ss_pred             CCeeecccccccCCCC-CceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCC
Q 043988           11 TPSFVCEICVESRSLY-DSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCE   66 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~   66 (151)
                      ...++|-||++.+... .+++..+|-|.|-..|++.|.++.-+++...-.||  .|.
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP--~Cq  243 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCP--ACQ  243 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCC--ccc
Confidence            4679999999988754 45677789999999999999999555555556898  566

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=90.82  E-value=0.39  Score=36.47  Aligned_cols=58  Identities=29%  Similarity=0.662  Sum_probs=39.1

Q ss_pred             ecccccccCCCCC--ceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhh-cCCHH
Q 043988           15 VCEICVESRSLYD--SFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRL-ILPDD   81 (151)
Q Consensus        15 ~C~iC~~~~~~~~--~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~-~l~~~   81 (151)
                      .||.|++++++.+  ++.. +||-+.|+-|+.. |++.+     .=.||  -|....+.+.|+- -|+++
T Consensus        16 ~cplcie~mditdknf~pc-~cgy~ic~fc~~~-irq~l-----ngrcp--acrr~y~denv~~~~~s~e   76 (480)
T COG5175          16 YCPLCIEPMDITDKNFFPC-PCGYQICQFCYNN-IRQNL-----NGRCP--ACRRKYDDENVRYVTLSPE   76 (480)
T ss_pred             cCcccccccccccCCcccC-CcccHHHHHHHHH-HHhhc-----cCCCh--HhhhhccccceeEEecCHH
Confidence            3999999988654  4443 7999999999864 34433     33788  5887766666642 24443

>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional

Probab=90.71  E-value=0.15  Score=26.99  Aligned_cols=29  Identities=17%  Similarity=0.460  Sum_probs=20.9

Q ss_pred             eecCcccCCccccccccccCcccCcccchhhh
Q 043988          101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFC  132 (151)
Q Consensus       101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C  132 (151)
                      +.||  +|+..+..+... ..+.||.||..+=
T Consensus         4 y~C~--~CG~~~~~~~~~-~~~~Cp~CG~~~~   32 (46)
T PRK00398          4 YKCA--RCGREVELDEYG-TGVRCPYCGYRIL   32 (46)
T ss_pred             EECC--CCCCEEEECCCC-CceECCCCCCeEE
Confidence            4688  899888776433 2789999987553

>PHA03096 p28-like protein; Provisional

Probab=90.43  E-value=0.19  Score=37.48  Aligned_cols=39  Identities=21%  Similarity=0.233  Sum_probs=29.7

Q ss_pred             eecccccccCCC----C-CceecCCCCCccchHHHHHHHHHHHh
Q 043988           14 FVCEICVESRSL----Y-DSFDVKGCSHFNCTSCIVRYIASKLE   52 (151)
Q Consensus        14 ~~C~iC~~~~~~----~-~~~~~~~C~H~fC~~Cl~~~~~~~i~   52 (151)
                      .+|.||++....    . .+-.+..|.|.||..|.+.|......
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~  222 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLY  222 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhh
Confidence            689999986552    2 22234579999999999999988763

>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C

Probab=90.01  E-value=0.11  Score=25.80  Aligned_cols=26  Identities=31%  Similarity=0.864  Sum_probs=15.1

Q ss_pred             ecCcccCCcccccc---ccccCcccCcccch
Q 043988          102 YCPYKDCSSMLIDE---GEAIRKSNCPHCRR  129 (151)
Q Consensus       102 ~Cp~~~C~~~~~~~---~~~~~~~~C~~C~~  129 (151)
                      +||  .|+..+...   ++......|+.|+.
T Consensus         2 fC~--~CG~~l~~~ip~gd~r~R~vC~~Cg~   30 (34)
T PF14803_consen    2 FCP--QCGGPLERRIPEGDDRERLVCPACGF   30 (34)
T ss_dssp             B-T--TT--B-EEE--TT-SS-EEEETTTTE
T ss_pred             ccc--cccChhhhhcCCCCCccceECCCCCC
Confidence            688  899877664   45677888888875

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=89.76  E-value=0.21  Score=27.93  Aligned_cols=28  Identities=32%  Similarity=0.870  Sum_probs=13.1

Q ss_pred             eeecCcccCCcccccc----ccccCcccCcccch
Q 043988          100 KFYCPYKDCSSMLIDE----GEAIRKSNCPHCRR  129 (151)
Q Consensus       100 ~~~Cp~~~C~~~~~~~----~~~~~~~~C~~C~~  129 (151)
                      .+.||  +|+..++..    ....+.+.||+||.
T Consensus        25 ~F~CP--nCG~~~I~RC~~CRk~~~~Y~CP~CGF   56 (59)
T PRK14890         25 KFLCP--NCGEVIIYRCEKCRKQSNPYTCPKCGF   56 (59)
T ss_pred             EeeCC--CCCCeeEeechhHHhcCCceECCCCCC
Confidence            34566  555543333    12334455555553

>PF12773 DZR: Double zinc ribbon

Probab=89.55  E-value=0.21  Score=26.74  Aligned_cols=27  Identities=30%  Similarity=0.752  Sum_probs=15.8

Q ss_pred             CeeecCcccCCccccccccccCcccCcccch
Q 043988           99 KKFYCPYKDCSSMLIDEGEAIRKSNCPHCRR  129 (151)
Q Consensus        99 ~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~  129 (151)
                      +..+||  .|+..+..  .....+.|+.|++
T Consensus        11 ~~~fC~--~CG~~l~~--~~~~~~~C~~Cg~   37 (50)
T PF12773_consen   11 DAKFCP--HCGTPLPP--PDQSKKICPNCGA   37 (50)
T ss_pred             cccCCh--hhcCChhh--ccCCCCCCcCCcC
Confidence            345777  77776662  2234566777754

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

Probab=88.10  E-value=0.13  Score=42.72  Aligned_cols=50  Identities=28%  Similarity=0.611  Sum_probs=35.6

Q ss_pred             eecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988           14 FVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus        14 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      +.|.+|.+   ....+. ..|+|.||.+|+...+...-.     ..||  .|...+....+
T Consensus       455 ~~c~ic~~---~~~~~i-t~c~h~~c~~c~~~~i~~~~~-----~~~~--~cr~~l~~~~l  504 (674)
T KOG1001|consen  455 HWCHICCD---LDSFFI-TRCGHDFCVECLKKSIQQSEN-----APCP--LCRNVLKEKKL  504 (674)
T ss_pred             cccccccc---ccccee-ecccchHHHHHHHhccccccC-----CCCc--HHHHHHHHHHH
Confidence            79999998   233444 479999999999998765431     2666  67766665554

>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=87.82  E-value=0.94  Score=33.59  Aligned_cols=62  Identities=18%  Similarity=0.358  Sum_probs=41.9

Q ss_pred             CCeeecccccccCCCCCceecCC-CCCccchHHHHHHHHHHHhCCccccCCCC-CCCC---CccChhHH
Q 043988           11 TPSFVCEICVESRSLYDSFDVKG-CSHFNCTSCIVRYIASKLEGNITNISCPQ-LGCE---ARLEFEDC   74 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~-~~C~---~~~~~~~i   74 (151)
                      ...+-|-+|-|-+...-+++... =.|.||.-|-++.|+.+-..+  .+.||. .+|.   ..++...|
T Consensus       266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sg--evYCPSGdkCPLvgS~vPWAFM  332 (352)
T KOG3579|consen  266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASG--EVYCPSGDKCPLVGSNVPWAFM  332 (352)
T ss_pred             CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCC--ceeCCCCCcCcccCCcccHHHh
Confidence            34588999988775444333211 169999999999999886544  689995 3565   34555544

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=87.47  E-value=0.26  Score=22.08  Aligned_cols=22  Identities=36%  Similarity=1.097  Sum_probs=11.9

Q ss_pred             ecCcccCCccccccccccCcccCcccchh
Q 043988          102 YCPYKDCSSMLIDEGEAIRKSNCPHCRRL  130 (151)
Q Consensus       102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~  130 (151)
                      +||  .|+..+..+     ...|+.||+.
T Consensus         1 ~Cp--~CG~~~~~~-----~~fC~~CG~~   22 (23)
T PF13240_consen    1 YCP--NCGAEIEDD-----AKFCPNCGTP   22 (23)
T ss_pred             CCc--ccCCCCCCc-----CcchhhhCCc
Confidence            466  777655432     2346666653

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=87.25  E-value=0.65  Score=31.53  Aligned_cols=30  Identities=20%  Similarity=0.464  Sum_probs=22.1

Q ss_pred             CeeecCcccCCccccccccccCcccCcccchh
Q 043988           99 KKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRL  130 (151)
Q Consensus        99 ~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~  130 (151)
                      ..+.||  .|+.-+...+.....+.||.||..
T Consensus       108 ~~Y~Cp--~c~~r~tf~eA~~~~F~Cp~Cg~~  137 (158)
T TIGR00373       108 MFFICP--NMCVRFTFNEAMELNFTCPRCGAM  137 (158)
T ss_pred             CeEECC--CCCcEeeHHHHHHcCCcCCCCCCE
Confidence            345799  788777666555578999999864

This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.

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

Probab=87.17  E-value=0.23  Score=36.83  Aligned_cols=35  Identities=23%  Similarity=0.526  Sum_probs=25.8

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHHHHH
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIA   48 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~   48 (151)
                      .-++.|.||-.++.  +++. ..|+|.||..|....+.
T Consensus       239 ~~Pf~c~icr~~f~--~pVv-t~c~h~fc~~ca~~~~q  273 (313)
T KOG1813|consen  239 LLPFKCFICRKYFY--RPVV-TKCGHYFCEVCALKPYQ  273 (313)
T ss_pred             cCCccccccccccc--cchh-hcCCceeehhhhccccc
Confidence            34578999998874  4444 48999999999766543

>PF14353 CpXC: CpXC protein

Probab=87.03  E-value=0.31  Score=31.70  Aligned_cols=14  Identities=29%  Similarity=0.795  Sum_probs=8.5

Q ss_pred             ccCcccCcccchhh
Q 043988          118 AIRKSNCPHCRRLF  131 (151)
Q Consensus       118 ~~~~~~C~~C~~~~  131 (151)
                      ....++||.||+.+
T Consensus        35 ~l~~~~CP~Cg~~~   48 (128)
T PF14353_consen   35 SLFSFTCPSCGHKF   48 (128)
T ss_pred             CcCEEECCCCCCce
Confidence            34566677666654

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=86.82  E-value=0.7  Score=32.04  Aligned_cols=30  Identities=23%  Similarity=0.672  Sum_probs=21.9

Q ss_pred             CeeecCcccCCccccccccccCcccCcccchh
Q 043988           99 KKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRL  130 (151)
Q Consensus        99 ~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~  130 (151)
                      ..+.||  .|+.-+...+.....+.||.||..
T Consensus       116 ~~Y~Cp--~C~~rytf~eA~~~~F~Cp~Cg~~  145 (178)
T PRK06266        116 MFFFCP--NCHIRFTFDEAMEYGFRCPQCGEM  145 (178)
T ss_pred             CEEECC--CCCcEEeHHHHhhcCCcCCCCCCC
Confidence            346799  688777666555678999988864

>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]

Probab=86.56  E-value=0.42  Score=26.71  Aligned_cols=27  Identities=30%  Similarity=0.707  Sum_probs=12.9

Q ss_pred             eecCcccCCcccccc----ccccCcccCcccch
Q 043988          101 FYCPYKDCSSMLIDE----GEAIRKSNCPHCRR  129 (151)
Q Consensus       101 ~~Cp~~~C~~~~~~~----~~~~~~~~C~~C~~  129 (151)
                      +.||  +|+..++..    ....+...||+||.
T Consensus        28 F~CP--nCGe~~I~Rc~~CRk~g~~Y~Cp~CGF   58 (61)
T COG2888          28 FPCP--NCGEVEIYRCAKCRKLGNPYRCPKCGF   58 (61)
T ss_pred             eeCC--CCCceeeehhhhHHHcCCceECCCcCc
Confidence            4566  666444443    11234455665553

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

Probab=86.45  E-value=0.53  Score=36.98  Aligned_cols=38  Identities=21%  Similarity=0.370  Sum_probs=27.7

Q ss_pred             CCCeeecccccccCCCCC-ceecCCCCCccchHHHHHHH
Q 043988           10 GTPSFVCEICVESRSLYD-SFDVKGCSHFNCTSCIVRYI   47 (151)
Q Consensus        10 ~~~~~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~   47 (151)
                      ..+.-+||||++-++.+- .+....|.|.|-..|+..|.
T Consensus       172 ~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~  210 (493)
T KOG0804|consen  172 LTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW  210 (493)
T ss_pred             cccCCCcchhHhhcCccccceeeeecccccchHHHhhcc
Confidence            355669999999876432 22223699999999998874

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

Probab=86.28  E-value=0.64  Score=35.10  Aligned_cols=47  Identities=26%  Similarity=0.528  Sum_probs=34.0

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCC
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEA   67 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~   67 (151)
                      ..-.||+|+-..-.  +..+..-|-.||..|+..|+..-       =.||..+++.
T Consensus       299 ~~~~CpvClk~r~N--ptvl~vSGyVfCY~Ci~~Yv~~~-------~~CPVT~~p~  345 (357)
T KOG0826|consen  299 DREVCPVCLKKRQN--PTVLEVSGYVFCYPCIFSYVVNY-------GHCPVTGYPA  345 (357)
T ss_pred             ccccChhHHhccCC--CceEEecceEEeHHHHHHHHHhc-------CCCCccCCcc
Confidence            34689999866533  33333579999999999999842       3788777664

>smart00531 TFIIE Transcription initiation factor IIE

Probab=86.19  E-value=0.79  Score=30.68  Aligned_cols=30  Identities=23%  Similarity=0.508  Sum_probs=19.7

Q ss_pred             CeeecCcccCCcccccccc-----ccCcccCcccchh
Q 043988           99 KKFYCPYKDCSSMLIDEGE-----AIRKSNCPHCRRL  130 (151)
Q Consensus        99 ~~~~Cp~~~C~~~~~~~~~-----~~~~~~C~~C~~~  130 (151)
                      ..+.||  .|+..+.....     ....+.||.||..
T Consensus        98 ~~Y~Cp--~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~  132 (147)
T smart00531       98 AYYKCP--NCQSKYTFLEANQLLDMDGTFTCPRCGEE  132 (147)
T ss_pred             cEEECc--CCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence            456899  89876665422     2233899988864

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

Probab=86.14  E-value=0.72  Score=35.18  Aligned_cols=40  Identities=30%  Similarity=0.624  Sum_probs=27.5

Q ss_pred             CcccCCC-CCeeecccccccCCCCCceecCCCCCccchHHHHHH
Q 043988            4 NAETDDG-TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRY   46 (151)
Q Consensus         4 ~a~~~~~-~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~   46 (151)
                      +|++++. +....|.||.+...   ...+.+|+|++|.-|....
T Consensus        51 tsSaddtDEen~~C~ICA~~~T---Ys~~~PC~H~~CH~Ca~Rl   91 (493)
T COG5236          51 TSSADDTDEENMNCQICAGSTT---YSARYPCGHQICHACAVRL   91 (493)
T ss_pred             cccccccccccceeEEecCCce---EEEeccCCchHHHHHHHHH
Confidence            3444443 45678999987552   2345689999999997654

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=85.58  E-value=0.39  Score=22.11  Aligned_cols=22  Identities=27%  Similarity=0.966  Sum_probs=11.6

Q ss_pred             eecCcccCCccccccccccCcccCcccch
Q 043988          101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRR  129 (151)
Q Consensus       101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~  129 (151)
                      +.||  .|+..+..     ....||.||+
T Consensus         3 ~~Cp--~Cg~~~~~-----~~~fC~~CG~   24 (26)
T PF13248_consen    3 MFCP--NCGAEIDP-----DAKFCPNCGA   24 (26)
T ss_pred             CCCc--ccCCcCCc-----ccccChhhCC
Confidence            3577  77763322     2235666654

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

Probab=85.28  E-value=1.2  Score=33.59  Aligned_cols=57  Identities=16%  Similarity=0.348  Sum_probs=41.1

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      +.+.||+=-+.....+++.++.|||.+=.+=+..    ..++|...++||  -|+..-..+.+
T Consensus       335 s~FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~----LS~nG~~~FKCP--YCP~~~~~~~~  391 (396)
T COG5109         335 SLFICPVLKELCTDENPPVMLECGHVISKEALSV----LSQNGVLSFKCP--YCPEMSKYENI  391 (396)
T ss_pred             ceeeccccHhhhcccCCCeeeeccceeeHHHHHH----HhhcCcEEeeCC--CCCcchhhhhh
Confidence            4578999777666677777889999987765544    345677789999  68865544443

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

Probab=85.22  E-value=1.2  Score=29.19  Aligned_cols=53  Identities=19%  Similarity=0.425  Sum_probs=39.7

Q ss_pred             CeeecccccccCCCCCceec-CCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           12 PSFVCEICVESRSLYDSFDV-KGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~-~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      +.++|.||-|......+..- .-||-..|.-|....++...    .-..||  -|+..+.
T Consensus        79 ~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~----~ypvCP--vCkTSFK  132 (140)
T PF05290_consen   79 KLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCN----LYPVCP--VCKTSFK  132 (140)
T ss_pred             CceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcc----cCCCCC--ccccccc
Confidence            78999999987765555442 23899999999999988763    346899  5876554

>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=84.79  E-value=0.34  Score=30.17  Aligned_cols=31  Identities=32%  Similarity=0.479  Sum_probs=24.1

Q ss_pred             eeecccccccCCCCCceecCCCCCccchHHHH
Q 043988           13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIV   44 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~   44 (151)
                      ...|++|...+..+. +.+.+|||.|...|+.
T Consensus        78 ~~~C~vC~k~l~~~~-f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   78 STKCSVCGKPLGNSV-FVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCccCcCCcCCCce-EEEeCCCeEEeccccc
Confidence            446999998887644 5555899999999974

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 [].

>PF14369 zf-RING_3: zinc-finger

Probab=83.91  E-value=0.89  Score=22.63  Aligned_cols=30  Identities=20%  Similarity=0.668  Sum_probs=19.0

Q ss_pred             eeecCcccCCccccccccccCcccCcccchhh
Q 043988          100 KFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLF  131 (151)
Q Consensus       100 ~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~  131 (151)
                      ..||-  .|+..+.........+.||.|+..|
T Consensus         2 ~ywCh--~C~~~V~~~~~~~~~~~CP~C~~gF   31 (35)
T PF14369_consen    2 RYWCH--QCNRFVRIAPSPDSDVACPRCHGGF   31 (35)
T ss_pred             CEeCc--cCCCEeEeCcCCCCCcCCcCCCCcE
Confidence            35787  8887777643223334788887654

>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]

Probab=83.13  E-value=0.2  Score=37.75  Aligned_cols=26  Identities=27%  Similarity=0.844  Sum_probs=22.1

Q ss_pred             ccCcccCcccchhhhhcCCCCCCCCC
Q 043988          118 AIRKSNCPHCRRLFCVQCKVPWHSEF  143 (151)
Q Consensus       118 ~~~~~~C~~C~~~~C~~C~~~~H~~~  143 (151)
                      ....+.|+.|+..||..|....|+-+
T Consensus       342 ~~~~y~C~~Ck~~FCldCDv~iHesL  367 (378)
T KOG2807|consen  342 SSGRYRCESCKNVFCLDCDVFIHESL  367 (378)
T ss_pred             CCCcEEchhccceeeccchHHHHhhh
Confidence            45678999999999999999888643

>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]

Probab=83.12  E-value=0.52  Score=29.14  Aligned_cols=29  Identities=34%  Similarity=0.913  Sum_probs=21.5

Q ss_pred             eecCcccCCccccccccc-cCcccCcccchhh
Q 043988          101 FYCPYKDCSSMLIDEGEA-IRKSNCPHCRRLF  131 (151)
Q Consensus       101 ~~Cp~~~C~~~~~~~~~~-~~~~~C~~C~~~~  131 (151)
                      .+||  .|+..++.+.+. .+.+.|+.|.+.+
T Consensus         2 ~FCP--~Cgn~Live~g~~~~rf~C~tCpY~~   31 (105)
T KOG2906|consen    2 LFCP--TCGNMLIVESGESCNRFSCRTCPYVF   31 (105)
T ss_pred             cccC--CCCCEEEEecCCeEeeEEcCCCCcee
Confidence            4788  899988887443 4788888887654

>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction

Probab=81.79  E-value=0.77  Score=22.86  Aligned_cols=27  Identities=30%  Similarity=0.493  Sum_probs=22.8

Q ss_pred             cCcccCcccchhhhhcCCCCCCCCCCc
Q 043988          119 IRKSNCPHCRRLFCVQCKVPWHSEFDC  145 (151)
Q Consensus       119 ~~~~~C~~C~~~~C~~C~~~~H~~~~C  145 (151)
                      ...+.|..|+..+|..|....|.++.-
T Consensus        10 ~~~~fC~~~~~~iC~~C~~~~H~~H~~   36 (39)
T cd00021          10 PLSLFCETDRALLCVDCDLSVHSGHRR   36 (39)
T ss_pred             ceEEEeCccChhhhhhcChhhcCCCCE
Confidence            567899999999999999877887653

>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]

Probab=81.65  E-value=0.47  Score=35.60  Aligned_cols=39  Identities=23%  Similarity=0.581  Sum_probs=28.1

Q ss_pred             ecCcccCCcccccc-------ccccCcccCcccchhhhhcCCCCCCCC
Q 043988          102 YCPYKDCSSMLIDE-------GEAIRKSNCPHCRRLFCVQCKVPWHSE  142 (151)
Q Consensus       102 ~Cp~~~C~~~~~~~-------~~~~~~~~C~~C~~~~C~~C~~~~H~~  142 (151)
                      .|-  .|+..+...       ......++|+.|+..||..|.+..|+.
T Consensus       364 ~Cf--~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~  409 (421)
T COG5151         364 HCF--VCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHET  409 (421)
T ss_pred             cce--eccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHHH
Confidence            455  566655443       123567899999999999999988753

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

Probab=81.58  E-value=0.66  Score=25.52  Aligned_cols=44  Identities=34%  Similarity=0.677  Sum_probs=28.9

Q ss_pred             eecccccccCCCCCceecCCCCCc-cchHHHHHHHHHHHhCCccccCCCCCCCCCc
Q 043988           14 FVCEICVESRSLYDSFDVKGCSHF-NCTSCIVRYIASKLEGNITNISCPQLGCEAR   68 (151)
Q Consensus        14 ~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~   68 (151)
                      -+|.||++.-.  +.+ +-.|||. +|.+|-.+..+..      .=.||  -|...
T Consensus         8 dECTICye~pv--dsV-lYtCGHMCmCy~Cg~rl~~~~------~g~CP--iCRap   52 (62)
T KOG4172|consen    8 DECTICYEHPV--DSV-LYTCGHMCMCYACGLRLKKAL------HGCCP--ICRAP   52 (62)
T ss_pred             cceeeeccCcc--hHH-HHHcchHHhHHHHHHHHHHcc------CCcCc--chhhH
Confidence            58999997432  222 2369998 8999988776541      23677  46643

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

Probab=80.89  E-value=1.4  Score=25.18  Aligned_cols=17  Identities=18%  Similarity=0.473  Sum_probs=12.4

Q ss_pred             ccchHHHHHHHHHHHhC
Q 043988           37 FNCTSCIVRYIASKLEG   53 (151)
Q Consensus        37 ~fC~~Cl~~~~~~~i~~   53 (151)
                      -||++||..|......+
T Consensus        11 gFCRNCLskWy~~aA~~   27 (68)
T PF06844_consen   11 GFCRNCLSKWYREAAEE   27 (68)
T ss_dssp             S--HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHh
Confidence            39999999999887654

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

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

Probab=80.86  E-value=0.89  Score=33.70  Aligned_cols=48  Identities=29%  Similarity=0.699  Sum_probs=34.6

Q ss_pred             CCeeecccccccCCC-CCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCC
Q 043988           11 TPSFVCEICVESRSL-YDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEA   67 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~   67 (151)
                      .....||||.+.+.. ...+..+.|||..-..|++.++...       .+||  -|..
T Consensus       156 ~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~-------y~CP--~C~~  204 (276)
T KOG1940|consen  156 SSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEG-------YTCP--ICSK  204 (276)
T ss_pred             cccCCCchhHHHhccccccCCccCcccchHHHHHHHHhccC-------CCCC--cccc
Confidence            334569999886553 3344556899999999998886542       6898  5777

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

Probab=80.78  E-value=0.36  Score=40.60  Aligned_cols=43  Identities=16%  Similarity=0.216  Sum_probs=24.7

Q ss_pred             CCCeeecccccccCCC----CCceecCCCCCccchHHHHHHHHHHHh
Q 043988           10 GTPSFVCEICVESRSL----YDSFDVKGCSHFNCTSCIVRYIASKLE   52 (151)
Q Consensus        10 ~~~~~~C~iC~~~~~~----~~~~~~~~C~H~fC~~Cl~~~~~~~i~   52 (151)
                      .....+|++|.-++..    .....+..|+|.+|..||..+....+.
T Consensus        93 ~a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~  139 (1134)
T KOG0825|consen   93 TAESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEE  139 (1134)
T ss_pred             cccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhc
Confidence            3444556666544443    112223357888888888887766654

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

Probab=80.62  E-value=1.1  Score=34.78  Aligned_cols=38  Identities=21%  Similarity=0.618  Sum_probs=27.3

Q ss_pred             eeecccccccCCCCCce-ecCCCCCccchHHHHHHHHHH
Q 043988           13 SFVCEICVESRSLYDSF-DVKGCSHFNCTSCIVRYIASK   50 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~-~~~~C~H~fC~~Cl~~~~~~~   50 (151)
                      +-.|.||-+-++...-. ..-.|||+|-..|+.+|+...
T Consensus         4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~   42 (465)
T KOG0827|consen    4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGD   42 (465)
T ss_pred             cceeeEeccCCccccccccccchhhHHHHHHHHHHHccC
Confidence            45899996656543322 222599999999999998764

>TIGR00622 ssl1 transcription factor ssl1

Probab=80.34  E-value=0.95  Score=28.87  Aligned_cols=39  Identities=26%  Similarity=0.709  Sum_probs=29.1

Q ss_pred             ecCcccCCccccccc-------cccCcccCcccchhhhhcCCCCCCCC
Q 043988          102 YCPYKDCSSMLIDEG-------EAIRKSNCPHCRRLFCVQCKVPWHSE  142 (151)
Q Consensus       102 ~Cp~~~C~~~~~~~~-------~~~~~~~C~~C~~~~C~~C~~~~H~~  142 (151)
                      .|-  +|...+....       .....+.|+.|+..||..|...+|+-
T Consensus        57 ~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~  102 (112)
T TIGR00622        57 FCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHES  102 (112)
T ss_pred             ccc--CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhh
Confidence            466  7777665321       23456889999999999999999874

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

>PLN00209 ribosomal protein S27; Provisional

Probab=80.20  E-value=1.2  Score=26.89  Aligned_cols=31  Identities=16%  Similarity=0.474  Sum_probs=24.5

Q ss_pred             eecCcccCCccccccccccCcccCcccchhhhh
Q 043988          101 FYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCV  133 (151)
Q Consensus       101 ~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~  133 (151)
                      +.||  +|...-...+.....+.|..|+...+.
T Consensus        37 VkCp--~C~n~q~VFShA~t~V~C~~Cg~~L~~   67 (86)
T PLN00209         37 VKCQ--GCFNITTVFSHSQTVVVCGSCQTVLCQ   67 (86)
T ss_pred             EECC--CCCCeeEEEecCceEEEccccCCEeec
Confidence            4699  999876666666788999999988764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	151
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	5e-13
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	7e-07

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

 Score = 60.3 bits (146), Expect = 5e-13
 Identities = 19/88 (21%), Positives = 38/88 (43%), Gaps = 3/88 (3%)

Query: 11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKL-EGNITNISCPQLGC--EA 67
          + S  C++C+    +     +  C    CT C+ +Y+   + EG  T ISCP   C  + 
Sbjct: 3  SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQG 62

Query: 68 RLEFEDCRLILPDDVFARWGLALCESAL 95
           L+  +   ++  ++  R+     E + 
Sbjct: 63 HLQENEIECMVAAEIMQRYKKLQFERSG 90

>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4 Length = 86

 Score = 43.8 bits (103), Expect = 7e-07
 Identities = 25/75 (33%), Positives = 32/75 (42%), Gaps = 7/75 (9%)

Query: 80  DDVFARWGLALCESALVGHKKF-YCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVP 138
               A +   L E  L+   KF +C    CS   I E E   ++ CP C + FCV+CK  
Sbjct: 4   GSSGALFHKKLTEGVLMRDPKFLWCA--QCSFGFIYERE-QLEATCPQCHQTFCVRCKRQ 60

Query: 139 W---HSEFDCSQFQK 150
           W   H    C  FQ 
Sbjct: 61  WEEQHRGRSCEDFQN 75

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	151
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.85
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	99.63
2jmo_A	80	Parkin; IBR, E3 ligase, zinc binding domain, RBR;	99.6
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.13
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.13
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.11
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.05
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.04
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.04
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.04
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.04
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.03
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.03
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	98.99
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	98.99
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	98.99
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	98.98
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	98.97
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	98.97
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	98.95
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	98.94
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	98.94
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	98.94
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	98.93
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	98.93
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.92
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.92
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	98.92
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	98.92
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	98.9
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	98.89
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	98.86
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	98.82
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	98.81
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.81
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	98.79
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	98.75
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	98.74
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	98.73
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.72
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.71
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.68
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	98.64
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	98.63
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.6
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	98.59
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.58
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	98.58
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.56
1z6u_A	150	NP95-like ring finger protein isoform B; structura	98.56
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	98.52
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	98.5
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.49
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	98.33
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.29
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.22
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	98.2
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.14
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	98.12
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.08
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.04
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	97.96
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	97.9
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	97.87
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	97.85
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	97.75
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	97.64
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	97.59
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	97.16
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	97.09
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	97.06
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	97.04
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	96.96
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	96.7
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	96.2
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	95.87
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	91.11
3nw0_A	238	Non-structural maintenance of chromosomes element	90.98
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	87.39
2d8v_A	67	Zinc finger FYVE domain-containing protein 19; zfy	86.06
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	84.29
1fre_A	42	Nuclear factor XNF7; zinc-binding protein, BBOX, d	82.82
1z60_A	59	TFIIH basal transcription factor complex P44 subun	82.74

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

Probab=99.85  E-value=1.9e-21  Score=120.41  Aligned_cols=87  Identities=20%  Similarity=0.474  Sum_probs=77.9

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCc-cccCCCCCCCCCc--cChhHHhhcCCHHHHHHHH
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNI-TNISCPQLGCEAR--LEFEDCRLILPDDVFARWG   87 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~-~~i~CP~~~C~~~--~~~~~i~~~l~~~~~~~~~   87 (151)
                      ...++|+||++++..++++.+.+|||.||++||..|+..+|.++. .+++||..+|+..  ++.+.++.+|+++++++|+
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~~~i~~ll~~~~~~ky~   82 (94)
T 1wim_A            3 SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQENEIECMVAAEIMQRYK   82 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECHHHHHHHSCHHHHHHHH
T ss_pred             CCCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCHHHHHHHCCHHHHHHHH
Confidence            457899999999988888877689999999999999999998764 5799998889999  9999999999999999999


Q ss_pred             HHHHhhhhcC
Q 043988           88 LALCESALVG   97 (151)
Q Consensus        88 ~~~~~~~~~~   97 (151)
                      +++++.++..
T Consensus        83 ~~~~~~~v~~   92 (94)
T 1wim_A           83 KLQFERSGPS   92 (94)
T ss_dssp             HHHHHSSCSS
T ss_pred             HHHHHhhhcc
Confidence            9999887754

>2ct7_A Ring finger protein 31; IBR, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.4

Probab=99.63  E-value=2.5e-18  Score=104.38  Aligned_cols=69  Identities=35%  Similarity=0.717  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHHHhhhhcCC-CeeecCcccCCccccccccccCcccCcccchhhhhcCCCCC---CCCCCchhhhhC
Q 043988           80 DDVFARWGLALCESALVGH-KKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPW---HSEFDCSQFQKL  151 (151)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~-~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~---H~~~~C~~~~~~  151 (151)
                      ++++++|++++.+.+|... +.+|||  +|+.+++.+.. ...+.||.|++.||+.|+.+|   |.|++|++|++|
T Consensus         4 ~~~~e~y~~~l~e~~v~~~~~~~wCP--~C~~~~~~~~~-~~~v~C~~C~~~FC~~C~~~w~~~H~~~sC~~~~~w   76 (86)
T 2ct7_A            4 GSSGALFHKKLTEGVLMRDPKFLWCA--QCSFGFIYERE-QLEATCPQCHQTFCVRCKRQWEEQHRGRSCEDFQNW   76 (86)
T ss_dssp             CCCCCSSSSCCCCSCCCSCCCEECCS--SSCCCEECCCS-CSCEECTTTCCEECSSSCSBCCTTTTTSCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCEeECc--CCCchheecCC-CCceEeCCCCCccccccCCchhhcCCCCChHHHHHH
Confidence            3567788888888888765 456999  99998887653 677999999999999999999   999999999998

>2jmo_A Parkin; IBR, E3 ligase, zinc binding domain, RBR; NMR {Homo sapiens}

Probab=99.60  E-value=7.3e-18  Score=100.86  Aligned_cols=70  Identities=26%  Similarity=0.569  Sum_probs=62.6

Q ss_pred             cCCHHHHHHHHHHHHhhhhcCCCeeecCcccCCccccccccccCcccCc-----ccchhhhhcCCCCCCCCCCchhh
Q 043988           77 ILPDDVFARWGLALCESALVGHKKFYCPYKDCSSMLIDEGEAIRKSNCP-----HCRRLFCVQCKVPWHSEFDCSQF  148 (151)
Q Consensus        77 ~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~C~-----~C~~~~C~~C~~~~H~~~~C~~~  148 (151)
                      +|+++++++|++++++.++..++.+|||+|+|+.++..+. +...+.|+     .|++.||+.|+.+||. .+|++.
T Consensus         2 ~l~~~~~~rY~~~~~e~~v~~~~~~~CP~p~C~~~v~~~~-~~~~v~C~~~~~~~C~~~FC~~C~~~wH~-~~C~~~   76 (80)
T 2jmo_A            2 HMGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEP-DQRKVTCEGGNGLGCGFAFCRECKEAYHE-GECSAV   76 (80)
T ss_dssp             CCCCCCCCSCCCSSSCCSSCCCSSCCCCSSSCCCCCCCCS-CTTSBCTTSSSTTCCSCCEETTTTEECCS-SCSSSC
T ss_pred             CCCHHHHHHHHHHHHHHHhhhCCcEECCCCCCCcccEECC-CCCcCCCCCCCCCCCCCeeccccCccccC-Cccccc
Confidence            6788899999999999999877788999999999998865 56779998     9999999999999999 999864

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

Probab=99.13  E-value=6.5e-11  Score=71.62  Aligned_cols=64  Identities=25%  Similarity=0.503  Sum_probs=47.6

Q ss_pred             CCCCCeeecccccccCCCCCc-eecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhc
Q 043988            8 DDGTPSFVCEICVESRSLYDS-FDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLI   77 (151)
Q Consensus         8 ~~~~~~~~C~iC~~~~~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~   77 (151)
                      +.....++|+||++.+...+. +..+.|||.||..|+..|++..    ...+.||  .|...+...++..+
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~----~~~~~CP--~Cr~~~~~~~i~~l   74 (88)
T 2ct2_A           10 DALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASS----INGVRCP--FCSKITRITSLTQL   74 (88)
T ss_dssp             CCCCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHC----SSCBCCT--TTCCCBCCSSTTTS
T ss_pred             hhccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcC----CCCcCCC--CCCCcccchhHHHH
Confidence            444667899999998865442 4445899999999999998764    1257999  68888777665544

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

Probab=99.13  E-value=6.1e-11  Score=69.24  Aligned_cols=60  Identities=28%  Similarity=0.528  Sum_probs=45.7

Q ss_pred             ccCCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhh
Q 043988            6 ETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRL   76 (151)
Q Consensus         6 ~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~   76 (151)
                      ..++....+.|+||++.+.  +++.+..|||.||..|+..|+..       ...||  .|...+...++..
T Consensus         8 ~~~~~~~~~~C~IC~~~~~--~p~~~~~CgH~fC~~Ci~~~~~~-------~~~CP--~Cr~~~~~~~~~~   67 (72)
T 2djb_A            8 NLSELTPYILCSICKGYLI--DATTITECLHTFCKSCIVRHFYY-------SNRCP--KCNIVVHQTQPLS   67 (72)
T ss_dssp             CCCCCCGGGSCTTTSSCCS--SCEECSSSCCEECHHHHHHHHHH-------CSSCT--TTCCCCCSSCSCC
T ss_pred             hHhhcCCCCCCCCCChHHH--CcCEECCCCCHHHHHHHHHHHHc-------CCcCC--CcCcccCcccccc
Confidence            3344566789999998774  45555589999999999999965       36899  6988887765543

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

Probab=99.11  E-value=1.1e-12  Score=85.29  Aligned_cols=101  Identities=22%  Similarity=0.520  Sum_probs=66.4

Q ss_pred             CCeeecccccccCCCC----CceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcCCHHHHHHH
Q 043988           11 TPSFVCEICVESRSLY----DSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARW   86 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~   86 (151)
                      ...++|+||++.+..+    +....+.|||.||.+|+..|++..       ..||  .|...+....+..+.        
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~-------~~CP--~Cr~~~~~~~l~~l~--------   67 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA-------NTCP--TCRKKINHKRYHPIY--------   67 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTC-------SBCT--TTCCBCTTTCEEECB--------
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhC-------CCCC--CCCCcCccccccccc--------
Confidence            3467999999887532    223445899999999999998642       4899  699888777664431        


Q ss_pred             HHHHHhhhhcCCCeeecCcccCCccccccccccCcccCcccchhhhhcCCCCC
Q 043988           87 GLALCESALVGHKKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPW  139 (151)
Q Consensus        87 ~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~  139 (151)
                               ...+...|+  -|...+..............||+.||..|...|
T Consensus        68 ---------i~~~~~~C~--iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~  109 (133)
T 4ap4_A           68 ---------IGSGTVSCP--ICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDS  109 (133)
T ss_dssp             ---------CSSSSCBCT--TTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHH
T ss_pred             ---------cCCCCCCCC--CCCCccccccccCcceEeCCCCChhhHHHHHHH
Confidence                     123345677  676555432111122233468888888888777

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

Probab=99.05  E-value=5.2e-10  Score=75.80  Aligned_cols=55  Identities=22%  Similarity=0.492  Sum_probs=42.4

Q ss_pred             CCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988            9 DGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus         9 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      .....+.|+||++.+.  +++. .+|||+||..|+..++...      ..+||  .|...+...++
T Consensus        14 ~~~~~~~C~IC~~~~~--~pv~-~~CgH~fC~~Ci~~~~~~~------~~~CP--~Cr~~~~~~~~   68 (170)
T 3hcs_A           14 PLESKYECPICLMALR--EAVQ-TPCGHRFCKACIIKSIRDA------GHKCP--VDNEILLENQL   68 (170)
T ss_dssp             CCCGGGBCTTTCSBCS--SEEE-CTTSCEEEHHHHHHHHHHH------CSBCT--TTCCBCCGGGC
T ss_pred             CCCCCCCCCCCChhhc--CcEE-CCCCCHHHHHHHHHHHHhC------CCCCC--CCccCcchhhh
Confidence            3456789999998774  4555 4899999999999998765      24899  58887776543

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

Probab=99.04  E-value=6.9e-11  Score=70.03  Aligned_cols=58  Identities=28%  Similarity=0.563  Sum_probs=45.1

Q ss_pred             CCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988            8 DDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus         8 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      +......+|+||++.+...+.+..+.|+|.||..|+..|++..       ..||  -|...+....+
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~-------~~CP--~Cr~~~~~~~~   67 (78)
T 2ect_A           10 EHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQH-------DSCP--VCRKSLTGQNT   67 (78)
T ss_dssp             TTSSSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTT-------CSCT--TTCCCCCCSCS
T ss_pred             ccCCCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcC-------CcCc--CcCCccCCccc
Confidence            3445678999999998766666566899999999999998532       4899  68887776554

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

Probab=99.04  E-value=3e-10  Score=68.09  Aligned_cols=61  Identities=21%  Similarity=0.483  Sum_probs=46.5

Q ss_pred             CCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988            8 DDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus         8 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      +.....++|+||++.+.  +++. ++|||.||..|+..++......+. .+.||  .|...+...++
T Consensus        14 ~~~~~~~~C~IC~~~~~--~p~~-~~CgH~fC~~Ci~~~~~~~~~~~~-~~~CP--~Cr~~~~~~~~   74 (85)
T 2ecv_A           14 VNVKEEVTCPICLELLT--QPLS-LDCGHSFCQACLTANHKKSMLDKG-ESSCP--VCRISYQPENI   74 (85)
T ss_dssp             CCCCCCCCCTTTCSCCS--SCBC-CSSSCCBCTTHHHHHHHHHHHTTS-CCCCT--TTCCSSCSSSC
T ss_pred             HHccCCCCCCCCCcccC--Ccee-CCCCCHHHHHHHHHHHHHhhcCCC-CCcCC--CCCCccCHHhc
Confidence            34456789999998874  3444 489999999999999988665443 57999  68888776554

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

Probab=99.04  E-value=1.4e-10  Score=67.76  Aligned_cols=57  Identities=19%  Similarity=0.519  Sum_probs=42.4

Q ss_pred             CCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988            9 DGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus         9 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      .....+.|+||++.+.  +++.+ .|||.||..|+..+++.    ......||  .|...+..+++
T Consensus        16 ~~~~~~~C~IC~~~~~--~~~~~-~CgH~fC~~Ci~~~~~~----~~~~~~CP--~Cr~~~~~~~~   72 (73)
T 2ysl_A           16 KLQEEVICPICLDILQ--KPVTI-DCGHNFCLKCITQIGET----SCGFFKCP--LCKTSVRKNAI   72 (73)
T ss_dssp             CCCCCCBCTTTCSBCS--SEEEC-TTCCEEEHHHHHHHCSS----SCSCCCCS--SSCCCCCCCCC
T ss_pred             hCccCCEeccCCcccC--CeEEc-CCCChhhHHHHHHHHHc----CCCCCCCC--CCCCcCCcccC
Confidence            3456789999998774  45554 89999999999998752    22357999  68887776543

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

Probab=99.04  E-value=2.7e-11  Score=71.90  Aligned_cols=65  Identities=23%  Similarity=0.471  Sum_probs=47.5

Q ss_pred             cccCCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988            5 AETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus         5 a~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      +..+.....++|+||++.+..  ++. ++|||.||..|+..|+............||  .|...+...++
T Consensus         4 ~~~~~~~~~~~C~IC~~~~~~--p~~-l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP--~Cr~~~~~~~l   68 (79)
T 2egp_A            4 GSSGNVQEEVTCPICLELLTE--PLS-LDCGHSLCRACITVSNKEAVTSMGGKSSCP--VCGISYSFEHL   68 (79)
T ss_dssp             SSSCCCCCCCEETTTTEECSS--CCC-CSSSCCCCHHHHSCCCCCCSSSCCCCCCCS--SSCCCCCSSGG
T ss_pred             chHhhcccCCCCcCCCcccCC--eeE-CCCCCHHHHHHHHHHHHhcccCCCCCCcCC--CCCCcCCHhhC
Confidence            344555678899999998743  444 489999999999998765433333467999  69888876655

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

Probab=99.03  E-value=3.4e-10  Score=64.89  Aligned_cols=56  Identities=18%  Similarity=0.482  Sum_probs=42.3

Q ss_pred             CCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988            8 DDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus         8 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      +.....+.|+||++.+.  +++. +.|||.||..|+..++.      .....||  .|...+..+++
T Consensus        10 ~~~~~~~~C~IC~~~~~--~p~~-~~CgH~fC~~Ci~~~~~------~~~~~CP--~Cr~~~~~~~i   65 (66)
T 2ecy_A           10 KTVEDKYKCEKCHLVLC--SPKQ-TECGHRFCESCMAALLS------SSSPKCT--ACQESIVKDKV   65 (66)
T ss_dssp             CSCCCCEECTTTCCEES--SCCC-CSSSCCCCHHHHHHHHT------TSSCCCT--TTCCCCCTTTC
T ss_pred             hcCCcCCCCCCCChHhc--CeeE-CCCCCHHHHHHHHHHHH------hCcCCCC--CCCcCCChhhc
Confidence            44566799999998874  3444 48999999999999985      1246899  68888776543

>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=99.03  E-value=4.8e-10  Score=64.75  Aligned_cols=57  Identities=19%  Similarity=0.454  Sum_probs=43.0

Q ss_pred             ccCCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988            6 ETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus         6 ~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      ..++.....+|+||++.+...+.+..+.|+|.||..|+..|+...       .+||  -|...+..
T Consensus         7 ~~~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~-------~~CP--~Cr~~~~~   63 (69)
T 2kiz_A            7 EGTEEDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITN-------KKCP--ICRVDIEA   63 (69)
T ss_dssp             TCCSTTCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHC-------SBCT--TTCSBSCS
T ss_pred             CcCcCCCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcC-------CCCc--CcCccccC
Confidence            334456678999999988665555556899999999999998762       3699  58766543

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

Probab=98.99  E-value=9.2e-10  Score=62.41  Aligned_cols=47  Identities=21%  Similarity=0.562  Sum_probs=35.7

Q ss_pred             CCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCC
Q 043988            9 DGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQ   62 (151)
Q Consensus         9 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   62 (151)
                      .....++|+||++.+.  +++.+ .|||.||..|+..+++..    .....||.
T Consensus        16 ~~~~~~~C~IC~~~~~--~p~~~-~CgH~fC~~Ci~~~~~~~----~~~~~CP~   62 (63)
T 2ysj_A           16 KLQEEVICPICLDILQ--KPVTI-DCGHNFCLKCITQIGETS----CGFFKCPL   62 (63)
T ss_dssp             CCCCCCBCTTTCSBCS--SCEEC-TTSSEECHHHHHHHHHHC----SSCCCCSC
T ss_pred             hCccCCCCCcCCchhC--CeEEe-CCCCcchHHHHHHHHHcC----CCCCcCcC
Confidence            4456789999998874  45554 899999999999998751    12468883

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

Probab=98.99  E-value=4.8e-10  Score=68.40  Aligned_cols=55  Identities=24%  Similarity=0.590  Sum_probs=41.5

Q ss_pred             cccCCCCCeeecccccccCCCCCceecCC-CCCccchHHHHHHHHHHHhCCccccCCCCCCCCCcc
Q 043988            5 AETDDGTPSFVCEICVESRSLYDSFDVKG-CSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARL   69 (151)
Q Consensus         5 a~~~~~~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~   69 (151)
                      ...+.....+.|+||++.+.  +++.+ . |||.||..|+..++...   +  ...||  .|...+
T Consensus         5 ~~~~~~~~~~~C~IC~~~~~--~p~~~-~~CgH~fC~~Ci~~~~~~~---~--~~~CP--~Cr~~~   60 (92)
T 3ztg_A            5 SEDDPIPDELLCLICKDIMT--DAVVI-PCCGNSYCDECIRTALLES---D--EHTCP--TCHQND   60 (92)
T ss_dssp             SSCCCCCTTTEETTTTEECS--SCEEC-TTTCCEECHHHHHHHHHHC---T--TCCCT--TTCCSS
T ss_pred             cccccCCcCCCCCCCChhhc--CceEC-CCCCCHHHHHHHHHHHHhc---C--CCcCc--CCCCcC
Confidence            34445566789999998874  55555 6 99999999999998742   1  36999  588775

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

Probab=98.99  E-value=5.7e-10  Score=65.32  Aligned_cols=54  Identities=19%  Similarity=0.532  Sum_probs=42.1

Q ss_pred             CCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988            8 DDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus         8 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      .+.....+|+||++.+.....+..+.|+|.||..|+..|++..       ..||  -|...+.
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~-------~~CP--~Cr~~~~   63 (74)
T 2ep4_A           10 KELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVR-------KVCP--LCNMPVL   63 (74)
T ss_dssp             CCCCCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHC-------SBCT--TTCCBCS
T ss_pred             ccCCCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcC-------CcCC--CcCcccc
Confidence            3445678999999998766666556899999999999998753       3899  5876554

>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=98.98  E-value=6.3e-10  Score=69.02  Aligned_cols=68  Identities=28%  Similarity=0.571  Sum_probs=49.3

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhc-CCHHHHHHHHHH
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLI-LPDDVFARWGLA   89 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~-l~~~~~~~~~~~   89 (151)
                      ..+.|+||++.+  .+++..+.|||.||..|+..|+...      ...||  .|...+...++... +-.+..+.+.++
T Consensus        21 ~~~~C~IC~~~~--~~p~~~~~CgH~FC~~Ci~~~~~~~------~~~CP--~Cr~~~~~~~l~~~~~~~~i~~~~~~l   89 (100)
T 3lrq_A           21 EVFRCFICMEKL--RDARLCPHCSKLCCFSCIRRWLTEQ------RAQCP--HCRAPLQLRELVNCRWAEEVTQQLDTL   89 (100)
T ss_dssp             HHTBCTTTCSBC--SSEEECTTTCCEEEHHHHHHHHHHT------CSBCT--TTCCBCCGGGCEECTTHHHHHHHHHHH
T ss_pred             CCCCCccCCccc--cCccccCCCCChhhHHHHHHHHHHC------cCCCC--CCCCcCCHHHhHhhHHHHHHHHHHHHH
Confidence            457899999887  4556536899999999999998764      26899  69998888776433 223444444443

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

Probab=98.97  E-value=4.4e-10  Score=64.78  Aligned_cols=56  Identities=20%  Similarity=0.544  Sum_probs=41.7

Q ss_pred             ccCCCCCeeecccccccCCCC----CceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988            6 ETDDGTPSFVCEICVESRSLY----DSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus         6 ~~~~~~~~~~C~iC~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      ..+......+|+||++.+...    +.+.++.|||.||..|+..|+..       ...||  -|...+.
T Consensus         8 ~~~~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-------~~~CP--~Cr~~~~   67 (69)
T 2ea6_A            8 TGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-------ANTCP--TCRKKIN   67 (69)
T ss_dssp             CCCCTTCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHH-------CSSCT--TTCCCCC
T ss_pred             cccCCCCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHc-------CCCCC--CCCCccC
Confidence            334456678999999987532    23355689999999999999875       25899  5887664

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

Probab=98.97  E-value=5.9e-10  Score=66.78  Aligned_cols=60  Identities=23%  Similarity=0.511  Sum_probs=44.7

Q ss_pred             CCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988            9 DGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus         9 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      +....++|+||++.+.  +++. ++|||.||..|+..|+.....++ ..+.||  .|...+...++
T Consensus        15 ~~~~~~~C~IC~~~~~--~p~~-~~CgH~fC~~Ci~~~~~~~~~~~-~~~~CP--~Cr~~~~~~~~   74 (85)
T 2ecw_A           15 MIKEEVTCPICLELLK--EPVS-ADCNHSFCRACITLNYESNRNTD-GKGNCP--VCRVPYPFGNL   74 (85)
T ss_dssp             CCCTTTSCTTTCSCCS--SCEE-CTTSCCBCHHHHHHHHHHSBCTT-SCBCCT--TTCCCCCTTCC
T ss_pred             hCccCCCCcCCChhhC--ccee-CCCCCHHHHHHHHHHHHhccCCC-CCCCCC--CCCCcCCHHhC
Confidence            3456789999998874  3444 48999999999999987754222 257999  69888876654

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

Probab=98.95  E-value=1.5e-10  Score=67.17  Aligned_cols=58  Identities=19%  Similarity=0.548  Sum_probs=44.0

Q ss_pred             CCCeeecccccccCCCC----CceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhh
Q 043988           10 GTPSFVCEICVESRSLY----DSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRL   76 (151)
Q Consensus        10 ~~~~~~C~iC~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~   76 (151)
                      .+...+|+||++.+..+    +.+..+.|||.||..|+..|++..       ..||  .|...+...++..
T Consensus         7 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~-------~~CP--~Cr~~~~~~~~~~   68 (71)
T 3ng2_A            7 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA-------NTCP--TCRKKINHKRYHP   68 (71)
T ss_dssp             CTTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHC-------SBCT--TTCCBCCCCSCCC
T ss_pred             CCCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcC-------CCCC--CCCCccChhheee
Confidence            34568999999887532    333556899999999999998753       4899  6988887766543

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

Probab=98.94  E-value=7.4e-10  Score=64.93  Aligned_cols=54  Identities=22%  Similarity=0.566  Sum_probs=40.1

Q ss_pred             cCCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCcc
Q 043988            7 TDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARL   69 (151)
Q Consensus         7 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~   69 (151)
                      .+.....+.|+||++.+.  +++.+..|||.||..|+..++...   +  ...||  .|...+
T Consensus         9 ~~~~~~~~~C~IC~~~~~--~p~~~~~CgH~fC~~Ci~~~~~~~---~--~~~CP--~Cr~~~   62 (74)
T 2yur_A            9 DDPIPDELLCLICKDIMT--DAVVIPCCGNSYCDECIRTALLES---D--EHTCP--TCHQND   62 (74)
T ss_dssp             CCCSCGGGSCSSSCCCCT--TCEECSSSCCEECTTHHHHHHHHS---S--SSCCS--SSCCSS
T ss_pred             cccCCCCCCCcCCChHHh--CCeEcCCCCCHHHHHHHHHHHHhc---C--CCcCC--CCCCcC
Confidence            344466789999998874  555553399999999999998753   1  46899  587654

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

Probab=98.94  E-value=1.7e-09  Score=64.38  Aligned_cols=52  Identities=21%  Similarity=0.541  Sum_probs=40.6

Q ss_pred             cCCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988            7 TDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus         7 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      .+.....+.|+||++.+  .+++. +.|||.||..|+..++..       ...||  .|...+.
T Consensus         9 ~~~~~~~~~C~IC~~~~--~~p~~-~~CgH~fC~~Ci~~~~~~-------~~~CP--~Cr~~~~   60 (81)
T 2csy_A            9 SEEEEIPFRCFICRQAF--QNPVV-TKCRHYFCESCALEHFRA-------TPRCY--ICDQPTG   60 (81)
T ss_dssp             SSCCCCCSBCSSSCSBC--CSEEE-CTTSCEEEHHHHHHHHHH-------CSBCS--SSCCBCC
T ss_pred             cccCCCCCCCcCCCchh--cCeeE-ccCCCHhHHHHHHHHHHC-------CCcCC--CcCcccc
Confidence            34456678999999887  34554 589999999999999864       35899  6888775

>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=98.94  E-value=2.8e-09  Score=67.98  Aligned_cols=85  Identities=20%  Similarity=0.425  Sum_probs=58.4

Q ss_pred             CCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcCCHHHHHHHHH
Q 043988            9 DGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARWGL   88 (151)
Q Consensus         9 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~   88 (151)
                      .....+.|+||++.+.  +++.+ .|||.||..|+..++...      ...||  .|...+...++.   ....++   +
T Consensus        14 ~~~~~~~C~IC~~~~~--~p~~~-~CgH~fC~~Ci~~~~~~~------~~~CP--~Cr~~~~~~~~~---~~~~l~---~   76 (118)
T 3hct_A           14 PLESKYECPICLMALR--EAVQT-PCGHRFCKACIIKSIRDA------GHKCP--VDNEILLENQLF---PDNFAK---R   76 (118)
T ss_dssp             CCCGGGBCTTTCSBCS--SEEEC-TTSCEEEHHHHHHHHHHH------CSBCT--TTCCBCCGGGCE---ECHHHH---H
T ss_pred             CCCCCCCCCcCChhhc--CeEEC-CcCChhhHHHHHHHHhhC------CCCCC--CCCCCcCHHhcc---cCHHHH---H
Confidence            3456689999998774  45554 899999999999998765      23899  688888765442   111111   1


Q ss_pred             HHHhhhhcCCCeeecCcccCCccccccc
Q 043988           89 ALCESALVGHKKFYCPYKDCSSMLIDEG  116 (151)
Q Consensus        89 ~~~~~~~~~~~~~~Cp~~~C~~~~~~~~  116 (151)
                      .     +. .-.++||+.+|+..+....
T Consensus        77 ~-----i~-~l~v~C~n~gC~~~~~~~~   98 (118)
T 3hct_A           77 E-----IL-SLMVKCPNEGCLHKMELRH   98 (118)
T ss_dssp             H-----HH-TSEEECSSTTCCCEEEGGG
T ss_pred             H-----Hc-cceeECCCCCCCCEEeeHH
Confidence            1     11 2357899989998777653

>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=98.93  E-value=1.2e-09  Score=60.10  Aligned_cols=50  Identities=24%  Similarity=0.448  Sum_probs=38.8

Q ss_pred             CCeeecccccccCCC-CCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCcc
Q 043988           11 TPSFVCEICVESRSL-YDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARL   69 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~   69 (151)
                      ....+|+||++++.. .+.+..+.|+|.||..|+..|++..       ..||  -|...+
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~-------~~CP--~Cr~~~   53 (55)
T 2ecm_A            3 SGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEG-------YRCP--LCSGPS   53 (55)
T ss_dssp             SCCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHT-------CCCT--TSCCSS
T ss_pred             CCCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcC-------CcCC--CCCCcC
Confidence            446789999998743 3345566899999999999998764       5899  577655

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

Probab=98.93  E-value=3.9e-10  Score=65.58  Aligned_cols=56  Identities=16%  Similarity=0.339  Sum_probs=43.1

Q ss_pred             CCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhh
Q 043988            9 DGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRL   76 (151)
Q Consensus         9 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~   76 (151)
                      ......+|+||++.+  .+.+.+ .|||.||..|+..|+..       ...||  -|...+....+..
T Consensus        11 ~~~~~~~C~IC~~~~--~~~~~~-~CgH~fC~~Ci~~~~~~-------~~~CP--~Cr~~~~~~~~~~   66 (71)
T 2d8t_A           11 PSLTVPECAICLQTC--VHPVSL-PCKHVFCYLCVKGASWL-------GKRCA--LCRQEIPEDFLDS   66 (71)
T ss_dssp             SSSSCCBCSSSSSBC--SSEEEE-TTTEEEEHHHHHHCTTC-------SSBCS--SSCCBCCHHHHSC
T ss_pred             cCCCCCCCccCCccc--CCCEEc-cCCCHHHHHHHHHHHHC-------CCcCc--CcCchhCHhhccC
Confidence            345668999999877  444554 79999999999988743       25899  6999988877643

>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=98.92  E-value=2e-09  Score=66.00  Aligned_cols=61  Identities=30%  Similarity=0.516  Sum_probs=46.4

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCc-cChhHH
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEAR-LEFEDC   74 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~-~~~~~i   74 (151)
                      ...+.||||++.+  .+++.+..|||+||+.|+..|+...-.. ....+||..+|... +...++
T Consensus         5 ~~~~~CPI~~~~~--~dPV~~~~cGh~f~r~cI~~~l~~~~~~-~~~~~CP~tgc~~~~l~~~~L   66 (94)
T 2yu4_A            5 SSGFTCPITKEEM--KKPVKNKVCGHTYEEDAIVRMIESRQKR-KKKAYCPQIGCSHTDIRKSDL   66 (94)
T ss_dssp             SSCCBCTTTCSBC--SSEEEESSSCCEEEHHHHHHHHHHHHTT-TCCBCCCSTTCCCCCBCGGGE
T ss_pred             CcEeECcCcCchh--cCCEEcCCCCCeecHHHHHHHHHHccCc-CCCCCCCcCcCcccccCHhhC
Confidence            4568999999877  5666653599999999999999875321 23579998889877 776654

>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=98.92  E-value=1.5e-09  Score=68.99  Aligned_cols=82  Identities=26%  Similarity=0.493  Sum_probs=57.1

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcCCHHHHHHHHHHHH
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARWGLALC   91 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~~~~   91 (151)
                      ..+.|+||++.+  .+++. ++|||.||..|+..++...      ...||  .|...+...++...+ ..    +.+.+.
T Consensus        22 ~~~~C~IC~~~~--~~p~~-~~CgH~fC~~Ci~~~~~~~------~~~CP--~Cr~~~~~~~~~~~~-~~----l~~~i~   85 (116)
T 1rmd_A           22 KSISCQICEHIL--ADPVE-TSCKHLFCRICILRCLKVM------GSYCP--SCRYPCFPTDLESPV-KS----FLNILN   85 (116)
T ss_dssp             HHTBCTTTCSBC--SSEEE-CTTSCEEEHHHHHHHHHHT------CSBCT--TTCCBCCGGGCBCCC-HH----HHHHHH
T ss_pred             CCCCCCCCCcHh--cCcEE-cCCCCcccHHHHHHHHhHC------cCcCC--CCCCCCCHhhccccH-HH----HHHHHH
Confidence            356899999877  44555 4899999999999998763      35899  699888887764321 11    112111


Q ss_pred             hhhhcCCCeeecCcccCCcccccc
Q 043988           92 ESALVGHKKFYCPYKDCSSMLIDE  115 (151)
Q Consensus        92 ~~~~~~~~~~~Cp~~~C~~~~~~~  115 (151)
                            .-.++||+.+|+..+...
T Consensus        86 ------~l~v~C~~~gC~~~~~~~  103 (116)
T 1rmd_A           86 ------SLMVKCPAQDCNEEVSLE  103 (116)
T ss_dssp             ------HCEEECCSTTCCCEEEHH
T ss_pred             ------HhcCCCCCCCCcchhhHh
Confidence                  125689988998877654

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

Probab=98.92  E-value=6.1e-10  Score=65.97  Aligned_cols=58  Identities=21%  Similarity=0.377  Sum_probs=41.5

Q ss_pred             CCCCeeecccccccCCCCCceec-CCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988            9 DGTPSFVCEICVESRSLYDSFDV-KGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus         9 ~~~~~~~C~iC~~~~~~~~~~~~-~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      ......+|+||++++...+...+ ..|||.||+.|+..++..      ....||  .|...+....+
T Consensus         7 ~~~~~~~CpICle~~~~~d~~~~p~~CGH~fC~~Cl~~~~~~------~~~~CP--~CR~~~~~~~~   65 (78)
T 1e4u_A            7 AKEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTD------ENGLCP--ACRKPYPEDPA   65 (78)
T ss_dssp             CCCCCCBCTTTCCBCCTTTTTCCSSTTSCCCCHHHHHHHTTS------SCSBCT--TTCCBCSSCSS
T ss_pred             ccccCCcCCccCccCccccccccccCCCCCcCHHHHHHHHhc------CCCCCC--CCCCccCCCch
Confidence            34556899999998765443322 249999999999887532      246899  69888776554

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

Probab=98.92  E-value=9e-10  Score=65.12  Aligned_cols=66  Identities=20%  Similarity=0.325  Sum_probs=47.3

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHh-hcCCHHHHHHHH
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR-LILPDDVFARWG   87 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~-~~l~~~~~~~~~   87 (151)
                      ...+.|+||++.+  .+++.+ .|||.||+.|+..|+..    +  ..+||  .|+..+...++. +..-.+.++.|.
T Consensus         6 ~~~~~C~IC~~~~--~~Pv~~-~CgH~fc~~Ci~~~~~~----~--~~~CP--~C~~~~~~~~l~~n~~l~~~i~~~~   72 (78)
T 1t1h_A            6 PEYFRCPISLELM--KDPVIV-STGQTYERSSIQKWLDA----G--HKTCP--KSQETLLHAGLTPNYVLKSLIALWC   72 (78)
T ss_dssp             SSSSSCTTTSCCC--SSEEEE-TTTEEEEHHHHHHHHTT----T--CCBCT--TTCCBCSSCCCEECTTTHHHHHHHH
T ss_pred             cccCCCCCccccc--cCCEEc-CCCCeecHHHHHHHHHH----C--cCCCC--CCcCCCChhhCccCHHHHHHHHHHH
Confidence            4568999999877  455555 89999999999999853    1  46899  688888766542 333345555554

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

Probab=98.90  E-value=1.9e-10  Score=71.23  Aligned_cols=68  Identities=24%  Similarity=0.513  Sum_probs=47.9

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHh-hcCCHHHHHHHHHHH
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR-LILPDDVFARWGLAL   90 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~-~~l~~~~~~~~~~~~   90 (151)
                      ..+.|+||++.+.  +++.+..|||.||..|+..|+..       ...||  .|...+...++. +..-.+.++.|.+..
T Consensus        21 ~~~~C~IC~~~~~--~p~~~~~CgH~fC~~Ci~~~~~~-------~~~CP--~Cr~~~~~~~l~~n~~l~~~i~~~~~~~   89 (99)
T 2y43_A           21 DLLRCGICFEYFN--IAMIIPQCSHNYCSLCIRKFLSY-------KTQCP--TCCVTVTEPDLKNNRILDELVKSLNFAR   89 (99)
T ss_dssp             HHTBCTTTCSBCS--SEEECTTTCCEEEHHHHHHHHTT-------CCBCT--TTCCBCCGGGCEECHHHHHHHHHHHHHH
T ss_pred             CCCCcccCChhhC--CcCEECCCCCHhhHHHHHHHHHC-------CCCCC--CCCCcCChhhCCcCHHHHHHHHHHHHHH
Confidence            4578999998874  45554589999999999999863       25899  699888876552 222234555555443

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

Probab=98.89  E-value=4.6e-10  Score=63.72  Aligned_cols=56  Identities=20%  Similarity=0.563  Sum_probs=42.7

Q ss_pred             CeeecccccccCCCC----CceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhh
Q 043988           12 PSFVCEICVESRSLY----DSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRL   76 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~   76 (151)
                      +..+|+||++.+..+    +.+..+.|||.||.+|+..|++.       ...||  .|...+...++..
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-------~~~CP--~Cr~~~~~~~~~~   61 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-------ANTCP--TCRKKINHKRYHP   61 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHH-------CSBCT--TTCCBCTTTCEEE
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHc-------CCCCC--CCCccCCccceee
Confidence            357899999987532    33345589999999999999875       25899  6998888776644

>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=98.86  E-value=6.3e-09  Score=65.57  Aligned_cols=70  Identities=17%  Similarity=0.412  Sum_probs=48.5

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhc-CCHHHHHHHHHHH
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLI-LPDDVFARWGLAL   90 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~-l~~~~~~~~~~~~   90 (151)
                      ..+.|+||++.+.  +++. ++|||.||..|+..++...    ...+.||  .|...+....+... .-.+..+.+.+.+
T Consensus        20 ~~~~C~IC~~~~~--~p~~-~~CgH~fC~~Ci~~~~~~~----~~~~~CP--~Cr~~~~~~~~~~~~~l~~~~~~~~~~~   90 (112)
T 1jm7_A           20 KILECPICLELIK--EPVS-TKCDHIFCKFCMLKLLNQK----KGPSQCP--LCKNDITKRSLQESTRFSQLVEELLKII   90 (112)
T ss_dssp             HHTSCSSSCCCCS--SCCB-CTTSCCCCSHHHHHHHHSS----SSSCCCT--TTSCCCCTTTCBCCCSSSHHHHHHHHHH
T ss_pred             CCCCCcccChhhc--CeEE-CCCCCHHHHHHHHHHHHhC----CCCCCCc--CCCCcCCHhhcCccHHHHHHHHHHHHHH
Confidence            3568999998774  4444 4899999999999998643    2247899  69988887776432 2234555554443

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

Probab=98.82  E-value=6e-10  Score=63.63  Aligned_cols=58  Identities=24%  Similarity=0.440  Sum_probs=42.0

Q ss_pred             eeecccccc-cCCCCCc-eecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcC
Q 043988           13 SFVCEICVE-SRSLYDS-FDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLIL   78 (151)
Q Consensus        13 ~~~C~iC~~-~~~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l   78 (151)
                      .++|+||++ .+..+.. +.++.|||.||.+|+..++..    +  ...||  .|+..+...+++..+
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~----~--~~~CP--~Cr~~~~~~~~~~~~   62 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR----G--AGNCP--ECGTPLRKSNFRVQL   62 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHT----T--SSSCT--TTCCCCSSCCCEEEC
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHc----C--CCcCC--CCCCccccccceeec
Confidence            468999998 5543332 123589999999999998753    1  46899  699988887775443

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

Probab=98.81  E-value=3e-09  Score=62.39  Aligned_cols=52  Identities=19%  Similarity=0.462  Sum_probs=41.1

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      ....+|+||++++...+.+..+.|+|.||..|+..|++..       ..||  -|...+..
T Consensus        21 ~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~-------~~CP--~Cr~~~~~   72 (75)
T 1x4j_A           21 SEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKAN-------RTCP--ICRADSGP   72 (75)
T ss_dssp             SSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHC-------SSCT--TTCCCCCC
T ss_pred             CCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcC-------CcCc--CcCCcCCC
Confidence            3557899999998776666666899999999999998652       4899  58776643

>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=98.81  E-value=1.2e-10  Score=76.63  Aligned_cols=92  Identities=17%  Similarity=0.369  Sum_probs=55.0

Q ss_pred             CCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcCCHHHHHHHHHH
Q 043988           10 GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARWGLA   89 (151)
Q Consensus        10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~~   89 (151)
                      ....+.|+||++.+  .+++.+ .|||+||..|+..++..    +  ...||  .|...+.......+++.+.+  |...
T Consensus        28 l~~~~~C~IC~~~~--~~pv~~-~CgH~FC~~Ci~~~~~~----~--~~~CP--~Cr~~~~~~~~~~~l~~~~~--~~d~   94 (141)
T 3knv_A           28 LEAKYLCSACRNVL--RRPFQA-QCGHRYCSFCLASILSS----G--PQNCA--ACVHEGIYEEGISILESSSA--FPDN   94 (141)
T ss_dssp             CCGGGBCTTTCSBC--SSEEEC-TTSCEEEHHHHHHHGGG----S--CEECH--HHHHTTCCCTTTTEECGGGC--EECH
T ss_pred             CCcCcCCCCCChhh--cCcEEC-CCCCccCHHHHHHHHhc----C--CCCCC--CCCCcccccccccccchhhh--cccH
Confidence            35668999999877  445554 89999999999998752    1  35899  57765543332222221100  0000


Q ss_pred             HHhhhhcCCCeeecCcccCCcccccc
Q 043988           90 LCESALVGHKKFYCPYKDCSSMLIDE  115 (151)
Q Consensus        90 ~~~~~~~~~~~~~Cp~~~C~~~~~~~  115 (151)
                      ..+..+. .-.++||+.+|+..+...
T Consensus        95 ~~~~~i~-~L~v~Cpn~GC~~~~~l~  119 (141)
T 3knv_A           95 AARREVE-SLPAVCPSDGCTWKGTLK  119 (141)
T ss_dssp             HHHHHHH-TSEEECCSTTCCCEEEHH
T ss_pred             HHHHHHc-ccccccCCCCCCCEeEHH
Confidence            1111111 235799998998777654

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

Probab=98.79  E-value=4.5e-09  Score=58.38  Aligned_cols=48  Identities=23%  Similarity=0.542  Sum_probs=34.9

Q ss_pred             CCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCC
Q 043988            8 DDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQ   62 (151)
Q Consensus         8 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   62 (151)
                      +.......|+||++.+..  ++. ++|||.||..|+..|+...    .....||.
T Consensus        10 ~~~~~~~~C~IC~~~~~~--p~~-~~CgH~fC~~Ci~~~~~~~----~~~~~CP~   57 (58)
T 2ecj_A           10 ENLQVEASCSVCLEYLKE--PVI-IECGHNFCKACITRWWEDL----ERDFPCPV   57 (58)
T ss_dssp             SCSCCCCBCSSSCCBCSS--CCC-CSSCCCCCHHHHHHHTTSS----CCSCCCSC
T ss_pred             hccccCCCCccCCcccCc--cEe-CCCCCccCHHHHHHHHHhc----CCCCCCCC
Confidence            344667899999988854  344 4899999999999986531    12467883

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

Probab=98.75  E-value=2.4e-09  Score=58.92  Aligned_cols=50  Identities=18%  Similarity=0.450  Sum_probs=37.4

Q ss_pred             CeeecccccccCCCCCceecCC-CCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           12 PSFVCEICVESRSLYDSFDVKG-CSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      ...+|+||++++...+.+..+. |+|.||.+|+..|++.       ...||  -|...+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~-------~~~CP--~Cr~~~~   54 (55)
T 1iym_A            4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGS-------HSTCP--LCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTT-------CCSCS--SSCCCSC
T ss_pred             CCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHc-------CCcCc--CCCCEeE
Confidence            4568999999987655444444 9999999999998743       24799  5776653

>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=98.74  E-value=1.2e-09  Score=68.58  Aligned_cols=56  Identities=27%  Similarity=0.666  Sum_probs=42.0

Q ss_pred             cccCCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988            5 AETDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus         5 a~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      ...+.....+.|+||++.+  .+++.+..|||.||..|+..++..       ...||  .|...+..
T Consensus         7 ~~~~~~~~~~~C~IC~~~~--~~p~~~~~CgH~fC~~Ci~~~~~~-------~~~CP--~Cr~~~~~   62 (108)
T 2ckl_A            7 IKITELNPHLMCVLCGGYF--IDATTIIECLHSFCKTCIVRYLET-------SKYCP--ICDVQVHK   62 (108)
T ss_dssp             EEHHHHGGGTBCTTTSSBC--SSEEEETTTCCEEEHHHHHHHHTS-------CSBCT--TTCCBSCS
T ss_pred             cchhccCCcCCCccCChHH--hCcCEeCCCCChhhHHHHHHHHHh-------CCcCc--CCCccccc
Confidence            3334445678999999887  456665589999999999999764       26899  68876654

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

Probab=98.73  E-value=6.9e-09  Score=63.18  Aligned_cols=52  Identities=19%  Similarity=0.468  Sum_probs=40.1

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      ....+|+||++++...+.+..+.|+|.||..|+..|++.       ...||  -|...+..
T Consensus        38 ~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~-------~~~CP--~Cr~~~~~   89 (91)
T 2l0b_A           38 GQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQK-------SGTCP--VCRCMFPP   89 (91)
T ss_dssp             SSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTT-------TCBCT--TTCCBSSC
T ss_pred             CCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHc-------CCcCc--CcCccCCC
Confidence            456789999998876665555689999999999999853       24899  58876653

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

Probab=98.72  E-value=3e-08  Score=59.57  Aligned_cols=53  Identities=13%  Similarity=-0.012  Sum_probs=41.9

Q ss_pred             CCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988           10 GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus        10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      ....+.|+||++.+  .+++.+ .|||+||+.|+..|+..       ..+||  .|+..+...++
T Consensus        11 ~p~~~~CpI~~~~m--~dPV~~-~cGhtf~r~~I~~~l~~-------~~~cP--~~~~~l~~~~l   63 (85)
T 2kr4_A           11 APDEFRDPLMDTLM--TDPVRL-PSGTVMDRSIILRHLLN-------SPTDP--FNRQMLTESML   63 (85)
T ss_dssp             CCTTTBCTTTCSBC--SSEEEC-TTSCEEEHHHHHHHHHH-------CSBCT--TTCCBCCGGGC
T ss_pred             CchheECcccCchh--cCCeEC-CCCCEECHHHHHHHHhc-------CCCCC--CCcCCCChHhc
Confidence            34578999999877  566665 79999999999999974       25899  58888876654

>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=98.71  E-value=1.1e-09  Score=69.60  Aligned_cols=52  Identities=23%  Similarity=0.624  Sum_probs=39.6

Q ss_pred             CCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988            9 DGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus         9 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      .....+.|+||++.+.  +++.+ .|||.||..|+..++..      ....||  .|...+..
T Consensus        11 ~~~~~~~C~iC~~~~~--~p~~~-~CgH~fC~~Ci~~~~~~------~~~~CP--~Cr~~~~~   62 (115)
T 3l11_A           11 PSLSECQCGICMEILV--EPVTL-PCNHTLCKPCFQSTVEK------ASLCCP--FCRRRVSS   62 (115)
T ss_dssp             CCHHHHBCTTTCSBCS--SCEEC-TTSCEECHHHHCCCCCT------TTSBCT--TTCCBCHH
T ss_pred             CCCCCCCCccCCcccC--ceeEc-CCCCHHhHHHHHHHHhH------CcCCCC--CCCcccCc
Confidence            3445689999998774  45555 89999999999988742      137899  69887765

>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=98.68  E-value=1.2e-08  Score=72.94  Aligned_cols=74  Identities=18%  Similarity=0.275  Sum_probs=52.1

Q ss_pred             CCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhh-cCCHHHHHHHHH
Q 043988           10 GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRL-ILPDDVFARWGL   88 (151)
Q Consensus        10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~-~l~~~~~~~~~~   88 (151)
                      ....+.||||++.+  .+++....|||.||+.|+..|+..    + ....||..+|...+...++.. ..-....+.++.
T Consensus       178 ~~~el~CPIcl~~f--~DPVts~~CGHsFcR~cI~~~~~~----~-~~~~CPvtGCr~~l~~~dL~pN~~L~~lve~~k~  250 (267)
T 3htk_C          178 GKIELTCPITCKPY--EAPLISRKCNHVFDRDGIQNYLQG----Y-TTRDCPQAACSQVVSMRDFVRDPIMELRCKIAKM  250 (267)
T ss_dssp             SBCCSBCTTTSSBC--SSEEEESSSCCEEEHHHHHHHSTT----C-SCEECSGGGCSCEECGGGEEECHHHHHHHHHHHH
T ss_pred             CceeeECcCccCcc--cCCeeeCCCCCcccHHHHHHHHHh----C-CCCCCCcccccCcCchhhCCcCHHHHHHHHHHHH
Confidence            45668999999877  567765589999999999999863    1 246899888999888776532 111234445544


Q ss_pred             HH
Q 043988           89 AL   90 (151)
Q Consensus        89 ~~   90 (151)
                      +.
T Consensus       251 r~  252 (267)
T 3htk_C          251 KE  252 (267)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=98.64  E-value=1.6e-08  Score=64.93  Aligned_cols=48  Identities=29%  Similarity=0.621  Sum_probs=37.9

Q ss_pred             eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988           13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      .+.|+||++.+.  +++.+ +|||.||..|+..++..      ....||  .|...+..
T Consensus        52 ~~~C~IC~~~~~--~p~~~-~CgH~fC~~Ci~~~~~~------~~~~CP--~Cr~~~~~   99 (124)
T 3fl2_A           52 TFQCICCQELVF--RPITT-VCQHNVCKDCLDRSFRA------QVFSCP--ACRYDLGR   99 (124)
T ss_dssp             HTBCTTTSSBCS--SEEEC-TTSCEEEHHHHHHHHHT------TCCBCT--TTCCBCCT
T ss_pred             CCCCCcCChHHc--CcEEe-eCCCcccHHHHHHHHhH------CcCCCC--CCCccCCC
Confidence            468999998874  45554 89999999999999872      246899  68887765

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

Probab=98.63  E-value=2.7e-08  Score=57.05  Aligned_cols=48  Identities=33%  Similarity=0.668  Sum_probs=36.7

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      ...+|+||++.+.  +....++|||.||..|+..|++..       ..||  -|...+.
T Consensus         4 ~~~~C~IC~~~~~--~~~~~~~C~H~fc~~Ci~~~~~~~-------~~CP--~Cr~~~~   51 (68)
T 1chc_A            4 VAERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQN-------PTCP--LCKVPVE   51 (68)
T ss_dssp             CCCCCSSCCSCCC--SCEEETTTTEEESTTHHHHHHHHS-------CSTT--TTCCCCC
T ss_pred             CCCCCeeCCcccc--CCcEecCCCCeeHHHHHHHHHhCc-------CcCc--CCChhhH
Confidence            3568999998874  333456899999999999998642       4899  5887665

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

Probab=98.60  E-value=6.2e-09  Score=66.29  Aligned_cols=65  Identities=20%  Similarity=0.454  Sum_probs=44.1

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHh-hcCCHHHHHHHHHH
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR-LILPDDVFARWGLA   89 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~-~~l~~~~~~~~~~~   89 (151)
                      ..+.|+||++.+.  +++.+..|||.||..|+..++.         ..||  .|...+...++. +..-.++++.+...
T Consensus        21 ~~~~C~IC~~~~~--~pv~~~~CgH~fC~~Ci~~~~~---------~~CP--~Cr~~~~~~~~~~n~~l~~l~~~~~~~   86 (117)
T 1jm7_B           21 KLLRCSRCTNILR--EPVCLGGCEHIFCSNCVSDCIG---------TGCP--VCYTPAWIQDLKINRQLDSMIQLCSKL   86 (117)
T ss_dssp             HTTSCSSSCSCCS--SCBCCCSSSCCBCTTTGGGGTT---------TBCS--SSCCBCSCSSCCCCHHHHHHHHHHHHH
T ss_pred             hCCCCCCCChHhh--CccEeCCCCCHHHHHHHHHHhc---------CCCc--CCCCcCccccccccHHHHHHHHHHHHH
Confidence            4578999998874  4454438999999999998864         5899  688877655442 22223444555443

>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=98.59  E-value=9.7e-08  Score=60.31  Aligned_cols=56  Identities=21%  Similarity=0.423  Sum_probs=39.5

Q ss_pred             CeeecccccccCCCCC---------------ceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988           12 PSFVCEICVESRSLYD---------------SFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~---------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      ...+|+||++++....               ...++.|+|.||..|+..|+....  ......||  -|...+..
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~--~~~~~~CP--~CR~~~~~   94 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGN--KDGSLQCP--SCKTIYGE   94 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTC--CSSCCBCT--TTCCBSSS
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHccc--CCCCCcCC--CCCCccCC
Confidence            3469999999985432               233568999999999999985432  12357999  58866643

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

Probab=98.58  E-value=9.5e-09  Score=56.86  Aligned_cols=47  Identities=21%  Similarity=0.518  Sum_probs=35.2

Q ss_pred             CCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988           10 GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus        10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      ....+.|+||++.+..  ++. ++|||.||..|+..          ..+.||  .|...+..
T Consensus         3 e~~~~~C~IC~~~~~~--p~~-l~CgH~fC~~Ci~~----------~~~~CP--~Cr~~~~~   49 (56)
T 1bor_A            3 EFQFLRCQQCQAEAKC--PKL-LPCLHTLCSGCLEA----------SGMQCP--ICQAPWPL   49 (56)
T ss_dssp             SCCCSSCSSSCSSCBC--CSC-STTSCCSBTTTCSS----------SSSSCS--SCCSSSSC
T ss_pred             cccCCCceEeCCccCC--eEE-cCCCCcccHHHHcc----------CCCCCC--cCCcEeec
Confidence            4556789999988753  333 58999999999766          257899  58766653

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

Probab=98.58  E-value=3.2e-09  Score=61.42  Aligned_cols=51  Identities=25%  Similarity=0.544  Sum_probs=37.8

Q ss_pred             CCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChh
Q 043988            9 DGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFE   72 (151)
Q Consensus         9 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~   72 (151)
                      ......+|+||++.+..   +. ++|+|.||..|+..|+..       ...||  -|...+...
T Consensus        11 ~~~~~~~C~IC~~~~~~---~~-~~CgH~fc~~Ci~~~~~~-------~~~CP--~Cr~~~~~~   61 (70)
T 2ecn_A           11 QLTDEEECCICMDGRAD---LI-LPCAHSFCQKCIDKWSDR-------HRNCP--ICRLQMTGA   61 (70)
T ss_dssp             CCCCCCCCSSSCCSCCS---EE-ETTTEEECHHHHHHSSCC-------CSSCH--HHHHCTTCC
T ss_pred             cCCCCCCCeeCCcCccC---cc-cCCCCcccHHHHHHHHHC-------cCcCC--CcCCcccCC
Confidence            44567899999988754   34 489999999999998651       46888  577665543

>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=98.56  E-value=5.6e-08  Score=59.92  Aligned_cols=51  Identities=20%  Similarity=0.114  Sum_probs=40.0

Q ss_pred             CeeecccccccCCCCCceecCCCC-CccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCS-HFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~-H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      ..+.||||++.+  .+++.+ .|| |+||+.|+..|+..       ..+||  .|+..+...++
T Consensus        21 ~~~~CpI~~~~m--~dPV~~-~cG~htf~r~cI~~~l~~-------~~~cP--~~~~~l~~~~L   72 (98)
T 1wgm_A           21 DEFLDPIMSTLM--CDPVVL-PSSRVTVDRSTIARHLLS-------DQTDP--FNRSPLTMDQI   72 (98)
T ss_dssp             TTTBCTTTCSBC--SSEEEC-TTTCCEEEHHHHHHHTTT-------SCBCT--TTCSBCCTTTS
T ss_pred             HhcCCcCccccc--cCCeEC-CCCCeEECHHHHHHHHHh-------CCCCC--CCCCCCChhhc
Confidence            468999999877  566665 899 99999999999864       24899  58888876543

>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=98.56  E-value=2.7e-08  Score=66.06  Aligned_cols=50  Identities=32%  Similarity=0.725  Sum_probs=39.4

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChh
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFE   72 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~   72 (151)
                      ..+.|+||++.+  .+++. +.|||.||..|+..++..      ..+.||  .|...+...
T Consensus        77 ~~~~C~IC~~~~--~~pv~-~~CgH~fC~~Ci~~~~~~------~~~~CP--~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELV--YQPVT-TECFHNVCKDCLQRSFKA------QVFSCP--ACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBC--SSEEE-CTTSCEEEHHHHHHHHHT------TCCBCT--TTCCBCCTT
T ss_pred             cCCEeecCChhh--cCCEE-cCCCCchhHHHHHHHHHh------CCCcCC--CCCccCCCC
Confidence            346899999877  44555 489999999999999874      246899  688887765

>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=98.52  E-value=3.4e-08  Score=66.51  Aligned_cols=49  Identities=31%  Similarity=0.794  Sum_probs=38.3

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      ..+.|+||++.+.  +++.+..|||.||..|+..|+...      ...||  .|...+.
T Consensus        53 ~~~~C~IC~~~~~--~p~~~~~CgH~fC~~Ci~~~~~~~------~~~CP--~Cr~~~~  101 (165)
T 2ckl_B           53 SELMCPICLDMLK--NTMTTKECLHRFCADCIITALRSG------NKECP--TCRKKLV  101 (165)
T ss_dssp             HHHBCTTTSSBCS--SEEEETTTCCEEEHHHHHHHHHTT------CCBCT--TTCCBCC
T ss_pred             CCCCCcccChHhh--CcCEeCCCCChhHHHHHHHHHHhC------cCCCC--CCCCcCC
Confidence            3468999998874  455555899999999999998731      46899  6887774

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

Probab=98.50  E-value=3.5e-08  Score=64.60  Aligned_cols=47  Identities=28%  Similarity=0.733  Sum_probs=35.9

Q ss_pred             eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988           13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      .++|+||++.+  .+++.+ +|||.||..|+..|+..       ...||  .|...+..
T Consensus        53 ~~~C~iC~~~~--~~~~~~-~CgH~fc~~Ci~~~~~~-------~~~CP--~Cr~~~~~   99 (138)
T 4ayc_A           53 ELQCIICSEYF--IEAVTL-NCAHSFCSYCINEWMKR-------KIECP--ICRKDIKS   99 (138)
T ss_dssp             HSBCTTTCSBC--SSEEEE-TTSCEEEHHHHHHHTTT-------CSBCT--TTCCBCCC
T ss_pred             cCCCcccCccc--CCceEC-CCCCCccHHHHHHHHHc-------CCcCC--CCCCcCCC
Confidence            45799999887  455554 89999999999998753       35799  58776643

>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=98.49  E-value=7.3e-08  Score=59.62  Aligned_cols=51  Identities=14%  Similarity=-0.001  Sum_probs=40.2

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      ..+.||||++.+  .+++.+ .|||+||+.|+..|+..       ..+||  -|+..+...++
T Consensus        28 ~~~~CpI~~~~m--~dPV~~-~cGhtf~r~~I~~~l~~-------~~~cP--~~~~~l~~~~L   78 (100)
T 2kre_A           28 DEFRDPLMDTLM--TDPVRL-PSGTIMDRSIILRHLLN-------SPTDP--FNRQTLTESML   78 (100)
T ss_dssp             TTTBCTTTCSBC--SSEEEE-TTTEEEEHHHHHHHTTS-------CSBCS--SSCCBCCTTSS
T ss_pred             HhhCCcCccCcc--cCCeEC-CCCCEEchHHHHHHHHc-------CCCCC--CCCCCCChhhc
Confidence            468999999877  566666 69999999999999863       25899  58887776543

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

Probab=98.33  E-value=2e-07  Score=55.34  Aligned_cols=54  Identities=19%  Similarity=0.362  Sum_probs=38.9

Q ss_pred             CCeeecccccccCCC-----------CC-ceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhH
Q 043988           11 TPSFVCEICVESRSL-----------YD-SFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFED   73 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~-----------~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~   73 (151)
                      ....+|+||++++..           .+ .+.+..|+|.|+.+|+..|++..       -+||  -|...+....
T Consensus        13 ~~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~-------~~CP--~CR~~~~~~~   78 (81)
T 2ecl_A           13 VECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQN-------NRCP--LCQQDWVVQR   78 (81)
T ss_dssp             CCCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTC-------CBCT--TTCCBCCEEE
T ss_pred             CCCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhC-------CCCC--CcCCCcchhh
Confidence            345679999888743           12 44555699999999999998653       3899  5887776543

>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=98.29  E-value=5.8e-07  Score=64.97  Aligned_cols=53  Identities=11%  Similarity=-0.065  Sum_probs=41.0

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      ...+.|+||++.+  .+++.+ +|||+||+.|+..|+...   +   .+||  .|+..++..++
T Consensus       206 ~~~~~c~i~~~~~--~dPv~~-~~gh~f~~~~i~~~~~~~---~---~~cP--~~~~~~~~~~l  258 (281)
T 2c2l_A          206 PDYLCGKISFELM--REPCIT-PSGITYDRKDIEEHLQRV---G---HFNP--VTRSPLTQEQL  258 (281)
T ss_dssp             CSTTBCTTTCSBC--SSEEEC-SSCCEEETTHHHHHHHHT---C---SSCT--TTCCCCCGGGC
T ss_pred             CcccCCcCcCCHh--cCCeEC-CCCCEECHHHHHHHHHHC---C---CCCc--CCCCCCchhcC
Confidence            3568999999877  566665 799999999999998752   2   2499  68888876553

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

Probab=98.22  E-value=4.2e-07  Score=58.55  Aligned_cols=57  Identities=19%  Similarity=0.548  Sum_probs=43.2

Q ss_pred             CCeeecccccccCCC----CCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhh
Q 043988           11 TPSFVCEICVESRSL----YDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRL   76 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~----~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~   76 (151)
                      +....|+||++.+..    ......+.|||.||..|+..|++..       .+||  .|...+..+++..
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~-------~~CP--~Cr~~~~~~~~~~  130 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA-------NTCP--TCRKKINHKRYHP  130 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHC-------SBCT--TTCCBCCGGGEEE
T ss_pred             CCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcC-------CCCC--CCCCcCChhccee
Confidence            456789999987643    1222445899999999999998752       4899  6999898877644

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

Probab=98.20  E-value=3.3e-06  Score=49.96  Aligned_cols=54  Identities=22%  Similarity=0.509  Sum_probs=40.9

Q ss_pred             CCeeecccccccCCCCCceecCCCC-----CccchHHHHHHHHHHHhCCccccCCCCCCCCCccChh
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCS-----HFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFE   72 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~   72 (151)
                      .....|.||++++...+.+. ++|.     |.|..+||..|+...   +  ...||  -|...+..+
T Consensus        13 ~~~~~C~IC~~~~~~~~~l~-~pC~C~Gs~h~fH~~Cl~~Wl~~~---~--~~~Cp--lCr~~~~~~   71 (80)
T 2d8s_A           13 SSQDICRICHCEGDDESPLI-TPCHCTGSLHFVHQACLQQWIKSS---D--TRCCE--LCKYEFIME   71 (80)
T ss_dssp             TTSCCCSSSCCCCCSSSCEE-CSSSCCSSSCCEETTHHHHHHHHH---C--CSBCS--SSCCBCCCC
T ss_pred             CCCCCCeEcCccccCCCeeE-eccccCCcCCeeCHHHHHHHHhhC---C--CCCCC--CCCCeeecC
Confidence            44568999999887555554 5786     999999999999875   1  36899  588766543

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.14  E-value=2.6e-06  Score=48.77  Aligned_cols=47  Identities=21%  Similarity=0.465  Sum_probs=33.9

Q ss_pred             CCCCeeecccccccCCCCCceecCCCCCc-cchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988            9 DGTPSFVCEICVESRSLYDSFDVKGCSHF-NCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus         9 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      .......|.||++..  .++ .+++|||. ||..|+..           ...||  -|...+..
T Consensus        11 ~~~~~~~C~IC~~~~--~~~-v~~pCgH~~~C~~C~~~-----------~~~CP--~CR~~i~~   58 (68)
T 2ea5_A           11 SEENSKDCVVCQNGT--VNW-VLLPCRHTCLCDGCVKY-----------FQQCP--MCRQFVQE   58 (68)
T ss_dssp             SCCCSSCCSSSSSSC--CCC-EETTTTBCCSCTTHHHH-----------CSSCT--TTCCCCCC
T ss_pred             cCCCCCCCCCcCcCC--CCE-EEECCCChhhhHHHHhc-----------CCCCC--CCCcchhc
Confidence            345578999999765  343 44599999 99999873           25899  58766543

>1wd2_A Ariadne-1 protein homolog; ring, IBR, triad, zinc finger, ligase; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.12  E-value=1.7e-06  Score=48.30  Aligned_cols=49  Identities=27%  Similarity=0.857  Sum_probs=39.8

Q ss_pred             CeeecCcccCCccccccccccCcccCcc--cchhhhhcCCCCC--CC--CCCchhhhh
Q 043988           99 KKFYCPYKDCSSMLIDEGEAIRKSNCPH--CRRLFCVQCKVPW--HS--EFDCSQFQK  150 (151)
Q Consensus        99 ~~~~Cp~~~C~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~--H~--~~~C~~~~~  150 (151)
                      +.+.||  .|+..++..+ ..++|+|..  |++.||+.|+.+|  |.  ..+|..|+.
T Consensus         5 ~~k~CP--~C~~~Iek~~-GCnhmtC~~~~C~~~FCw~C~~~~~~~~~~~y~C~~y~~   59 (60)
T 1wd2_A            5 NTKECP--KCHVTIEKDG-GCNHMVCRNQNCKAEFCWVCLGPWEPHGSAWYNCNRYNE   59 (60)
T ss_dssp             CCCCCT--TTCCCCSSCC-SCCSSSCCSSGGGSCCSSSSCSCSGGGGTSSSSSCSCCC
T ss_pred             cceECc--CCCCeeEeCC-CCCcEEECCCCcCCEEeeCcCCCcccCCCccccCCCccc
Confidence            345788  9999999975 589999987  9999999999998  43  347877664

>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A {Danio rerio} PDB: 2c2v_S 2oxq_C

Probab=98.08  E-value=3.4e-06  Score=57.34  Aligned_cols=53  Identities=9%  Similarity=-0.079  Sum_probs=41.2

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      ...+.||||++.+  .+++.+ +|||+||+.|+..|+...   +   .+||  .|+..++..++
T Consensus       104 p~~f~CPI~~elm--~DPV~~-~~Ghtfer~~I~~~l~~~---~---~tcP--~t~~~l~~~~L  156 (179)
T 2f42_A          104 PDYLCGKISFELM--REPCIT-PSGITYDRKDIEEHLQRV---G---HFDP--VTRSPLTQDQL  156 (179)
T ss_dssp             CGGGBCTTTCSBC--SSEEEC-TTSCEEEHHHHHHHHHHT---C---SBCT--TTCCBCCGGGC
T ss_pred             cHhhcccCccccC--CCCeEC-CCCCEECHHHHHHHHHhC---C---CCCC--CCcCCCChhhC
Confidence            4568999999877  566665 899999999999999762   2   2699  58888876544

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

Probab=98.04  E-value=2e-06  Score=50.06  Aligned_cols=42  Identities=24%  Similarity=0.652  Sum_probs=32.3

Q ss_pred             eeecccccccCCCCCceecCCCCCc-cchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           13 SFVCEICVESRSLYDSFDVKGCSHF-NCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      ...|+||++..  .+++. ++|||. ||..|+..+           ..||  -|...+.
T Consensus        24 ~~~C~iC~~~~--~~~~~-~pCgH~~~C~~C~~~~-----------~~CP--~Cr~~i~   66 (74)
T 4ic3_A           24 EKLCKICMDRN--IAIVF-VPCGHLVTCKQCAEAV-----------DKCP--MCYTVIT   66 (74)
T ss_dssp             HTBCTTTSSSB--CCEEE-ETTCCBCCCHHHHTTC-----------SBCT--TTCCBCS
T ss_pred             CCCCCCCCCCC--CCEEE-cCCCChhHHHHhhhcC-----------ccCC--CcCcCcc
Confidence            46899999866  44544 489999 999997765           5899  5887665

>2ecg_A Baculoviral IAP repeat-containing protein 4; BIRC4, ring domian, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.96  E-value=5e-06  Score=48.45  Aligned_cols=43  Identities=26%  Similarity=0.682  Sum_probs=31.5

Q ss_pred             eeecccccccCCCCCceecCCCCCc-cchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988           13 SFVCEICVESRSLYDSFDVKGCSHF-NCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      ..+|+||++..  .+++. ++|||. ||..|+..           ...||  -|...+..
T Consensus        25 ~~~C~IC~~~~--~~~~~-~pCgH~~~C~~C~~~-----------~~~CP--~Cr~~i~~   68 (75)
T 2ecg_A           25 EKLCKICMDRN--IAIVF-VPCGHLVTCKQCAEA-----------VDKCP--MCYTVITF   68 (75)
T ss_dssp             HHSCSSSCSSC--CCBCC-SSSCCCCBCHHHHHH-----------CSBCT--TTCCBCCC
T ss_pred             CCCCCcCCCCC--CCEEE-ecCCCHHHHHHHhhC-----------CCCCc--cCCceecC
Confidence            45899999876  34443 589999 99999842           25899  58876643

>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=97.90  E-value=1e-05  Score=61.10  Aligned_cols=50  Identities=30%  Similarity=0.682  Sum_probs=37.8

Q ss_pred             eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhH
Q 043988           13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFED   73 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~   73 (151)
                      ..+|+||++..  .+++. .+|||.||..|+..++..      ....||  -|...+....
T Consensus       332 ~~~C~ICle~~--~~pv~-lpCGH~FC~~Ci~~wl~~------~~~~CP--~CR~~i~~~~  381 (389)
T 2y1n_A          332 FQLCKICAEND--KDVKI-EPCGHLMCTSCLTSWQES------EGQGCP--FCRCEIKGTE  381 (389)
T ss_dssp             SSBCTTTSSSB--CCEEE-ETTCCEECHHHHHHHHHH------TCSBCT--TTCCBCCEEE
T ss_pred             CCCCCccCcCC--CCeEE-eCCCChhhHHHHHHHHhc------CCCCCC--CCCCccCCce
Confidence            36999999877  34444 489999999999998864      135899  6887766543

>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=97.87  E-value=4.6e-06  Score=51.99  Aligned_cols=49  Identities=24%  Similarity=0.398  Sum_probs=36.6

Q ss_pred             eecccccccCCCCC---------------ceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988           14 FVCEICVESRSLYD---------------SFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus        14 ~~C~iC~~~~~~~~---------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      .+|.||++.+...-               .+..+.|+|.|+..|+..|+..       ..+||  -|...+..
T Consensus        38 d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~-------~~~CP--~Cr~~~~~  101 (106)
T 3dpl_R           38 DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-------RQVCP--LDNREWEF  101 (106)
T ss_dssp             CCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTT-------CSBCS--SSCSBCCE
T ss_pred             CCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHc-------CCcCc--CCCCccee
Confidence            47999998876431               2344589999999999999764       25899  58876653

>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=97.85  E-value=3.6e-06  Score=47.43  Aligned_cols=50  Identities=20%  Similarity=0.437  Sum_probs=34.3

Q ss_pred             CCeeecccccccCCCCCceecCCCCCc-cchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHF-NCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      +....|+||++...... +.+.+|||. ||.+|...+.+.       .-+||  -|...+.
T Consensus         5 ~~~~~C~IC~~~~~~~~-~~~~pCgH~~~C~~C~~~~~~~-------~~~CP--iCR~~i~   55 (63)
T 2vje_B            5 NLLKPCSLCEKRPRDGN-IIHGRTGHLVTCFHCARRLKKA-------GASCP--ICKKEIQ   55 (63)
T ss_dssp             GGGSBCTTTSSSBSCEE-EEETTEEEEEECHHHHHHHHHT-------TCBCT--TTCCBCC
T ss_pred             CcCCCCcccCCcCCCeE-EEecCCCCHhHHHHHHHHHHHh-------CCcCC--CcCchhh
Confidence            34568999998653211 223489999 999999886542       14899  5877664

>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=97.75  E-value=7.3e-06  Score=46.28  Aligned_cols=48  Identities=21%  Similarity=0.480  Sum_probs=33.8

Q ss_pred             CeeecccccccCCCCCcee-cCCCCCc-cchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           12 PSFVCEICVESRSLYDSFD-VKGCSHF-NCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~-~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      ...+|.||++...  +... .++|||. ||.+|+..+.+.       .-.||  -|...+.
T Consensus         7 ~~~~C~IC~~~~~--~~~~~~~pCgH~~~C~~C~~~~~~~-------~~~CP--iCR~~i~   56 (64)
T 2vje_A            7 AIEPCVICQGRPK--NGCIVHGKTGHLMACFTCAKKLKKR-------NKPCP--VCRQPIQ   56 (64)
T ss_dssp             GGSCCTTTSSSCS--CEEEEETTEEEEEECHHHHHHHHHT-------TCCCT--TTCCCCC
T ss_pred             CcCCCCcCCCCCC--CEEEECCCCCChhhHHHHHHHHHHc-------CCcCC--CcCcchh
Confidence            3458999998653  3332 2389999 899999987642       24799  5877664

>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=97.64  E-value=1.6e-05  Score=46.81  Aligned_cols=43  Identities=35%  Similarity=0.808  Sum_probs=32.1

Q ss_pred             eeecccccccCCCCCceecCCCCCc-cchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988           13 SFVCEICVESRSLYDSFDVKGCSHF-NCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      ...|+||++..  .+++. ++|||. ||..|+..+           ..||  -|...+..
T Consensus        18 ~~~C~IC~~~~--~~~v~-~pCgH~~~C~~C~~~~-----------~~CP--~Cr~~i~~   61 (79)
T 2yho_A           18 AMLCMVCCEEE--INSTF-CPCGHTVCCESCAAQL-----------QSCP--VCRSRVEH   61 (79)
T ss_dssp             HTBCTTTSSSB--CCEEE-ETTCBCCBCHHHHTTC-----------SBCT--TTCCBCCE
T ss_pred             CCEeEEeCccc--CcEEE-ECCCCHHHHHHHHHhc-----------CcCC--CCCchhhC
Confidence            45899999765  44444 489999 999998753           2899  58876654

>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=97.59  E-value=1.2e-05  Score=50.95  Aligned_cols=50  Identities=24%  Similarity=0.417  Sum_probs=0.0

Q ss_pred             eecccccccCCCCC---------------ceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChh
Q 043988           14 FVCEICVESRSLYD---------------SFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFE   72 (151)
Q Consensus        14 ~~C~iC~~~~~~~~---------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~   72 (151)
                      -+|.||++++....               .+..+.|+|.|+..|+..|++..       -.||  -|...+...
T Consensus        49 d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~-------~~CP--~Cr~~~~~~  113 (117)
T 4a0k_B           49 DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTR-------QVCP--LDNREWEFQ  113 (117)
T ss_dssp             --------------------------------------------------------------------------
T ss_pred             CcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcC-------CcCC--CCCCeeeee
Confidence            48999999885321               22234799999999999998773       4799  587765443

>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=97.16  E-value=0.00059  Score=37.95  Aligned_cols=52  Identities=13%  Similarity=0.185  Sum_probs=38.6

Q ss_pred             eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHh
Q 043988           13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR   75 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~   75 (151)
                      .+.|+|+++.+.  +++....+||.|++.++.+|++..   +    +||.  .+..+...++.
T Consensus         3 ~~~CpIs~~~m~--dPV~~~~sG~~yer~~I~~~l~~~---~----~cP~--t~~~L~~~~Li   54 (61)
T 2bay_A            3 HMLCAISGKVPR--RPVLSPKSRTIFEKSLLEQYVKDT---G----NDPI--TNEPLSIEEIV   54 (61)
T ss_dssp             -CCCTTTCSCCS--SEEEETTTTEEEEHHHHHHHHHHH---S----BCTT--TCCBCCGGGCE
T ss_pred             eEEecCCCCCCC--CCEEeCCCCcEEcHHHHHHHHHhC---C----CCcC--CcCCCChhhcE
Confidence            478999998774  555543799999999999999864   2    4884  56677766653

>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=97.09  E-value=0.00013  Score=54.51  Aligned_cols=42  Identities=21%  Similarity=0.706  Sum_probs=32.3

Q ss_pred             eeecccccccCCCCCceecCCCCCc-cchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           13 SFVCEICVESRSLYDSFDVKGCSHF-NCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      ...|+||++..  .+++.+ +|||. ||..|+..+           ..||  -|...+.
T Consensus       295 ~~~C~IC~~~~--~~~v~l-pCgH~~fC~~C~~~~-----------~~CP--~CR~~i~  337 (345)
T 3t6p_A          295 ERTCKVCMDKE--VSVVFI-PCGHLVVCQECAPSL-----------RKCP--ICRGIIK  337 (345)
T ss_dssp             TCBCTTTSSSB--CCEEEE-TTCCEEECTTTGGGC-----------SBCT--TTCCBCC
T ss_pred             CCCCCccCCcC--CceEEc-CCCChhHhHHHHhcC-----------CcCC--CCCCCcc
Confidence            46899999876  445544 89999 999998754           5899  5887664

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

Probab=97.06  E-value=0.00034  Score=40.50  Aligned_cols=51  Identities=20%  Similarity=0.434  Sum_probs=37.6

Q ss_pred             CCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      +...+|.||++.+...  .....|+|.|-..|+..|++.+-     .-+||  .|...+.
T Consensus        13 ~~i~~C~IC~~~i~~g--~~C~~C~h~fH~~Ci~kWl~~~~-----~~~CP--~Cr~~w~   63 (74)
T 2ct0_A           13 DAVKICNICHSLLIQG--QSCETCGIRMHLPCVAKYFQSNA-----EPRCP--HCNDYWP   63 (74)
T ss_dssp             SSSCBCSSSCCBCSSS--EECSSSCCEECHHHHHHHSTTCS-----SCCCT--TTCSCCC
T ss_pred             CCCCcCcchhhHcccC--CccCCCCchhhHHHHHHHHHhcC-----CCCCC--CCcCcCC
Confidence            4457899999887542  23448999999999999986531     25899  5776654

>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=97.04  E-value=0.0022  Score=37.20  Aligned_cols=60  Identities=20%  Similarity=0.335  Sum_probs=42.6

Q ss_pred             cccCCCCCeeecccccccCCCCCceecCC-CCCccchHHHHHHHHHHHhCCccccCCCCC-CCC
Q 043988            5 AETDDGTPSFVCEICVESRSLYDSFDVKG-CSHFNCTSCIVRYIASKLEGNITNISCPQL-GCE   66 (151)
Q Consensus         5 a~~~~~~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~-~C~   66 (151)
                      +........+.|.+|-+.+...-+++... =.|+||..|-+.+|+.+...  ..+.||.. +|.
T Consensus         7 ~~~~~~~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~q~~~--~EvyCPSG~kCp   68 (93)
T 2cs3_A            7 GSPMANSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKAQGAT--GEVYCPSGEKCP   68 (93)
T ss_dssp             SCSSCSCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHHHHSS--SCCCCTTSSCCB
T ss_pred             CCCCCCCCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHhcCCC--CcEECCCCCccc
Confidence            33444567889999998886655554321 26999999999999998643  46888852 454

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

Probab=96.96  E-value=0.001  Score=49.51  Aligned_cols=63  Identities=21%  Similarity=0.429  Sum_probs=44.4

Q ss_pred             CCCCeeecccccccCCC-CCce----ecCCCCCccchHHHHHHHHHHHhC----CccccCCCCCCCCCccChhH
Q 043988            9 DGTPSFVCEICVESRSL-YDSF----DVKGCSHFNCTSCIVRYIASKLEG----NITNISCPQLGCEARLEFED   73 (151)
Q Consensus         9 ~~~~~~~C~iC~~~~~~-~~~~----~~~~C~H~fC~~Cl~~~~~~~i~~----~~~~i~CP~~~C~~~~~~~~   73 (151)
                      +++...+|+|||+.+.. ..++    ....|+|.|-..|+.+|+++.-..    ++..=.||  -|+..++...
T Consensus       304 ~ee~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CP--yCr~pIs~sf  375 (381)
T 3k1l_B          304 EDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCP--FCKAKLSTSF  375 (381)
T ss_dssp             CCCSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECT--TTCCEEEGGG
T ss_pred             cccCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCC--CCCCcCCccH
Confidence            34567899999988765 2222    124799999999999999987543    12234799  6988877443

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=96.70  E-value=0.0012  Score=40.06  Aligned_cols=46  Identities=22%  Similarity=0.542  Sum_probs=30.3

Q ss_pred             ecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           15 VCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        15 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      -|++|--  +......+.+|.|.||.+|...+.+..      .-.||  .|...+.
T Consensus         3 fC~~C~~--Pi~iygRmIPCkHvFCydCa~~~~~~~------~k~Cp--~C~~~V~   48 (101)
T 3vk6_A            3 FCDKCGL--PIKVYGRMIPCKHVFCYDCAILHEKKG------DKMCP--GCSDPVQ   48 (101)
T ss_dssp             BCTTTCS--BCSEEEEEETTCCEEEHHHHHHHHHTT------CCBCT--TTCCBCS
T ss_pred             ecCccCC--CeEEEeeeccccccHHHHHHHHHHhcc------CCCCc--CcCCeee
Confidence            4778853  434444566899999999998876543      12566  4665443

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=96.20  E-value=0.003  Score=38.50  Aligned_cols=28  Identities=21%  Similarity=0.464  Sum_probs=23.5

Q ss_pred             ccCcccCcccchhhhhcCCC-CCCCCCCc
Q 043988          118 AIRKSNCPHCRRLFCVQCKV-PWHSEFDC  145 (151)
Q Consensus       118 ~~~~~~C~~C~~~~C~~C~~-~~H~~~~C  145 (151)
                      ....+.|..|+..+|..|.. ..|.+++-
T Consensus        68 e~l~~fC~~~~~~iC~~C~~~~~H~~H~~   96 (101)
T 2jun_A           68 EKVNMYCVTDDQLICALCKLVGRHRDHQV   96 (101)
T ss_dssp             SCCCEEETTTTEEECHHHHHHTTTSSSCB
T ss_pred             CcceEECCCCCCccchhcCCCCCcCCCCe
Confidence            45788999999999999986 67988764

>1vyx_A ORF K3, K3RING; zinc-binding protein, ring domain, cross-brace motif; NMR {Human herpesvirus 8} SCOP: g.44.1.3

Probab=95.87  E-value=0.018  Score=31.72  Aligned_cols=50  Identities=22%  Similarity=0.394  Sum_probs=34.9

Q ss_pred             CCeeecccccccCCCCCceecCCCC--C---ccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           11 TPSFVCEICVESRSLYDSFDVKGCS--H---FNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~~~~~C~--H---~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      +....|-||+++... . .. .+|.  +   .|-.+||..|+..+-     ...||  -|+..+.
T Consensus         4 ~~~~~CrIC~~~~~~-~-l~-~PC~C~gs~~~~H~~Cl~~W~~~~~-----~~~C~--~C~~~~~   58 (60)
T 1vyx_A            4 EDVPVCWICNEELGN-E-RF-RACGCTGELENVHRSCLSTWLTISR-----NTACQ--ICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSC-C-CC-CSCCCSSGGGSCCHHHHHHHHHHHT-----CSBCT--TTCCBCC
T ss_pred             CCCCEeEEeecCCCC-c-ee-cCcCCCCchhhhHHHHHHHHHHhCC-----CCccC--CCCCeee
Confidence            445689999987432 2 22 4654  4   899999999997652     36899  5876654

>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=91.11  E-value=0.19  Score=33.24  Aligned_cols=86  Identities=16%  Similarity=0.335  Sum_probs=49.3

Q ss_pred             ecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhhcCCHHHHHHHHHHHHhhh
Q 043988           15 VCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRLILPDDVFARWGLALCESA   94 (151)
Q Consensus        15 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~~~~~~~~~~~~~   94 (151)
                      .||+|...+...+.+..             ..+...+.+  +.+.||+.+|+..+...+++..+..              
T Consensus        55 ~CP~Cr~~~~~~~~~~~-------------~~~~~~i~~--l~v~C~n~GC~~~~~~~~l~~H~~~--------------  105 (170)
T 3hcs_A           55 KCPVDNEILLENQLFPD-------------NFAKREILS--LMVKCPNEGCLHKMELRHLEDHQAH--------------  105 (170)
T ss_dssp             BCTTTCCBCCGGGCEEC-------------HHHHHHHHT--SEEECCSTTCCCEEEGGGHHHHHTT--------------
T ss_pred             CCCCCccCcchhhhhhh-------------HHHHHHHhh--cccCCCCCCCCceecHhHHHHHHhc--------------
Confidence            78888766644332221             223333432  4789998899998887775422110              


Q ss_pred             hcCCCeeecCcccCCccccccc--------cccCcccCcccchhhh
Q 043988           95 LVGHKKFYCPYKDCSSMLIDEG--------EAIRKSNCPHCRRLFC  132 (151)
Q Consensus        95 ~~~~~~~~Cp~~~C~~~~~~~~--------~~~~~~~C~~C~~~~C  132 (151)
                       =....+.||  +|+..+....        -..+.+.|+.|+..+-
T Consensus       106 -C~~~~v~C~--~C~~~~~r~~l~~H~~~~C~~r~~~C~~C~~~~~  148 (170)
T 3hcs_A          106 -CEFALMDCP--QCQRPFQKFHINIHILKDCPRRQVSCDNCAASMA  148 (170)
T ss_dssp             -CTTSEEECT--TTCCEEEGGGHHHHHHHTCTTCEEECTTTCCEEE
T ss_pred             -CCceeeECC--CCChHHHHHHHHHHhhhhCCCCCeECCCCCCccC
Confidence             012346788  8998776552        1344556666665543

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

Probab=90.98  E-value=0.13  Score=36.25  Aligned_cols=52  Identities=21%  Similarity=0.488  Sum_probs=38.2

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChh
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFE   72 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~   72 (151)
                      ...+|.+|.+-...  -.....|+|+|-..|+..|++..     ....||  .|+..++.+
T Consensus       179 ~i~~C~iC~~iv~~--g~~C~~C~~~~H~~C~~~~~~~~-----~~~~CP--~C~~~W~~~  230 (238)
T 3nw0_A          179 AVKICNICHSLLIQ--GQSCETCGIRMHLPCVAKYFQSN-----AEPRCP--HCNDYWPHE  230 (238)
T ss_dssp             TCCBCTTTCSBCSS--CEECSSSCCEECHHHHHHHTTTC-----SSCBCT--TTCCBCCSC
T ss_pred             CCCcCcchhhHHhC--CcccCccChHHHHHHHHHHHHhC-----CCCCCC--CCCCCCCCC
Confidence            46789999976653  24444699999999999998642     246899  688776554

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=87.39  E-value=3.8  Score=26.40  Aligned_cols=77  Identities=19%  Similarity=0.308  Sum_probs=44.3

Q ss_pred             cCCCCCeeecccccccCCCCCceecCCCCCccchHHHHHHHH----HHHhCCccccCCCCCCCCCccChhHHhhcCCHHH
Q 043988            7 TDDGTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIA----SKLEGNITNISCPQLGCEARLEFEDCRLILPDDV   82 (151)
Q Consensus         7 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~----~~i~~~~~~i~CP~~~C~~~~~~~~i~~~l~~~~   82 (151)
                      .++......|.+|.   ...+.+-...|.-.||..|+..-+.    ..|.....+-.||  .|... +...+...+ ..+
T Consensus        57 ~d~Dg~~d~C~vC~---~GG~LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~--~C~~~-pl~~l~~~c-~~~  129 (142)
T 2lbm_A           57 RDSDGMDEQCRWCA---EGGNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCY--ICHPE-PLLDLVTAC-NSV  129 (142)
T ss_dssp             BCTTSCBCSCSSSC---CCSSEEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCT--TTCCC-TTHHHHHHH-HHH
T ss_pred             ecCCCCCCeecccC---CCCcEEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEee--cccCc-cHHHHHHHH-HHH
Confidence            34444566899997   3456677778999999999997663    2331111234788  46532 223332222 235


Q ss_pred             HHHHHHHH
Q 043988           83 FARWGLAL   90 (151)
Q Consensus        83 ~~~~~~~~   90 (151)
                      ++.+++++
T Consensus       130 ~~~~~~~~  137 (142)
T 2lbm_A          130 FENLEQLL  137 (142)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            55555544

>2d8v_A Zinc finger FYVE domain-containing protein 19; zfyve19, ZF- B_BOX, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.43.1.1

Probab=86.06  E-value=0.51  Score=26.22  Aligned_cols=36  Identities=22%  Similarity=0.517  Sum_probs=27.4

Q ss_pred             CCCCeeecccccccCCCCCceecCCC-CCccchHHHHHHHH
Q 043988            9 DGTPSFVCEICVESRSLYDSFDVKGC-SHFNCTSCIVRYIA   48 (151)
Q Consensus         9 ~~~~~~~C~iC~~~~~~~~~~~~~~C-~H~fC~~Cl~~~~~   48 (151)
                      ++++..-|.||.++.    .+....| +-.||..|+++...
T Consensus         4 ~~ee~pWC~ICneDA----tlrC~gCdgDLYC~rC~rE~H~   40 (67)
T 2d8v_A            4 GSSGLPWCCICNEDA----TLRCAGCDGDLYCARCFREGHD   40 (67)
T ss_dssp             SCCCCSSCTTTCSCC----CEEETTTTSEEECSSHHHHHTT
T ss_pred             cCcCCCeeEEeCCCC----eEEecCCCCceehHHHHHHHcc
Confidence            344556799998875    3556689 88999999999763

>3qt1_I DNA-directed RNA polymerases I, II, and III subun; transferase-transcription complex, RNA polymerase II, transc elongation; 4.30A {Saccharomyces cerevisiae}

Probab=84.29  E-value=0.54  Score=30.06  Aligned_cols=32  Identities=22%  Similarity=0.470  Sum_probs=24.2

Q ss_pred             CCeeecCcccCCcccccccc---ccCcccCcccchhh
Q 043988           98 HKKFYCPYKDCSSMLIDEGE---AIRKSNCPHCRRLF  131 (151)
Q Consensus        98 ~~~~~Cp~~~C~~~~~~~~~---~~~~~~C~~C~~~~  131 (151)
                      ....+||  .|+.++....+   ....+.|+.|++..
T Consensus        22 ~~~~FCP--eCgNmL~pked~~~~~l~~~CrtCgY~~   56 (133)
T 3qt1_I           22 TTFRFCR--DCNNMLYPREDKENNRLLFECRTCSYVE   56 (133)
T ss_dssp             CCCCBCT--TTCCBCBCCBCTTTCCBCCBCSSSCCBC
T ss_pred             cCCeeCC--CCCCEeeECccCCCceeEEECCCCCCcE
Confidence            3456999  99999987743   35679999998853

>1fre_A Nuclear factor XNF7; zinc-binding protein, BBOX, development, MID-blastula- transition; NMR {Xenopus laevis} SCOP: g.43.1.1

Probab=82.82  E-value=0.74  Score=22.73  Aligned_cols=27  Identities=26%  Similarity=0.385  Sum_probs=22.9

Q ss_pred             ccCcccCcccchhhhhcCCC-CCCCCCC
Q 043988          118 AIRKSNCPHCRRLFCVQCKV-PWHSEFD  144 (151)
Q Consensus       118 ~~~~~~C~~C~~~~C~~C~~-~~H~~~~  144 (151)
                      ....+.|..++..+|..|.. ..|.+++
T Consensus        11 e~l~lfC~~d~~~iC~~C~~~~~H~~H~   38 (42)
T 1fre_A           11 ERLKLYCKDDGTLSCVICRDSLKHASHN   38 (42)
T ss_dssp             SSCCCCCCSSSSSSCCTTSSCSSCTTCC
T ss_pred             CeeeEEeCCCCeEEeccCCCCCCCCCCc
Confidence            56788999999999999998 6688775

>1z60_A TFIIH basal transcription factor complex P44 subunit; basic transcription factor, zinc binding protein, ring finger; NMR {Homo sapiens} SCOP: g.49.1.2

Probab=82.74  E-value=0.15  Score=27.91  Aligned_cols=36  Identities=33%  Similarity=0.820  Sum_probs=26.4

Q ss_pred             ecCcccCCccccccccccCcccCcccchhhhhcCCCCCCCCC
Q 043988          102 YCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPWHSEF  143 (151)
Q Consensus       102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~  143 (151)
                      .|-  .|...+..    ...+.|+.|+..||..|-.-.|+.+
T Consensus        17 ~C~--~C~~~~~~----~~~y~C~~C~~~FC~dCD~fiHe~L   52 (59)
T 1z60_A           17 FCY--GCQGELKD----QHVYVCAVCQNVFCVDCDVFVHDSL   52 (59)
T ss_dssp             EET--TTTEECTT----SEEECCTTTTCCBCHHHHHTTTTTS
T ss_pred             ccc--ccCcccCC----CccEECCccCcCcccchhHHHHhhc
Confidence            465  67665532    1237899999999999999888743

---

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	151
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	2e-07

>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 = 44.3 bits (104), Expect = 2e-07
 Identities = 18/79 (22%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 11 TPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKL-EGNITNISCPQLGC--EA 67
          + S  C++C+    +     +  C    CT C+ +Y+   + EG  T ISCP   C  + 
Sbjct: 3  SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQG 62

Query: 68 RLEFEDCRLILPDDVFARW 86
           L+  +   ++  ++  R+
Sbjct: 63 HLQENEIECMVAAEIMQRY 81

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	151
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	99.83
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	99.59
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	98.99
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	98.95
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	98.92
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	98.84
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.8
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	98.78
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	98.74
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	98.74
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	98.72
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	98.7
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.68
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	98.62
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	98.61
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.28
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.21
d1wd2a_	60	Ariadne-1 protein homolog {Human (Homo sapiens) [T	98.19
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	97.93
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	96.61
d1frea_	39	Nuclear factor XNF7 {African clawed frog (Xenopus	88.12
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	86.44
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	85.6
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	83.58
d2csva1	59	Tripartite motif-containing protein 29 {Human (Hom	81.72
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	81.4
d2o35a1	79	Hypothetical protein SMc04008 {Rhizobium meliloti	80.03

>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=99.83  E-value=5e-21  Score=117.06  Aligned_cols=87  Identities=20%  Similarity=0.450  Sum_probs=75.9

Q ss_pred             CCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCC-ccccCCCCCCCCC--ccChhHHhhcCCHHHHHHH
Q 043988           10 GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGN-ITNISCPQLGCEA--RLEFEDCRLILPDDVFARW   86 (151)
Q Consensus        10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~-~~~i~CP~~~C~~--~~~~~~i~~~l~~~~~~~~   86 (151)
                      +.+..+|+||+++++..+++.++.|+|.||.+||..|++.+|.++ ..+|+||..+|+.  .+...+|+.+|+++++++|
T Consensus         2 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~~~i~~ll~~~~~~ky   81 (94)
T d1wima_           2 SSGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQENEIECMVAAEIMQRY   81 (94)
T ss_dssp             CCSBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECHHHHHHHSCHHHHHHH
T ss_pred             CCCCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCCCCCcccCHHHHHHhCCHHHHHHH
Confidence            456779999999998888888889999999999999999999865 4579999888864  5788999999999999999


Q ss_pred             HHHHHhhhhc
Q 043988           87 GLALCESALV   96 (151)
Q Consensus        87 ~~~~~~~~~~   96 (151)
                      +++.++....
T Consensus        82 ~~~~l~~~~~   91 (94)
T d1wima_          82 KKLQFERSGP   91 (94)
T ss_dssp             HHHHHHSSCS
T ss_pred             HHHHHHhccc
Confidence            9998886543

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: IBR domain
domain: Ring finger protein 31
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.4e-17  Score=96.61  Aligned_cols=64  Identities=34%  Similarity=0.771  Sum_probs=54.7

Q ss_pred             HHHHHHHhhhhcCC-CeeecCcccCCccccccccccCcccCcccchhhhhcCCCCC---CCCCCchhhhhC
Q 043988           85 RWGLALCESALVGH-KKFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPW---HSEFDCSQFQKL  151 (151)
Q Consensus        85 ~~~~~~~~~~~~~~-~~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~---H~~~~C~~~~~~  151 (151)
                      +|++++++..|... +.+|||  +|+..++.++ +.+.++|+.|++.||+.|+.+|   |.|.+|++|++|
T Consensus         2 ~Y~~~l~~~~l~~~~~~k~CP--~C~~~~~~~~-~~~~~~C~~C~~~fC~~C~~~w~~~H~~~tC~~~~~w   69 (73)
T d2ct7a1           2 LFHKKLTEGVLMRDPKFLWCA--QCSFGFIYER-EQLEATCPQCHQTFCVRCKRQWEEQHRGRSCEDFQNW   69 (73)
T ss_dssp             SSSSCCCCSCCCSCCCEECCS--SSCCCEECCC-SCSCEECTTTCCEECSSSCSBCCTTTTTSCHHHHHHH
T ss_pred             hHHHHHHHHHHHHCCCCCCCC--CCCCEeEECC-CCCEEEcCCCCCeECcccCcchhcCCCCCCHHHHHHH
Confidence            35566667777764 567998  8999999875 4788999999999999999999   999999999998

>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=98.99  E-value=4.6e-11  Score=64.05  Aligned_cols=50  Identities=26%  Similarity=0.495  Sum_probs=37.4

Q ss_pred             eecccccccCCCCCc-eecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988           14 FVCEICVESRSLYDS-FDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus        14 ~~C~iC~~~~~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      .+|+||++++...+. +....|||.||.+|+..|++..      ..+||  .|...++.
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~------~~~CP--~CR~~~~~   51 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDE------NGLCP--ACRKPYPE   51 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTS------CCBCT--TTCCBCSC
T ss_pred             CCCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhc------CCCCC--ccCCcCCC
Confidence            489999998865433 3445899999999999987532      34799  68877754

>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=98.95  E-value=5.6e-10  Score=68.16  Aligned_cols=69  Identities=17%  Similarity=0.403  Sum_probs=48.1

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHh-hcCCHHHHHHHHHH
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR-LILPDDVFARWGLA   89 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~-~~l~~~~~~~~~~~   89 (151)
                      +.++|+||++.+  .+++.+ .|||.||..|+..|+...    .....||  -|+..+...+++ ...-.+.++++.+.
T Consensus        20 ~~l~CpIC~~~~--~~pv~~-~CgH~fC~~Ci~~~~~~~----~~~~~CP--~Cr~~~~~~~l~~n~~l~~~ve~l~~~   89 (103)
T d1jm7a_          20 KILECPICLELI--KEPVST-KCDHIFCKFCMLKLLNQK----KGPSQCP--LCKNDITKRSLQESTRFSQLVEELLKI   89 (103)
T ss_dssp             HHTSCSSSCCCC--SSCCBC-TTSCCCCSHHHHHHHHSS----SSSCCCT--TTSCCCCTTTCBCCCSSSHHHHHHHHH
T ss_pred             cCcCCCccCchh--CCeEEc-CCCCchhhHHHHHHHHHC----CCCCcCc--CCCCcCChhhCCcCHHHHHHHHHHHHH
Confidence            346899999877  455554 799999999999987542    2246899  699888877763 22223556666543

>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=98.92  E-value=3.7e-10  Score=66.53  Aligned_cols=53  Identities=28%  Similarity=0.615  Sum_probs=41.1

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHh
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR   75 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~   75 (151)
                      +.+.|+||++.+  .+++. +.|||.||+.|+..|++..      .-+||  .|+..+...++.
T Consensus        22 ~~l~C~IC~~~~--~~pv~-~~CgH~FC~~Ci~~~~~~~------~~~CP--~Cr~p~~~~~l~   74 (86)
T d1rmda2          22 KSISCQICEHIL--ADPVE-TSCKHLFCRICILRCLKVM------GSYCP--SCRYPCFPTDLE   74 (86)
T ss_dssp             HHTBCTTTCSBC--SSEEE-CTTSCEEEHHHHHHHHHHT------CSBCT--TTCCBCCGGGCB
T ss_pred             cCcCCccCCcch--hccee-cCCCChhhHHHHHHHHhhC------CCcCc--ccCCCCChhhcc
Confidence            446899999877  45555 4899999999999998653      23799  688888777654

>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=98.84  E-value=4.2e-10  Score=62.97  Aligned_cols=55  Identities=24%  Similarity=0.455  Sum_probs=39.4

Q ss_pred             eeecccccccCCC--CCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHh
Q 043988           13 SFVCEICVESRSL--YDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR   75 (151)
Q Consensus        13 ~~~C~iC~~~~~~--~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~   75 (151)
                      ..+|+||++++..  ...+.+..|||.||.+|+..|+...      .-.||  .|+..+...+++
T Consensus         3 d~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~------~~~CP--~CR~~i~~~~~~   59 (65)
T d1g25a_           3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRG------AGNCP--ECGTPLRKSNFR   59 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTT------SSSCT--TTCCCCSSCCCE
T ss_pred             CCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcC------cCCCC--CCCcCccccccc
Confidence            3589999986432  2223345899999999999998532      23699  699888776654

>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=98.80  E-value=1.4e-09  Score=62.95  Aligned_cols=65  Identities=20%  Similarity=0.322  Sum_probs=46.5

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHh-hcCCHHHHHHHH
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCR-LILPDDVFARWG   87 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~-~~l~~~~~~~~~   87 (151)
                      ..+.|+||++.+  .+++.+ .|||.||+.|+..|+...      .-.||  .|...+...++. ++.-.+.++.|.
T Consensus         7 ~~l~CpIc~~~m--~dPV~~-~cgh~fc~~ci~~~~~~~------~~~cP--~~~~~l~~~~l~pN~~L~~~I~~~~   72 (78)
T d1t1ha_           7 EYFRCPISLELM--KDPVIV-STGQTYERSSIQKWLDAG------HKTCP--KSQETLLHAGLTPNYVLKSLIALWC   72 (78)
T ss_dssp             SSSSCTTTSCCC--SSEEEE-TTTEEEEHHHHHHHHTTT------CCBCT--TTCCBCSSCCCEECTTTHHHHHHHH
T ss_pred             ccCCCcCcCchh--hCceEc-cCCCcchHHHHHHHHHHC------CCCCC--cccccCCcccccchHHHHHHHHHHH
Confidence            468999999877  566665 899999999999998642      24688  577777766653 343345566553

>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=98.78  E-value=3.1e-09  Score=57.55  Aligned_cols=51  Identities=14%  Similarity=0.102  Sum_probs=41.3

Q ss_pred             ecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHHhh
Q 043988           15 VCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDCRL   76 (151)
Q Consensus        15 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i~~   76 (151)
                      .|+||++.+  .+++....|||.||++|+.+|++..       -+||  -|+..+..+++-.
T Consensus         2 ~C~Ic~~~~--~~Pv~~~~cGh~fc~~cI~~~l~~~-------~~CP--~c~~~l~~~dLip   52 (56)
T d2baya1           2 LCAISGKVP--RRPVLSPKSRTIFEKSLLEQYVKDT-------GNDP--ITNEPLSIEEIVE   52 (56)
T ss_dssp             CCTTTCSCC--SSEEEETTTTEEEEHHHHHHHHHHH-------SBCT--TTCCBCCGGGCEE
T ss_pred             CCccCCchH--HhcCccCCCCCcccHHHHHHHHhhc-------cCCC--ccCCcCCHHhcee
Confidence            699999877  5666666799999999999999874       2699  5888888877643

>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=98.74  E-value=1.6e-09  Score=58.46  Aligned_cols=48  Identities=19%  Similarity=0.509  Sum_probs=36.8

Q ss_pred             eeecccccccCCCCCcee-cCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCcc
Q 043988           13 SFVCEICVESRSLYDSFD-VKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARL   69 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~   69 (151)
                      ..+|+||++++...+.+. +..|+|.|+.+|+..|++.+       -+||  -|+..|
T Consensus         5 ~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~-------~~CP--~CR~~i   53 (55)
T d1iyma_           5 GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSH-------STCP--LCRLTV   53 (55)
T ss_dssp             SCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTC-------CSCS--SSCCCS
T ss_pred             CCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhC-------CcCC--CCCCEe
Confidence            357999999998665554 45799999999999998542       3799  577654

>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=98.74  E-value=2.8e-09  Score=61.99  Aligned_cols=52  Identities=12%  Similarity=-0.066  Sum_probs=40.0

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      ..+.|+||++.+  .+++. +.|||+||++|+..|+...      .-.||  .|+..++..++
T Consensus         6 ~~l~CpIc~~l~--~dPv~-~~cGhtfc~~ci~~~l~~~------~~~cP--~c~~~l~~~~l   57 (80)
T d2c2la2           6 DYLCGKISFELM--REPCI-TPSGITYDRKDIEEHLQRV------GHFNP--VTRSPLTQEQL   57 (80)
T ss_dssp             STTBCTTTCSBC--SSEEE-CSSCCEEETTHHHHHHHHT------CSSCT--TTCCCCCGGGC
T ss_pred             ccccCcCcCchh--hhhcc-cCCcCeecHHHHHHHHhcC------CccCC--Ccccccccccc
Confidence            457899999877  55665 4899999999999998652      24688  57777776654

>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=98.72  E-value=4.9e-09  Score=59.01  Aligned_cols=47  Identities=34%  Similarity=0.695  Sum_probs=36.2

Q ss_pred             eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      ..+|+||++.+.  +....++|||.||..|+..|++.+       -+||  -|+..+.
T Consensus         5 ~d~C~IC~~~~~--~~~~~~~C~H~Fc~~Ci~~w~~~~-------~~CP--~CR~~i~   51 (68)
T d1chca_           5 AERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQN-------PTCP--LCKVPVE   51 (68)
T ss_dssp             CCCCSSCCSCCC--SCEEETTTTEEESTTHHHHHHHHS-------CSTT--TTCCCCC
T ss_pred             CCCCccCCcCcc--CCcEEeCCCCcCcHHHHHHHHHhC-------CcCC--CCCcchH
Confidence            347999998874  344556999999999999998752       4799  5887654

>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=98.70  E-value=5.3e-09  Score=60.59  Aligned_cols=48  Identities=31%  Similarity=0.749  Sum_probs=36.0

Q ss_pred             eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988           13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      ...|+||++.+  .+++ +++|||.||.+|+..|+...      .-+||  -|+..|..
T Consensus        23 ~~~C~IC~~~~--~~~~-~~~CgH~fC~~Ci~~wl~~~------~~~CP--~Cr~~i~~   70 (79)
T d1fbva4          23 FQLCKICAEND--KDVK-IEPCGHLMCTSCLTSWQESE------GQGCP--FCRCEIKG   70 (79)
T ss_dssp             TTBCTTTSSSB--CCEE-CSSSCCEECHHHHHHHHHTT------CCSCT--TTCCCCCC
T ss_pred             CCCCccCCCcC--CCeE-EeCCCCeeeHHHHHHHHHHC------cCcCC--CCCcCccC
Confidence            34799999876  3444 45899999999999998642      24799  58877653

>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=98.68  E-value=1.1e-09  Score=66.07  Aligned_cols=50  Identities=24%  Similarity=0.623  Sum_probs=37.5

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      ..++|+||++.+.  +++.+..|||.||.+|+..|+.         -.||  .|+..+...++
T Consensus        21 ~~l~C~IC~~~~~--~pv~~~~CgH~fC~~Ci~~~~~---------~~CP--~Cr~~~~~~~l   70 (97)
T d1jm7b_          21 KLLRCSRCTNILR--EPVCLGGCEHIFCSNCVSDCIG---------TGCP--VCYTPAWIQDL   70 (97)
T ss_dssp             HTTSCSSSCSCCS--SCBCCCSSSCCBCTTTGGGGTT---------TBCS--SSCCBCSCSSC
T ss_pred             hcCCCccCCchhh--cCceeCCCCCchhHHHHHHHHh---------cccc--ccCCcCchhhC
Confidence            3468999999884  4555557999999999988862         2599  68877765544

>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=98.62  E-value=4.5e-09  Score=56.78  Aligned_cols=48  Identities=21%  Similarity=0.490  Sum_probs=35.2

Q ss_pred             CCCeeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChh
Q 043988           10 GTPSFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFE   72 (151)
Q Consensus        10 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~   72 (151)
                      ..+..+|+||++.+.  +++. ++|||.||..|+.+          ...+||  -|+..++..
T Consensus         3 e~~~l~C~IC~~~~~--~p~~-lpCgH~fC~~Ci~~----------~~~~CP--~Cr~~~~~~   50 (56)
T d1bora_           3 EFQFLRCQQCQAEAK--CPKL-LPCLHTLCSGCLEA----------SGMQCP--ICQAPWPLG   50 (56)
T ss_dssp             SCCCSSCSSSCSSCB--CCSC-STTSCCSBTTTCSS----------SSSSCS--SCCSSSSCC
T ss_pred             ccCCCCCcccCcccC--CCEE-ecCCCHHhHHHHHc----------CCCcCc--CCCCcccCC
Confidence            345679999998874  4444 48999999999742          246899  688777644

>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=98.61  E-value=1.7e-08  Score=62.38  Aligned_cols=56  Identities=21%  Similarity=0.417  Sum_probs=40.2

Q ss_pred             CeeecccccccCCC---------------CCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988           12 PSFVCEICVESRSL---------------YDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus        12 ~~~~C~iC~~~~~~---------------~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      ...+|+||++++..               ...+.++.|+|.||.+||..|++..-.  ...++||  -|+..+..
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~--~~~~~CP--~CR~~~~~   94 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNK--DGSLQCP--SCKTIYGE   94 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCC--SSCCBCT--TTCCBSSS
T ss_pred             ccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCc--CCCCccc--cccchhcc
Confidence            34579999998642               123455689999999999999976432  2357999  58766543

>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=98.28  E-value=4.9e-07  Score=49.22  Aligned_cols=53  Identities=21%  Similarity=0.274  Sum_probs=37.2

Q ss_pred             CCeeecccccccCCCCCce--ecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccC
Q 043988           11 TPSFVCEICVESRSLYDSF--DVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLE   70 (151)
Q Consensus        11 ~~~~~C~iC~~~~~~~~~~--~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~   70 (151)
                      +....|.||++++......  ...+|+|.|+..||..|+..+-     ..+||  -|...+.
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~-----~~~CP--~Cr~~~~   58 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISR-----NTACQ--ICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHT-----CSBCT--TTCCBCC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCC-----CCCCc--ccCCeee
Confidence            4456899999987643322  1234569999999999997752     35899  5877654

>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=98.21  E-value=4.9e-07  Score=54.19  Aligned_cols=51  Identities=18%  Similarity=0.101  Sum_probs=37.6

Q ss_pred             eeecccccccCCCCCceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccChhHH
Q 043988           13 SFVCEICVESRSLYDSFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEFEDC   74 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~~~i   74 (151)
                      .+.||||.+.+  .+++.+..|+|.||+.|+..|+...       -.||  -|+..+...++
T Consensus        22 ~f~CPI~~~lm--~dPV~~~~~~~ty~r~~I~~~l~~~-------~~~P--~~~~~l~~~~L   72 (98)
T d1wgma_          22 EFLDPIMSTLM--CDPVVLPSSRVTVDRSTIARHLLSD-------QTDP--FNRSPLTMDQI   72 (98)
T ss_dssp             TTBCTTTCSBC--SSEEECTTTCCEEEHHHHHHHTTTS-------CBCT--TTCSBCCTTTS
T ss_pred             HhCCcCchhHH--HHHHhcccccchhhHHHHHHHHHhc-------CCcc--cccccccchhh
Confidence            58999999877  6677664455789999999997531       2678  46777776554

>d1wd2a_ g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Ariadne-1 protein homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.19  E-value=4.7e-07  Score=49.18  Aligned_cols=49  Identities=27%  Similarity=0.862  Sum_probs=38.9

Q ss_pred             CeeecCcccCCccccccccccCcccCc--ccchhhhhcCCCCC--C--CCCCchhhhh
Q 043988           99 KKFYCPYKDCSSMLIDEGEAIRKSNCP--HCRRLFCVQCKVPW--H--SEFDCSQFQK  150 (151)
Q Consensus        99 ~~~~Cp~~~C~~~~~~~~~~~~~~~C~--~C~~~~C~~C~~~~--H--~~~~C~~~~~  150 (151)
                      +...||  .|+..++..+ +.++|+|.  .|+..||+.|+++|  |  ....|..|++
T Consensus         5 ntK~CP--~C~~~ieK~~-GCnhM~C~~~~C~~~fCw~C~~~~~~~~~~~~~C~~~~e   59 (60)
T d1wd2a_           5 NTKECP--KCHVTIEKDG-GCNHMVCRNQNCKAEFCWVCLGPWEPHGSAWYNCNRYNE   59 (60)
T ss_dssp             CCCCCT--TTCCCCSSCC-SCCSSSCCSSGGGSCCSSSSCSCSGGGGTSSSSSCSCCC
T ss_pred             cCcCCC--CCCCeEEECC-CCCCeEeCCCCCCCeEECCCCCccccCCCCCCCCcCCcc
Confidence            356788  9999999864 58999994  69999999999988  3  3456777654

>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=97.93  E-value=2.8e-06  Score=49.70  Aligned_cols=50  Identities=24%  Similarity=0.399  Sum_probs=36.1

Q ss_pred             eeecccccccCCCCC---------------ceecCCCCCccchHHHHHHHHHHHhCCccccCCCCCCCCCccCh
Q 043988           13 SFVCEICVESRSLYD---------------SFDVKGCSHFNCTSCIVRYIASKLEGNITNISCPQLGCEARLEF   71 (151)
Q Consensus        13 ~~~C~iC~~~~~~~~---------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~~~~   71 (151)
                      ..+|.||++++....               .+..+.|||.|+.+||..|++.+       -+||  -|...+..
T Consensus        21 ~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~-------~~CP--~CR~~~~~   85 (88)
T d3dplr1          21 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTR-------QVCP--LDNREWEF   85 (88)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTC-------SBCS--SSCSBCCE
T ss_pred             CCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHC-------CcCC--CCCCcccc
Confidence            346999987765322               23445899999999999998652       3799  58876654

>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=96.61  E-value=0.0031  Score=34.23  Aligned_cols=51  Identities=22%  Similarity=0.384  Sum_probs=38.3

Q ss_pred             CCCeeecccccccCCCCCceecCC-CCCccchHHHHHHHHHHHhCCccccCCCC
Q 043988           10 GTPSFVCEICVESRSLYDSFDVKG-CSHFNCTSCIVRYIASKLEGNITNISCPQ   62 (151)
Q Consensus        10 ~~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   62 (151)
                      +...+.|.+|-+-+...-+++..+ =+|.||..|-+.+|+.+..++  .+.||.
T Consensus         5 ~~~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~q~~~~--evyCPS   56 (80)
T d2cs3a1           5 NSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKAQGATG--EVYCPS   56 (80)
T ss_dssp             SCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHHHHSSS--CCCCTT
T ss_pred             CCCceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHhcCCCC--cEECCC
Confidence            344589999998886655554321 279999999999999987554  688885

>d1frea_ g.43.1.1 (A:) Nuclear factor XNF7 {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Small proteins
fold: B-box zinc-binding domain
superfamily: B-box zinc-binding domain
family: B-box zinc-binding domain
domain: Nuclear factor XNF7
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=88.12  E-value=0.14  Score=24.17  Aligned_cols=29  Identities=24%  Similarity=0.381  Sum_probs=24.0

Q ss_pred             cccCcccCcccchhhhhcCCC-CCCCCCCc
Q 043988          117 EAIRKSNCPHCRRLFCVQCKV-PWHSEFDC  145 (151)
Q Consensus       117 ~~~~~~~C~~C~~~~C~~C~~-~~H~~~~C  145 (151)
                      ++...+.|..|+..+|..|.. ..|.+++-
T Consensus         7 ~e~l~lfC~~d~~~iC~~C~~~~~H~~H~v   36 (39)
T d1frea_           7 DERLKLYCKDDGTLSCVICRDSLKHASHNF   36 (39)
T ss_dssp             CSSCCCCCCSSSSSSCCTTSSCSSCTTCCC
T ss_pred             CcceeEEcccCCcEeeccCcCCCCcCCCcE
Confidence            456789999999999999976 46988763

>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=86.44  E-value=0.056  Score=28.11  Aligned_cols=37  Identities=30%  Similarity=0.717  Sum_probs=27.6

Q ss_pred             eeecCcccCCccccccccccCcccCcccchhhhhcCCCCCCCC
Q 043988          100 KFYCPYKDCSSMLIDEGEAIRKSNCPHCRRLFCVQCKVPWHSE  142 (151)
Q Consensus       100 ~~~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~  142 (151)
                      ..+|-  +|+..+.    +...+.|++|+..||..|-.-.|+.
T Consensus        15 ~~~C~--gC~~~l~----~~~~y~C~~C~~~FC~dCD~fiHe~   51 (59)
T d1z60a1          15 ERFCY--GCQGELK----DQHVYVCAVCQNVFCVDCDVFVHDS   51 (59)
T ss_dssp             CCEET--TTTEECT----TSEEECCTTTTCCBCHHHHHTTTTT
T ss_pred             CCCcc--CCCCcCC----CCceEECcCCCCccccccchhhhhh
Confidence            34666  6765442    2345889999999999999988874

>d2akla2 g.41.3.5 (A:3-40) Hypothetical protein PA0128, N-terminal domain {Pseudomonas aeruginosa [TaxId: 287]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: PhnA zinc-binding domain
domain: Hypothetical protein PA0128, N-terminal domain
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=85.60  E-value=0.089  Score=24.73  Aligned_cols=26  Identities=31%  Similarity=0.643  Sum_probs=17.8

Q ss_pred             ecCcccCCccccccccccCcccCcccchhh
Q 043988          102 YCPYKDCSSMLIDEGEAIRKSNCPHCRRLF  131 (151)
Q Consensus       102 ~Cp~~~C~~~~~~~~~~~~~~~C~~C~~~~  131 (151)
                      .||  .|+.-....+  ...+.||.|+++|
T Consensus         5 ~CP--~C~seytYed--g~l~vCPeC~hEW   30 (38)
T d2akla2           5 PCP--QCNSEYTYED--GALLVCPECAHEW   30 (38)
T ss_dssp             CCT--TTCCCCCEEC--SSSEEETTTTEEE
T ss_pred             cCC--CCCCcceEcC--CCEEECCcccCcC
Confidence            466  8887666654  3557888887764

>d1z60a1 g.49.1.2 (A:328-386) TFIIH p44 subunit cysteine-rich domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: TFIIH p44 subunit cysteine-rich domain
domain: TFIIH p44 subunit cysteine-rich domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.58  E-value=0.33  Score=25.06  Aligned_cols=31  Identities=16%  Similarity=0.353  Sum_probs=24.4

Q ss_pred             CeeecccccccCCCCCceecCCCCCccchHH
Q 043988           12 PSFVCEICVESRSLYDSFDVKGCSHFNCTSC   42 (151)
Q Consensus        12 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~C   42 (151)
                      ....|--|..++.....+....|++.||.+|
T Consensus        14 ~~~~C~gC~~~l~~~~~y~C~~C~~~FC~dC   44 (59)
T d1z60a1          14 GERFCYGCQGELKDQHVYVCAVCQNVFCVDC   44 (59)
T ss_dssp             SCCEETTTTEECTTSEEECCTTTTCCBCHHH
T ss_pred             CCCCccCCCCcCCCCceEECcCCCCcccccc
Confidence            4567989987776555566778999999999

>d2csva1 g.43.1.1 (A:8-66) Tripartite motif-containing protein 29 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: B-box zinc-binding domain
superfamily: B-box zinc-binding domain
family: B-box zinc-binding domain
domain: Tripartite motif-containing protein 29
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.72  E-value=0.075  Score=27.65  Aligned_cols=31  Identities=13%  Similarity=0.233  Sum_probs=26.3

Q ss_pred             cccCcccCcccchhhhhcCCCCCCCCCCchh
Q 043988          117 EAIRKSNCPHCRRLFCVQCKVPWHSEFDCSQ  147 (151)
Q Consensus       117 ~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~  147 (151)
                      +....+.|..|+..+|..|....|.|++-..
T Consensus        18 ~e~l~lyC~~c~~~iC~~C~~~~H~~H~~~~   48 (59)
T d2csva1          18 GKTMELFCQTDQTCICYLCMFQEHKNHSTVT   48 (59)
T ss_dssp             CCBCCEEESSSCCEECHHHHHTTTSSSCEEE
T ss_pred             CCccceECCCCCceECcccCcccCCCCCeeC
Confidence            4567899999999999999888899987543

>d2cura1 g.39.1.3 (A:33-63) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.40  E-value=1  Score=19.62  Aligned_cols=30  Identities=17%  Similarity=0.483  Sum_probs=20.8

Q ss_pred             cccccccCCCCCceecCCCCCccchHHHHHHH
Q 043988           16 CEICVESRSLYDSFDVKGCSHFNCTSCIVRYI   47 (151)
Q Consensus        16 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~   47 (151)
                      |.-|-.++....+..+  =.+.||.+|.+..+
T Consensus         2 C~~C~K~Lag~rFTa~--eDq~yCVdCYK~~v   31 (31)
T d2cura1           2 CVTCSKKLAGQRFTAV--EDQYYCVDCYKNFV   31 (31)
T ss_dssp             CTTTCCBCTTSCEEEC--SSCEEEHHHHHHHH
T ss_pred             cccccchhcCceeEEe--cceEEEeeeecccC
Confidence            5667666666555554  47899999988753

>d2o35a1 a.293.1.1 (A:2-80) Hypothetical protein SMc04008 {Rhizobium meliloti [TaxId: 382]}

class: All alpha proteins
fold: SMc04008-like
superfamily: SMc04008-like
family: SMc04008-like
domain: Hypothetical protein SMc04008
species: Rhizobium meliloti [TaxId: 382]

Probab=80.03  E-value=0.57  Score=25.43  Aligned_cols=17  Identities=18%  Similarity=0.452  Sum_probs=14.1

Q ss_pred             ccchHHHHHHHHHHHhC
Q 043988           37 FNCTSCIVRYIASKLEG   53 (151)
Q Consensus        37 ~fC~~Cl~~~~~~~i~~   53 (151)
                      -||++||..|......+
T Consensus        39 GFCRNCLskWy~~~a~~   55 (79)
T d2o35a1          39 GFCRNCLSNWYREAAEA   55 (79)
T ss_dssp             SCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            39999999999877654