Citrus Sinensis ID: 048114

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230----
Protein Sequence
LHILNFVPQNTPFGKAKKPFSSRSVTEKGQCSNSKNEVTIEERIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRCSSNPQL
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccccccccccccccHHHHHccccHHHHHHHHHHHHHHHHccccEEcccccccccEEEcccccccccEEccccccccccccccccccccccHHHHHHHHccccHHHHHHHHHHHcccccccccccccEEEccccccEEccccccc
Secondary Structure Prediction (SSPRO)
cEEEEccccccccccHHHHHHHHcHHcccccccccccccccccccccccccEEEcccccHHcccccccccHHHHHHHHHHHHEEHHcccEEEEcccccccccccHHHHHHHccHHHHHHHHHHHHHHHccccccEEccccccccEEEEcccccccccEEcccccEEEEcccccccccccHHHHHHHHcccccccHHHHHHHHHHcccccccccccEEEEcccccEEEEEccccc
Coil and Loop (DISEMBL)
lhilnfvpqntpfgkakkpfssrsvtekgqcsnsknevtIEERIETSFICdicvepkstdesfsikgcshsycTECMTKYVASKLQEnitsincpvadckgvlepeycrdilpedvfnRWGNALCEAVILGAQkfycpfkdcsallIDDGGEairesvcpdcnrmfcaqckvpwhagircaefqklhkderepeDIMLMTLAQKenwrrcpnckifvekkegcrymrcssnpql
Flexible Loop (DISEMBL)
lhilnfvpqntpfgkakkpfssrsvtekgqcsnsknevtieeriETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQklhkderepEDIMLMTLaqkenwrrcpnckifvekkegcrymrcssnpql
Low Complexity Region (SEG)
LHILNFVPQNTPFGKAKKPFSSRSVTEKGQCSNSKNEVTIEERIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRCSSNPQL
Disordered region (IsUnstruct)
**************************************TIEERIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKD****EDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMR*******
Disordered Region (DISOPRED)
LHILNFVPQ***************************************ICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQ**************MTLAQKENWRRCPNCKIFVEKKEGCRYMRCSSNPQL
Disordered Region (DISEMBL)
LHILNFVPQNTPFGKAK*******************EVTIEERIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRCSSNPQL
Disordered Region (DISPRO)
LHILNFVPQNTPFGKAKKPFSSRSVTEK*****************TSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRCSSNPQL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
LHILNFVPQNTPFGKAKKPFSSRSVTEKGQCSNSKNEVTIEERIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRCSSNPQL
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	234	2.2.26 [Sep-21-2011]
Q4KLT0	282	Probable E3 ubiquitin-pro	N/A	no	0.739	0.613	0.272	7e-14
P50876	292	Probable E3 ubiquitin-pro	yes	no	0.846	0.678	0.258	3e-13
A4IIY1	292	Probable E3 ubiquitin-pro	no	no	0.846	0.678	0.248	4e-13
Q925F3	292	Probable E3 ubiquitin-pro	yes	no	0.846	0.678	0.253	6e-13
D3YYI7	515	Probable E3 ubiquitin-pro	no	no	0.730	0.332	0.269	7e-13
Q7Z419	303	E3 ubiquitin-protein liga	no	no	0.752	0.580	0.280	2e-12
A5PK27	304	E3 ubiquitin-protein liga	no	no	0.747	0.575	0.279	7e-12
Q8BKD6	301	E3 ubiquitin-protein liga	no	no	0.743	0.578	0.275	9e-12
Q9JI90	485	E3 ubiquitin-protein liga	no	no	0.773	0.373	0.234	9e-12
Q9UBS8	474	E3 ubiquitin-protein liga	no	no	0.773	0.381	0.244	2e-11

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

 Score = 77.4 bits (189), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 51/187 (27%), Positives = 87/187 (46%), Gaps = 14/187 (7%)

Query: 50  CDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR 109
           C +C+E +S      +  C    C EC+ +Y++S++Q     I CP+ +C   L+     
Sbjct: 3   CRVCLEDRSIK---PLPCCKKPVCDECLKRYLSSQVQLGQAEIQCPITECNKHLDESTIL 59

Query: 110 DILPEDVFNRWGNALCEAVILGAQKFYCP-------FKDCSALLIDDGGEAIRESVCPDC 162
             LP D   ++   L E   + +    CP       FK  + +      E   +  CP C
Sbjct: 60  YSLPHDDIIKYKYFL-ELSRMDSSTKPCPQCKHFTTFKRKTHIPNPTKSENKLKIQCPSC 118

Query: 163 NRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEG 222
             ++C +C  PWH G+ C E++K  K  R   + +      + N ++CP CK+ +++ EG
Sbjct: 119 QFIWCFRCHAPWHEGVNCREYKKGDKLLRHWANEIEHG---QRNAQKCPRCKVHIQRTEG 175

Query: 223 CRYMRCS 229
           C +M CS
Sbjct: 176 CDHMTCS 182

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: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

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

 Score = 75.5 bits (184), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 53/205 (25%), Positives = 93/205 (45%), Gaps = 7/205 (3%)

Query: 32  SNSKNEVTIEERIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENI-T 90
           + ++   T +  ++    C +C+     ++  +I  C   +CT C+ +YV   ++E + T
Sbjct: 2   TTTRYRPTWDLALDPLVSCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLET 61

Query: 91  SINCPVADC--KGVLEPEYCRDILPEDVFNRWGNALCE-AVILGAQKFYCPFKDCSAL-- 145
           +I+CP A C  +G L+      ++  ++  R+     E  V+    + +CP   C A+  
Sbjct: 62  AISCPDAACPKQGHLQENEIECMVAAEIMQRYKKLQFEREVLFDPCRTWCPASTCQAVCQ 121

Query: 146 LIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKE 205
           L D G +  +   C  C   FC+ CK  WH G  C E   +     E      M      
Sbjct: 122 LQDVGLQTPQPVQCKACRMEFCSTCKASWHPGQGCPETMPITFLPGETSAAFKME-EDDA 180

Query: 206 NWRRCPNCKIFVEKKEGCRYMRCSS 230
             +RCP CK+++E+ EGC  M C +
Sbjct: 181 PIKRCPKCKVYIERDEGCAQMMCKN 205

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|A4IIY1|R144A_XENTR Probable E3 ubiquitin-protein ligase RNF144A OS=Xenopus tropicalis GN=rnf144a PE=2 SV=1

 Score = 75.1 bits (183), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 51/205 (24%), Positives = 97/205 (47%), Gaps = 7/205 (3%)

Query: 32  SNSKNEVTIEERIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENI-T 90
           + ++   T +  +E    C +C+   + ++  +I  C   +CT C+ +YV   ++E + T
Sbjct: 2   TTARYRPTWDLALEPLVSCKLCLGEYTVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLET 61

Query: 91  SINCPVADC--KGVLEPEYCRDILPEDVFNRWGNALCEA-VILGAQKFYCPFKDCSAL-- 145
           +I+CP A C  +G L+      ++  ++  ++     E  ++L   + +CP   C A+  
Sbjct: 62  AISCPDASCPKRGHLQENEIECMVAAEIMQKYKKLQFEKEILLDPCRTWCPSSSCQAVCK 121

Query: 146 LIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKE 205
           L + G +  +   C  C+  FC+ CK  WH G  C E   +     +       +L    
Sbjct: 122 LQEKGIQNPQLVQCSACDIEFCSACKANWHPGQGCPENMAITFLPGDSSSF-FKSLEDDV 180

Query: 206 NWRRCPNCKIFVEKKEGCRYMRCSS 230
             +RCP CK+++E+ EGC  M C +
Sbjct: 181 PIKRCPKCKVYIERDEGCAQMMCKN 205

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.

Xenopus tropicalis (taxid: 8364)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q925F3|R144A_MOUSE Probable E3 ubiquitin-protein ligase RNF144A OS=Mus musculus GN=Rnf144a PE=1 SV=1

 Score = 74.3 bits (181), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 52/205 (25%), Positives = 94/205 (45%), Gaps = 7/205 (3%)

Query: 32  SNSKNEVTIEERIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENI-T 90
           + ++   T +  ++    C +C+     ++  +I  C   +CT C+ +YV   ++E + T
Sbjct: 2   TTARYRPTWDLALDPLVSCKLCLGEYPAEQMTTIAQCQCIFCTLCLKQYVELLIKEGLET 61

Query: 91  SINCPVADC--KGVLEPEYCRDILPEDVFNRWGNALCE-AVILGAQKFYCPFKDCSAL-- 145
           +I+CP A C  +G L+      ++  ++  R+     E  V+    + +CP   C A+  
Sbjct: 62  AISCPDAACPKQGHLQENEIECMVAAEIMQRYKKLQFEREVLFDPCRTWCPASTCQAVCQ 121

Query: 146 LIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKE 205
           L D G +  +   C  C+  FC+ CK  WH G  C E   +     E      M      
Sbjct: 122 LQDIGLQTPQLVQCKACDMEFCSACKARWHPGQGCPETMPITFLPGETSSAFKMEEGDAP 181

Query: 206 NWRRCPNCKIFVEKKEGCRYMRCSS 230
             +RCP C++++E+ EGC  M C +
Sbjct: 182 I-KRCPKCRVYIERDEGCAQMMCKN 205

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.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|D3YYI7|RN217_MOUSE Probable E3 ubiquitin-protein ligase RNF217 OS=Mus musculus GN=Rnf217 PE=3 SV=2

 Score = 74.3 bits (181), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 52/193 (26%), Positives = 82/193 (42%), Gaps = 22/193 (11%)

Query: 48  FICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY 107
            +C +C+E K       +  C  + C EC+  Y++S++Q     I CPV +C   LE   
Sbjct: 234 LMCRVCLEDKPIK---PLPCCKKAVCEECLKIYLSSQVQLGQVEIKCPVTECFEFLEETT 290

Query: 108 C------RDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPD 161
                   D +    F   G            K +  FK    +      E+  +  CP 
Sbjct: 291 VVYNLTHEDSIKYKYFLELGRIDSSTKPCPQCKHFTTFKKKGHIPTPSRSESRYKIQCPT 350

Query: 162 CNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQ-----KENWRRCPNCKIF 216
           C  ++C +C  PWH G+ C E++K         D +L   A      + N ++CP CKI 
Sbjct: 351 CQLIWCFKCHSPWHEGVNCKEYKK--------GDKLLRHWASEIEHGQRNAQKCPKCKIH 402

Query: 217 VEKKEGCRYMRCS 229
           +++ EGC +M CS
Sbjct: 403 IQRTEGCDHMTCS 415

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.

Mus musculus (taxid: 10090)

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 = 72.8 bits (177), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 53/189 (28%), Positives = 87/189 (46%), Gaps = 13/189 (6%)

Query: 48  FICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITS-INCPVADC--KGVLE 104
             C +C+  +S D+  +++ C   +CT C+ +Y+   ++E   S I CP   C   G L+
Sbjct: 28  ITCKLCLCEQSLDKMTTLQECQCIFCTACLKQYMQLAIREGCGSPITCPDMVCLNHGTLQ 87

Query: 105 PEYCRDILPEDVFNRWGNALCE-AVILGAQKFYCPFKDCSALL----IDDGGEAIRESVC 159
                 ++P D F  +     E  V L   + +CP  DC  +      D G   + E  C
Sbjct: 88  EAEIACLVPVDQFQLYQRLKFEREVHLDPYRTWCPVADCQTVCPVASSDPGQPVLVE--C 145

Query: 160 PDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEK 219
           P C+  FC+ CK  WHA + C + Q +       E   L     +   ++CP C++++E+
Sbjct: 146 PSCHLKFCSCCKDAWHAEVSCRDSQPI---VLPTEHRALFGTDAEAPIKQCPVCRVYIER 202

Query: 220 KEGCRYMRC 228
            EGC  M C
Sbjct: 203 NEGCAQMMC 211

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

 Score = 70.9 bits (172), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 52/186 (27%), Positives = 85/186 (45%), Gaps = 11/186 (5%)

Query: 50  CDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITS-INCPVADC--KGVLEPE 106
           C +C+  +S D+  +++ C   +CT C+ +Y+   ++E   S I CP   C   G L+  
Sbjct: 31  CKLCLCEQSLDKMTTLQECRCIFCTACLKQYMQLAIREGCGSPITCPDMVCLNHGTLQEA 90

Query: 107 YCRDILPEDVFNRWGNALCE-AVILGAQKFYCPFKDCSAL---LIDDGGEAIRESVCPDC 162
               ++P D F  +     E  V L   + +CP  DC  +      D G+ +    CP C
Sbjct: 91  EIACLVPVDQFQLYQRLKFEREVHLDPCRTWCPVADCQTVCPVATSDPGQPVLVE-CPSC 149

Query: 163 NRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEG 222
           +  FC+ CK  WHA + C + Q         E   L         ++CP C++++E+ EG
Sbjct: 150 HLKFCSCCKDAWHAEVSCRDSQ---PGILPTEHGTLFGTETDAPIKQCPVCRVYIERNEG 206

Query: 223 CRYMRC 228
           C  M C
Sbjct: 207 CAQMMC 212

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 = 70.5 bits (171), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 51/185 (27%), Positives = 83/185 (44%), Gaps = 11/185 (5%)

Query: 50  CDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITS-INCPVADC--KGVLEPE 106
           C +C+  +S D+   ++ C   +CT C+ +Y+   ++E   S I CP   C   G L+  
Sbjct: 30  CKLCLCEQSLDKMTMLQECQCIFCTPCLKQYMVLSIREGCGSPITCPDMVCLNHGTLQET 89

Query: 107 YCRDILPEDVFNRWGNALCE-AVILGAQKFYCPFKDCSALLIDDGGEAIRESV--CPDCN 163
               ++P D F  +     E  V +   + +CP  DC  +     G+  +  +  CP C+
Sbjct: 90  EIACLVPLDEFQLYQRLKFEREVHMDPLRTWCPVADCQTVCHISAGDPGQPVLVECPSCH 149

Query: 164 RMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGC 223
             FC+ CK  WH    C + Q        PE   L         ++CP C+I++E+ EGC
Sbjct: 150 LKFCSCCKDAWHEESSCRDSQ-----SAMPEHGALFGTDADAPIKQCPVCRIYIERNEGC 204

Query: 224 RYMRC 228
             M C
Sbjct: 205 AQMMC 209

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|Q9JI90|RNF14_MOUSE E3 ubiquitin-protein ligase RNF14 OS=Mus musculus GN=Rnf14 PE=2 SV=2

 Score = 70.5 bits (171), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 49/209 (23%), Positives = 89/209 (42%), Gaps = 28/209 (13%)

Query: 48  FICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQEN-ITSINCPVADCKGVLEPE 106
           F+C IC   K   +      C H YC  C+  Y   ++++  +  +NCP   C  V  P 
Sbjct: 219 FLCSICFCEKLGSDCMYFLECKHVYCKACLKDYFEIQIKDGQVKCLNCPEPQCPSVATPG 278

Query: 107 YCRDILPEDVFNRWGNALCEAVI-LGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRM 165
             ++++  D+F R+   L ++ + L A   YCP   C   ++ + G  +  ++C  CN  
Sbjct: 279 QVKELVEADLFARYDRLLLQSTLDLMADVVYCPRPCCQLPVMQEPGGTM--AICSSCNFA 336

Query: 166 FCAQCKVPWHA-----------------GIRCAEFQKLHKDEREPEDIMLMTLAQKE--- 205
           FC  C++ +H                   ++  E  K   ++R  + ++   L + E   
Sbjct: 337 FCTLCRLTYHGLSPCKVTAEKLIDLRNEYLQADEATKRFLEQRYGKRVIQKALEEMESKD 396

Query: 206 ----NWRRCPNCKIFVEKKEGCRYMRCSS 230
               N + CP C   ++K +GC  M C+ 
Sbjct: 397 WLEKNSKSCPCCGTPIQKLDGCNKMTCTG 425

Might act as an E3 ubiquitin-protein ligase which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates, which could be nuclear proteins. Could play a role as a coactivator for androgen- and, to a lesser extent, progesterone-dependent transcription.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9UBS8|RNF14_HUMAN E3 ubiquitin-protein ligase RNF14 OS=Homo sapiens GN=RNF14 PE=1 SV=1

 Score = 69.7 bits (169), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 51/209 (24%), Positives = 88/209 (42%), Gaps = 28/209 (13%)

Query: 48  FICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQEN-ITSINCPVADCKGVLEPE 106
           F+C IC   K   E      C H YC  C+  Y   ++++  +  +NCP   C  V  P 
Sbjct: 218 FLCSICFCEKLGSECMYFLECRHVYCKACLKDYFEIQIRDGQVQCLNCPEPKCPSVATPG 277

Query: 107 YCRDILPEDVFNRWGNALCEAVI-LGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRM 165
             ++++  ++F R+   L ++ + L A   YCP   C   ++ + G  +   +C  CN  
Sbjct: 278 QVKELVEAELFARYDRLLLQSSLDLMADVVYCPRPCCQLPVMQEPGCTM--GICSSCNFA 335

Query: 166 FCAQCKVPWHA-----------------GIRCAEFQKLHKDEREPEDIMLMTLAQKE--- 205
           FC  C++ +H                   ++  E  K   D+R  + ++   L + E   
Sbjct: 336 FCTLCRLTYHGVSPCKVTAEKLMDLRNEYLQADEANKRLLDQRYGKRVIQKALEEMESKE 395

Query: 206 ----NWRRCPNCKIFVEKKEGCRYMRCSS 230
               N + CP C   +EK +GC  M C+ 
Sbjct: 396 WLEKNSKSCPCCGTPIEKLDGCNKMTCTG 424

Might act as an E3 ubiquitin-protein ligase which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates, which could be nuclear proteins. Could play a role as a coactivator for androgen- and, to a lesser extent, progesterone-dependent transcription.

Homo sapiens (taxid: 9606)

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	234
224142755	307	predicted protein [Populus trichocarpa]	0.965	0.736	0.649	7e-85
255550303	400	zinc finger protein, putative [Ricinus c	0.927	0.542	0.625	2e-81
225444595	358	PREDICTED: probable E3 ubiquitin-protein	0.948	0.620	0.620	6e-80
297738503	329	unnamed protein product [Vitis vinifera]	0.948	0.674	0.620	8e-80
356558463	685	PREDICTED: uncharacterized protein LOC10	0.905	0.309	0.545	2e-67
356530471	333	PREDICTED: putative uncharacterized prot	0.905	0.636	0.537	9e-63
297820104	322	zinc finger family protein [Arabidopsis	0.854	0.621	0.523	1e-60
224032067	332	unknown [Zea mays] gi|414885478|tpg|DAA6	0.914	0.644	0.504	2e-60
224035271	349	unknown [Zea mays]	0.888	0.595	0.513	2e-59
414885476	349	TPA: putative RING zinc finger domain su	0.888	0.595	0.513	2e-59

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

 Score =  319 bits (817), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 152/234 (64%), Positives = 180/234 (76%), Gaps = 8/234 (3%)

Query: 1   LHILNFVPQNTPFGKAKKPFSSRSVTEKGQCSNSKNEVTIEERIETSFICDICVEPKSTD 60
           + +L+F+P+  P  K K+P    SV EKGQ SNS+        I+  F+C ICVEP    
Sbjct: 59  IKVLDFLPEVIPSRKQKEPTFIESVAEKGQSSNSQ--------IDPDFVCQICVEPTILK 110

Query: 61  ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRW 120
            SF IKGC+H+YCTECM KYV+SKLQENIT I CPV DCKG LEPE CR +LPE+VF+RW
Sbjct: 111 NSFLIKGCTHAYCTECMVKYVSSKLQENITKICCPVPDCKGALEPEDCRSVLPENVFDRW 170

Query: 121 GNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRC 180
           GNALCEAVILG+QKFYCPFKDCSA+LIDDG E +RES CP+C RMFCAQCKVPWH+ I C
Sbjct: 171 GNALCEAVILGSQKFYCPFKDCSAMLIDDGEEVVRESECPNCWRMFCAQCKVPWHSQISC 230

Query: 181 AEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRCSSNPQL 234
            E++ LHKDERE +DI+LM LA+ +NWRRCP C+IFVEK EGCRYM+C    Q 
Sbjct: 231 EEYKMLHKDERERDDILLMNLAKNKNWRRCPKCRIFVEKIEGCRYMKCRCGTQF 284

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  308 bits (788), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 145/232 (62%), Positives = 175/232 (75%), Gaps = 15/232 (6%)

Query: 1   LHILNFVP----QNTPFGKAKKPFSSRSVTEKGQCSNSKNEVTIEERIETSFICDICVEP 56
           L +L+F P         GK +  FS   VTEKG  S        E      F+C+ICVE 
Sbjct: 165 LRVLDFTPLPATSKKEMGKNRFGFS---VTEKGHSS--------EPNDHPQFVCEICVES 213

Query: 57  KSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDV 116
           K+ DES +I+GC+H+YCT+CM KYVASK+QENIT I CPV+ C G+LEPEYCR ILP++V
Sbjct: 214 KTADESLAIRGCTHAYCTDCMAKYVASKIQENITGIYCPVSGCGGLLEPEYCRSILPQEV 273

Query: 117 FNRWGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHA 176
           F+RWGNALCEA+ LG+QKFYCPFKDCSA+LI+DGGE IRES CP C R+FCA CKVPWH+
Sbjct: 274 FDRWGNALCEALNLGSQKFYCPFKDCSAMLINDGGEVIRESECPHCRRLFCAHCKVPWHS 333

Query: 177 GIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRC 228
           GI C +FQ LHKDERE EDIMLM LA+ + WRRCP C+I+VE+ EGCRYM+C
Sbjct: 334 GIDCNKFQTLHKDEREKEDIMLMKLAENKKWRRCPICRIYVERTEGCRYMKC 385

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  302 bits (774), Expect = 6e-80,   Method: Compositional matrix adjust.
 Identities = 142/229 (62%), Positives = 175/229 (76%), Gaps = 7/229 (3%)

Query: 1   LHILNFVPQNTPFG-KAKKPFSSRSVTEKGQCSNSKNEVTIEERIETSFICDICVEPKST 59
           L IL   P  TP     +KPF+  SVTE GQ SNSK +         +F+C+IC++PK  
Sbjct: 81  LQILGINPPTTPHAFSTRKPFTFPSVTETGQPSNSKPDPP------PTFVCEICIDPKPL 134

Query: 60  DESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNR 119
           + SFSIKGC HSYC++CMTKYVASKLQ+N++ I+CP  +C GVLEP+ CR ILP  VF+R
Sbjct: 135 NHSFSIKGCPHSYCSDCMTKYVASKLQDNVSRISCPAPNCTGVLEPQQCRPILPSHVFDR 194

Query: 120 WGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIR 179
           WGNALCEA+ILG+QKFYCP+KDCSALLI D GE I+ES CP+C R+FCAQC+VPWH+GI 
Sbjct: 195 WGNALCEALILGSQKFYCPYKDCSALLIRDEGEVIKESECPNCRRLFCAQCEVPWHSGID 254

Query: 180 CAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRC 228
           C EFQKL+KDER  EDI++M LA+  NW+RCP CK +VEK  GC Y+RC
Sbjct: 255 CGEFQKLNKDERGREDILMMNLAKTNNWKRCPKCKFYVEKSFGCMYIRC 303

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  302 bits (773), Expect = 8e-80,   Method: Compositional matrix adjust.
 Identities = 142/229 (62%), Positives = 175/229 (76%), Gaps = 7/229 (3%)

Query: 1   LHILNFVPQNTPFG-KAKKPFSSRSVTEKGQCSNSKNEVTIEERIETSFICDICVEPKST 59
           L IL   P  TP     +KPF+  SVTE GQ SNSK +         +F+C+IC++PK  
Sbjct: 81  LQILGINPPTTPHAFSTRKPFTFPSVTETGQPSNSKPDPP------PTFVCEICIDPKPL 134

Query: 60  DESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNR 119
           + SFSIKGC HSYC++CMTKYVASKLQ+N++ I+CP  +C GVLEP+ CR ILP  VF+R
Sbjct: 135 NHSFSIKGCPHSYCSDCMTKYVASKLQDNVSRISCPAPNCTGVLEPQQCRPILPSHVFDR 194

Query: 120 WGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIR 179
           WGNALCEA+ILG+QKFYCP+KDCSALLI D GE I+ES CP+C R+FCAQC+VPWH+GI 
Sbjct: 195 WGNALCEALILGSQKFYCPYKDCSALLIRDEGEVIKESECPNCRRLFCAQCEVPWHSGID 254

Query: 180 CAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRC 228
           C EFQKL+KDER  EDI++M LA+  NW+RCP CK +VEK  GC Y+RC
Sbjct: 255 CGEFQKLNKDERGREDILMMNLAKTNNWKRCPKCKFYVEKSFGCMYIRC 303

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  261 bits (666), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 125/229 (54%), Positives = 160/229 (69%), Gaps = 17/229 (7%)

Query: 1   LHILNFVPQNTPFGKAKKPFSSRSVTEKGQCSNSKNEVTIEERIETSFICDICVEPKSTD 60
           + ILNF P NT FGK +K  SS     KG+CS++             F+C+IC E K+  
Sbjct: 95  VRILNFTPPNTSFGKRRKKSSS-----KGECSST-----------APFLCEICTETKTDR 138

Query: 61  ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRW 120
           +SFSI GC H YC  C+ +YV SKL++N+ +I CPV  C+G+LE +YCR+IL   VF+RW
Sbjct: 139 DSFSITGCRHVYCNSCVAQYVESKLEDNVVNIPCPVPGCRGLLEADYCREILSPRVFDRW 198

Query: 121 GNALCEAVILGAQKFYCPFKDCSALLIDDGGEA-IRESVCPDCNRMFCAQCKVPWHAGIR 179
           GNALCEAVI   +KFYCPF DCSA+LI    +A IRE  CP+C R+FCA C+VPWH  I 
Sbjct: 199 GNALCEAVIDAEEKFYCPFADCSAMLIRASEDADIRECECPNCRRLFCALCRVPWHENIP 258

Query: 180 CAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRC 228
           C EFQKL+ +ERE EDIMLM+LA++  W+RCP+C+ +V K EGC YMRC
Sbjct: 259 CEEFQKLNAEEREREDIMLMSLAKQMQWKRCPHCRFYVAKSEGCMYMRC 307

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  245 bits (626), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 123/229 (53%), Positives = 154/229 (67%), Gaps = 17/229 (7%)

Query: 1   LHILNFVPQNTPFGKAKKPFSSRSVTEKGQCSNSKNEVTIEERIETSFICDICVEPKSTD 60
           + ILNF P NT FGK  K       + KG+CSNS            SF+C+IC E K+  
Sbjct: 95  VRILNFTPINTSFGKRSK-----KSSSKGECSNS-----------ASFVCEICTETKTAR 138

Query: 61  ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRW 120
           +SFSI GC H YC  C+ +YV SKL+ENI SI CPV  C+G+LE + CR+IL   VF+RW
Sbjct: 139 DSFSIIGCHHVYCNSCVAQYVESKLEENIVSIPCPVPGCRGLLEADDCREILAPRVFDRW 198

Query: 121 GNALCEAVILGAQKFYCPFKDCSALLIDDGGE-AIRESVCPDCNRMFCAQCKVPWHAGIR 179
           G ALCEAVI   +KFYCPF DCS +LI    E  IRE+ CP+C R+FCAQC+VPWH  + 
Sbjct: 199 GKALCEAVIAAEEKFYCPFADCSVMLIRGIEENNIREAECPNCRRLFCAQCRVPWHDNMP 258

Query: 180 CAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRC 228
           C +FQKL+ DER+ EDIMLM LA +  W+RCP C+ +V K +GC YM+C
Sbjct: 259 CEDFQKLNADERDKEDIMLMNLANQMQWKRCPRCRFYVAKSDGCMYMKC 307

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  238 bits (607), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 110/210 (52%), Positives = 152/210 (72%), Gaps = 10/210 (4%)

Query: 19  PFSSRSVTEKGQCSNSKNEVTIEERIETSFICDICVEPKSTDESFSIKGCSHSYCTECMT 78
           P  ++S+ EKGQ S+S            +F C+ICVE KS  E+F I GCSH YC +C++
Sbjct: 97  PIHTKSL-EKGQSSSSAT---------VTFDCEICVETKSIIETFRIGGCSHFYCNDCVS 146

Query: 79  KYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCEAVILGAQKFYCP 138
           KY+A+KLQ+NI SI CPV+ C G LEP+ CR ILP +VF+RWG+ALCEAV++ +++FYCP
Sbjct: 147 KYIAAKLQDNILSIECPVSGCSGRLEPDQCRQILPREVFDRWGDALCEAVVMRSKRFYCP 206

Query: 139 FKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIML 198
           +KDCSALL  D  E +++S CP C+RM C +C   WH  + C EFQKL ++ER  +DI+L
Sbjct: 207 YKDCSALLFMDESEVMKDSECPHCHRMVCVECGTKWHPEMTCEEFQKLAENERGRDDILL 266

Query: 199 MTLAQKENWRRCPNCKIFVEKKEGCRYMRC 228
            T+A+K+ W+RCP+CK ++EK  GC YM+C
Sbjct: 267 ATMAKKKKWKRCPSCKFYIEKSHGCLYMKC 296

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224032067|gb|ACN35109.1| unknown [Zea mays] gi|414885478|tpg|DAA61492.1| TPA: putative RING zinc finger domain superfamily protein [Zea mays]

 Score =  238 bits (606), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 113/224 (50%), Positives = 152/224 (67%), Gaps = 10/224 (4%)

Query: 15  KAKKPFSSRSVTEKGQCSNSKNEVTIEERIETSFICDICVEPKSTDESFSIKGCSHSYCT 74
           K KKP  S ++ E GQCS   +       I +   C IC+E     ESF + GC+H++C 
Sbjct: 110 KGKKPLGSSTIQELGQCSRGAST-----NISSELYCAICMETVHIGESFPVDGCTHTFCI 164

Query: 75  ECMTKYVASKLQENITSINCPVADCK-GVLEPEYCRDILPEDVFNRWGNALCEAVILGAQ 133
            C+++ +A+K++EN+ SI CP   CK GVL P+ CRD++P  +F RWG ALC++  LG+ 
Sbjct: 165 SCVSQCIAAKVEENVLSIGCPAPGCKDGVLHPDACRDVIPAQLFQRWGAALCDSS-LGSL 223

Query: 134 KFYCPFKDCSALLIDDGG---EAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDE 190
           KFYCPFK+CSALL+DD G   E I    CP C RMFCAQCKVPWHAG+ CAEFQ+L KDE
Sbjct: 224 KFYCPFKECSALLVDDPGHGEEVITNVECPHCCRMFCAQCKVPWHAGVTCAEFQRLGKDE 283

Query: 191 REPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRCSSNPQL 234
           R  ED++L  +AQ+  W+RCP CKI+VE+ EGC ++ C  + Q+
Sbjct: 284 RGREDLLLRKVAQESKWQRCPKCKIYVERIEGCVFIICRYSSQI 327

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224035271|gb|ACN36711.1| unknown [Zea mays]

 Score =  234 bits (598), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 112/218 (51%), Positives = 149/218 (68%), Gaps = 10/218 (4%)

Query: 15  KAKKPFSSRSVTEKGQCSNSKNEVTIEERIETSFICDICVEPKSTDESFSIKGCSHSYCT 74
           K KKP  S ++ E GQCS   +       I +   C IC+E     ESF + GC+H++C 
Sbjct: 110 KGKKPLGSSTIQELGQCSRGAST-----NISSELYCAICMETVHIGESFPVDGCTHTFCI 164

Query: 75  ECMTKYVASKLQENITSINCPVADCK-GVLEPEYCRDILPEDVFNRWGNALCEAVILGAQ 133
            C+++ +A+K++EN+ SI CP   CK GVL P+ CRD++P  +F RWG ALC++  LG+ 
Sbjct: 165 SCVSQCIAAKVEENVLSIGCPAPGCKDGVLHPDACRDVIPAQLFQRWGAALCDSS-LGSL 223

Query: 134 KFYCPFKDCSALLIDDGG---EAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDE 190
           KFYCPFK+CSALL+DD G   E I    CP C RMFCAQCKVPWHAG+ CAEFQ+L KDE
Sbjct: 224 KFYCPFKECSALLVDDPGHGEEVITNVECPHCCRMFCAQCKVPWHAGVTCAEFQRLGKDE 283

Query: 191 REPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRC 228
           R  ED++L  +AQ+  W+RCP CKI+VE+ EGC ++ C
Sbjct: 284 RGREDLLLRKVAQESKWQRCPKCKIYVERIEGCVFIIC 321

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414885476|tpg|DAA61490.1| TPA: putative RING zinc finger domain superfamily protein isoform 1 [Zea mays] gi|414885477|tpg|DAA61491.1| TPA: putative RING zinc finger domain superfamily protein isoform 2 [Zea mays]

 Score =  234 bits (598), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 112/218 (51%), Positives = 149/218 (68%), Gaps = 10/218 (4%)

Query: 15  KAKKPFSSRSVTEKGQCSNSKNEVTIEERIETSFICDICVEPKSTDESFSIKGCSHSYCT 74
           K KKP  S ++ E GQCS   +       I +   C IC+E     ESF + GC+H++C 
Sbjct: 110 KGKKPLGSSTIQELGQCSRGAST-----NISSELYCAICMETVHIGESFPVDGCTHTFCI 164

Query: 75  ECMTKYVASKLQENITSINCPVADCK-GVLEPEYCRDILPEDVFNRWGNALCEAVILGAQ 133
            C+++ +A+K++EN+ SI CP   CK GVL P+ CRD++P  +F RWG ALC++  LG+ 
Sbjct: 165 SCVSQCIAAKVEENVLSIGCPAPGCKDGVLHPDACRDVIPAQLFQRWGAALCDSS-LGSL 223

Query: 134 KFYCPFKDCSALLIDDGG---EAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDE 190
           KFYCPFK+CSALL+DD G   E I    CP C RMFCAQCKVPWHAG+ CAEFQ+L KDE
Sbjct: 224 KFYCPFKECSALLVDDPGHGEEVITNVECPHCCRMFCAQCKVPWHAGVTCAEFQRLGKDE 283

Query: 191 REPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRC 228
           R  ED++L  +AQ+  W+RCP CKI+VE+ EGC ++ C
Sbjct: 284 RGREDLLLRKVAQESKWQRCPKCKIYVERIEGCVFIIC 321

Source: Zea mays

Species: Zea mays

Genus: Zea

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	234
TAIR|locus:2084116	320	AT3G53690 [Arabidopsis thalian	0.824	0.603	0.527	2.7e-61
TAIR|locus:2091030	303	AT3G14250 [Arabidopsis thalian	0.820	0.633	0.445	5.1e-51
TAIR|locus:2133935	532	AT4G19670 [Arabidopsis thalian	0.914	0.402	0.348	9e-33
TAIR|locus:2151689	444	AT5G37560 [Arabidopsis thalian	0.777	0.409	0.335	3.4e-29
TAIR|locus:2085622	222	AT3G45470 [Arabidopsis thalian	0.752	0.792	0.344	2.4e-28
TAIR|locus:2143995	655	AT5G60250 [Arabidopsis thalian	0.756	0.270	0.315	9.4e-27
TAIR|locus:1006230127	384	AT2G26135 [Arabidopsis thalian	0.752	0.458	0.349	2.5e-26
TAIR|locus:2040065	373	AT2G25360 [Arabidopsis thalian	0.760	0.477	0.324	4e-26
TAIR|locus:2050100	468	AT2G21420 [Arabidopsis thalian	0.752	0.376	0.344	4.8e-26
TAIR|locus:504955785	213	AT3G45555 [Arabidopsis thalian	0.756	0.830	0.304	2e-24

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

 Score = 627 (225.8 bits), Expect = 2.7e-61, P = 2.7e-61
 Identities = 107/203 (52%), Positives = 149/203 (73%)

Query:    27 EKGQCSNSKNEVTIEERIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQ 86
             EKGQ S+SK           +F C+ICV+ KS  ESF I GCSH YC +C++KY+A+KLQ
Sbjct:   101 EKGQSSSSKT---------ATFDCEICVDSKSIIESFRIGGCSHFYCNDCVSKYIAAKLQ 151

Query:    87 ENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALL 146
             +NI SI CPV+ C G LEP+ CR ILP++VF+RWG+ALCEAV++ ++KFYCP+KDCSAL+
Sbjct:   152 DNILSIECPVSGCSGRLEPDQCRQILPKEVFDRWGDALCEAVVMRSKKFYCPYKDCSALV 211

Query:   147 IDDGGEA-IRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKE 205
               +  E  +++S CP C+RM C +C   WH  + C EFQKL  +ER  +DI+L T+A+++
Sbjct:   212 FLEESEVKMKDSECPHCHRMVCVECGTQWHPEMTCEEFQKLAANERGRDDILLATMAKQK 271

Query:   206 NWRRCPNCKIFVEKKEGCRYMRC 228
              W+RCP+CK ++EK +GC YM+C
Sbjct:   272 KWKRCPSCKFYIEKSQGCLYMKC 294

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 530 (191.6 bits), Expect = 5.1e-51, P = 5.1e-51
 Identities = 89/200 (44%), Positives = 139/200 (69%)

Query:    37 EVTIE-ERIETSF-ICDICVEPKSTDESF-SIKGCSHSYCTECMTKYVASKLQENITSIN 93
             E+  E E +E S  +C IC++ K + + F     C+H+YCT+C  +YVA+K++EN + I 
Sbjct:    80 EIKAENEPMEPSRRLCMICMDEKPSSDIFRGTTNCTHAYCTDCTVRYVATKIKENASRIK 139

Query:    94 CPVADCKGVLEPEYCRDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALLID-DGGE 152
             CP  +C  ++EP  CRD++P+DVF+RW   LCE++I    KFYCPFKDCSA++++ + G+
Sbjct:   140 CPDVECTRLIEPYTCRDLIPKDVFDRWEKILCESLISSWDKFYCPFKDCSAMMVNNENGD 199

Query:   153 A-IRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKL---HKDEREPEDIMLMTLAQKENWR 208
             A + ++ C  C+R+FC QCKV WHAGI C EFQ+     K   + +D +L+ +A+ + WR
Sbjct:   200 ANVTQTECRSCHRLFCVQCKVTWHAGIGCDEFQRFGNTKKKSSDEDDALLIQMAKNKQWR 259

Query:   209 RCPNCKIFVEKKEGCRYMRC 228
             RCP+CK +V+K EGC++++C
Sbjct:   260 RCPSCKFYVDKVEGCQHIKC 279

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 359 (131.4 bits), Expect = 9.0e-33, P = 9.0e-33
 Identities = 84/241 (34%), Positives = 112/241 (46%)

Query:     4 LN-FVPQNTPFGKAKKPFSSRSVTEKGQCSNSKNEVTIEERIETSFICDICVEPKSTDES 62
             LN FV +  PF    +  S   V      SN   +  IE        C IC E + ++  
Sbjct:   167 LNGFVLKLAPFCDLDEALSLAQVAVGIVSSNLDGDKPIEN-------CSICCEDRQSEMM 219

Query:    63 FSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGN 122
              S+K C+H +C+ CM  YV  K++ +   I CP   CK  L    C+  LP   F  +  
Sbjct:   220 LSLK-CTHKFCSHCMKTYVEGKVKTSEVPIRCPQVQCKHYLSAAECKSFLPVTTFKSFEE 278

Query:   123 A-LCEAVILGAQKFYCPFKDCSALL-----IDDGGEAIRESV---------CPDCNRMFC 167
             A +C        K YCP+ +CS LL     +  G  +   S          CP C R  C
Sbjct:   279 ANVCSK---NNGKIYCPYPNCSFLLDPQECLSSGRASSSSSTQSENSCCVECPVCERFVC 335

Query:   168 AQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMR 227
               C VPWHA + C EFQ L  DER P+DI L  LA+ + WRRC  C+I +E  +GC +M 
Sbjct:   336 VDCGVPWHASMSCEEFQILPVDERYPDDITLHRLARYKRWRRCQQCRIMIELAQGCNHMT 395

Query:   228 C 228
             C
Sbjct:   396 C 396

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 324 (119.1 bits), Expect = 3.4e-29, P = 3.4e-29
 Identities = 63/188 (33%), Positives = 95/188 (50%)

Query:    45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE 104
             E    C IC +    +       C H +C  C+ + V  KL+  I    C    CK  L 
Sbjct:   176 EKPLTCSICSDKTDAEHMLLNDKCLHRHCFSCVKQQVKVKLRSGIVP-PCLEDGCKSELT 234

Query:   105 PEYCRDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALL--IDDGGEAIRESV--CP 160
              E C  +L   +   W   + E +I  A+K YCP++ CS L+   +   EA + +V  C 
Sbjct:   235 LESCSMVLTPKLIEMWKRKMEEDLIPDAEKIYCPYRSCSMLMSKTELSREAEQSNVRACI 294

Query:   161 DCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKK 220
              C+ +FC  CKVPWH+ + CA+++++H  ER   D+ML  LA  + WR+C  CK  +E  
Sbjct:   295 KCSELFCIDCKVPWHSDLSCADYKRIHS-ERLVNDMMLKVLANDQMWRQCSECKHMIELT 353

Query:   221 EGCRYMRC 228
             EGC ++ C
Sbjct:   354 EGCNHITC 361

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 316 (116.3 bits), Expect = 2.4e-28, P = 2.4e-28
 Identities = 63/183 (34%), Positives = 95/183 (51%)

Query:    50 CDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR 109
             C IC+E    D  F +  C H +C  C+ + V  KL+ N T   C   +CK  L  E C 
Sbjct:     6 CVICLEETKADRMFVMDKCLHRHCYPCVNQLVEVKLR-NGTVPTCLDYECKLKLSLENCF 64

Query:   110 DILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALL----IDDGGEAIRESVCPDCNRM 165
              +L   V   W + + E  I  A++ YCP+ +CS L+    I    ++  +  C  C+ +
Sbjct:    65 KVLKPKVIELWKHMMKEESIPLAKRIYCPYINCSTLMSKTEISRSNKS-NDRACIKCSGL 123

Query:   166 FCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRY 225
              C  CKVPWH+ + CAE++KLH D    +D+ L  LA  + WR+C  C+  +E  +GC +
Sbjct:   124 VCIDCKVPWHSDLSCAEYKKLHPDP-VLDDLTLKLLANDQKWRQCVKCRHLIELNQGCNH 182

Query:   226 MRC 228
             M C
Sbjct:   183 MTC 185

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 309 (113.8 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 60/190 (31%), Positives = 95/190 (50%)

Query:    50 CDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR 109
             C IC      +  FS+  C H +C +C+ ++V  KL   +    CP   CK  L  + C 
Sbjct:   301 CAICFNDIVAEGMFSVDKCRHRFCFQCVKQHVEVKLLHGMAP-KCPHDGCKSELVIDACG 359

Query:   110 DILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALL----IDDGGEAI-----RESV-- 158
              +L   +   W   L E  I   ++ YCP+  CSAL+    I +  +++     +  V  
Sbjct:   360 KLLTPKLSKLWQQRLQENAIPVTERVYCPYPRCSALMSKTKISESAKSLLSLYPKSGVRR 419

Query:   159 CPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVE 218
             C +C  +FC  CKVPWH  + C E++KLH  E   +D+ L +LA  + WR+C  C+  +E
Sbjct:   420 CVECRGLFCVDCKVPWHGNLSCTEYKKLHP-EPPADDVKLKSLANNKMWRQCGKCQHMIE 478

Query:   219 KKEGCRYMRC 228
               +GC ++ C
Sbjct:   479 LSQGCNHITC 488

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 297 (109.6 bits), Expect = 2.5e-26, P = 2.5e-26
 Identities = 64/183 (34%), Positives = 91/183 (49%)

Query:    50 CDICVEPK-STDESFSIKGCSHSYCTECMTKYV-ASKLQENITSINCPVADCKGVLEPEY 107
             C IC +   + D  F I  C H +C+EC+ +++  S LQ ++  I CP   CK  L    
Sbjct:   153 CTICFDDDINADMMFYIDQCGHMFCSECVKRHIEVSLLQGSL--ITCPSYRCKSKLTYGS 210

Query:   108 CRDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRES--VCPDCNRM 165
             C +IL   V   W   + E  I    + YCP   CSAL+     + +  S   C  C   
Sbjct:   211 CVNILTPKVKEMWIQRMGEDSIPVTDRVYCPNPTCSALMSVTELDQLTGSKRCCVKCGES 270

Query:   166 FCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRY 225
             FC +CKVPWH  + C  ++KLH + R   D  L  LA +E+WR+C  CK  +E  +GC  
Sbjct:   271 FCIKCKVPWHDNLSCKRYKKLHSN-RTTNDKQLNELANQESWRQCSKCKHMIELTQGCVR 329

Query:   226 MRC 228
             + C
Sbjct:   330 VIC 332

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 = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 60/185 (32%), Positives = 91/185 (49%)

Query:    49 ICDICVEPKSTDESF-SIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY 107
             IC IC E    +  F + + C H +C  C+ +YV  KL    T   C    CK  L  E 
Sbjct:    89 ICSICFEETEGERMFFTTEKCVHRHCFPCVKQYVEVKLLSG-TVPTCLDDGCKFKLTLES 147

Query:   108 CRDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALL----IDDGGEAIRESVCPDCN 163
             C  +L  ++   W   + E  I  A++ YCP+ +CS L+    +    +   +  C  C 
Sbjct:   148 CSKVLTLELIEMWKQKMKEDSIPAAERIYCPYPNCSMLMSKTELSSESDLSNDRSCVKCC 207

Query:   164 RMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGC 223
              +FC  CKVP H+ + CAE++KLH D    E + L +LA+ + WR+C  C+  +E    C
Sbjct:   208 GLFCIDCKVPSHSDLSCAEYKKLHHDPLVDE-LKLKSLAKDKKWRQCKMCRHMIELSHAC 266

Query:   224 RYMRC 228
              +M C
Sbjct:   267 NHMTC 271

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 297 (109.6 bits), Expect = 4.8e-26, P = 4.8e-26
 Identities = 63/183 (34%), Positives = 90/183 (49%)

Query:    50 CDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR 109
             C IC E    D  F  + C H  C  C+ ++V   L   I S  C    C   L  E C 
Sbjct:   187 CCICRENTDADRMFFTENCFHRQCFSCVNRHVQRMLLCGI-SPTCLHFPCNSELTFESCS 245

Query:   110 DILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALLIDDG--GEAIRESV--CPDCNRM 165
              +L  ++   W   + E ++  A K YCP++ CS L+       E  + +V  C  C R+
Sbjct:   246 KVLTPNLIEFWKRKIEEDLVPAADKIYCPYRRCSMLMSKTALSRETDQSNVRACIKCCRL 305

Query:   166 FCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRY 225
             FC  CKVP HAG+ C +++KL+ D     D+ L +LA K+ WR+C  C   VE  EGC +
Sbjct:   306 FCIDCKVPSHAGLSCVDYKKLNPDPLY--DVKLKSLANKKKWRQCVQCSNLVELFEGCNH 363

Query:   226 MRC 228
             + C
Sbjct:   364 ITC 366

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:504955785 AT3G45555 [Arabidopsis thaliana (taxid:3702)]

 Score = 279 (103.3 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 56/184 (30%), Positives = 90/184 (48%)

Query:    50 CDICVEPK-STDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYC 108
             C IC      +++ + +  C+H +C ECM +Y+  +L E  T + CP   C+  L  + C
Sbjct:    17 CSICFNDDFKSEQMYYVALCNHKFCLECMKRYIEVRLLEG-TVLICPYYQCESKLTLKSC 75

Query:   109 RDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALL--IDDGGEAIRESV--CPDCNR 164
               IL   +   W   + E  I   ++FYCP   CSAL+  I+     + +    C  C  
Sbjct:    76 FHILTSKLKAMWEQKIEEESIPVTERFYCPNPRCSALMSKIELSKSTLEDGFVRCFQCGE 135

Query:   165 MFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCR 224
              FC  CKV W + + C   +KL  +    +D ML  LA ++ WR+C  C+  ++  EGC 
Sbjct:   136 RFCINCKVSWQSNLSCDNCKKLGNNPTS-DDKMLKVLANEKKWRQCEKCQHMIKLSEGCI 194

Query:   225 YMRC 228
             ++ C
Sbjct:   195 HVTC 198

GO:0005737 "cytoplasm" evidence=ISM

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

Your Input: gw1.XVIII.567.1 hypothetical protein (303 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	234
smart00647	64	smart00647, IBR, In Between Ring fingers	2e-09
pfam01485	63	pfam01485, IBR, IBR domain	5e-05

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

 Score = 52.0 bits (125), Expect = 2e-09
 Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 118 NRWGNALCEAVIL-GAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHA 176
            ++   L E+ +       +CP  DCSA +I    E      CP C   FC +CKVPWH+
Sbjct: 1   EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHS 60

Query: 177 GIRC 180
            + C
Sbjct: 61  PVSC 64

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

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

 Score = 39.9 bits (93), Expect = 5e-05
 Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 1/45 (2%)

Query: 136 YCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRC 180
           +CP  DC  ++    G + +   C  C   FC  CK PWH G+ C
Sbjct: 20  WCPTPDCGNIIEKTDGGS-QNVTCSKCGTEFCFSCKEPWHEGLTC 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	234
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	100.0
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	100.0
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	99.95
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	99.92
smart00647	64	IBR In Between Ring fingers. the domains occurs be	99.34
PF01485	64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	99.26
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.88
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.77
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.74
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	98.74
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.74
PF14634	44	zf-RING_5: zinc-RING finger domain	98.7
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.68
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	98.63
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.49
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.4
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.18
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	98.17
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.17
PHA02926	242	zinc finger-like protein; Provisional	98.17
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.11
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.08
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.08
PHA02929	238	N1R/p28-like protein; Provisional	98.07
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.07
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.01
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	97.85
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	97.69
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.5
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	97.49
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.4
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	97.34
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	97.32
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.22
smart00647	64	IBR In Between Ring fingers. the domains occurs be	97.22
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.06
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	97.02
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.0
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	97.0
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	96.67
PF01485	64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	96.55
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	96.33
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	96.32
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	96.22
KOG2660	331	consensus Locus-specific chromosome binding protei	96.01
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	95.75
KOG4367	699	consensus Predicted Zn-finger protein [Function un	95.69
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	95.46
smart00661	52	RPOL9 RNA polymerase subunit 9.	95.31
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	95.29
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	95.24
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	95.22
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	95.19
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	95.17
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	95.15
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	95.13
PHA00626	59	hypothetical protein	95.13
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	95.11
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	94.85
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	94.76
KOG0297	391	consensus TNF receptor-associated factor [Signal t	94.71
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	94.62
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	94.55
COG5152	259	Uncharacterized conserved protein, contains RING a	94.35
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	94.25
KOG4739	233	consensus Uncharacterized protein involved in syna	94.11
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	94.07
PRK00432	50	30S ribosomal protein S27ae; Validated	93.85
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	93.82
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	93.77
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	93.65
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	93.47
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	93.11
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	93.05
KOG3039	303	consensus Uncharacterized conserved protein [Funct	92.93
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	92.27
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	91.95
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	91.91
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	91.68
KOG4445	368	consensus Uncharacterized conserved protein, conta	91.66
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	91.46
COG5222	427	Uncharacterized conserved protein, contains RING Z	91.41
PF14952	44	zf-tcix: Putative treble-clef, zinc-finger, Zn-bin	91.41
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	91.34
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	90.77
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	90.5
PF04641	260	Rtf2: Rtf2 RING-finger	90.42
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	89.93
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	89.89
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	89.75
CHL00174	296	accD acetyl-CoA carboxylase beta subunit; Reviewed	89.37
PF14569	80	zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.	89.25
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	89.2
smart00661	52	RPOL9 RNA polymerase subunit 9.	89.2
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	89.15
KOG1001	674	consensus Helicase-like transcription factor HLTF/	89.09
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	88.71
PHA03096	284	p28-like protein; Provisional	88.66
COG1998	51	RPS31 Ribosomal protein S27AE [Translation, riboso	88.54
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	88.09
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	87.13
KOG3579	352	consensus Predicted E3 ubiquitin ligase [Posttrans	86.84
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	86.79
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	86.23
PLN03086	567	PRLI-interacting factor K; Provisional	86.14
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	86.08
COG5175	480	MOT2 Transcriptional repressor [Transcription]	85.88
KOG1941	518	consensus Acetylcholine receptor-associated protei	85.34
KOG3002	299	consensus Zn finger protein [General function pred	84.63
PF03119	28	DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f	84.26
PRK08665	752	ribonucleotide-diphosphate reductase subunit alpha	84.06
PF12773	50	DZR: Double zinc ribbon	84.03
COG1645	131	Uncharacterized Zn-finger containing protein [Gene	83.98
PF01599	47	Ribosomal_S27: Ribosomal protein S27a; InterPro: I	83.72
KOG2807	378	consensus RNA polymerase II transcription initiati	83.68
PF13248	26	zf-ribbon_3: zinc-ribbon domain	83.59
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	83.57
PRK14714	1337	DNA polymerase II large subunit; Provisional	83.53
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	82.92
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	82.64
PRK14559	645	putative protein serine/threonine phosphatase; Pro	82.62
KOG1940	276	consensus Zn-finger protein [General function pred	82.53
COG1997	89	RPL43A Ribosomal protein L37AE/L43A [Translation,	81.47
TIGR03655	53	anti_R_Lar restriction alleviation protein, Lar fa	81.17
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	81.15
PF08271	43	TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013	80.28

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

Probab=100.00  E-value=7.1e-36  Score=250.29  Aligned_cols=185  Identities=36%  Similarity=0.838  Sum_probs=157.0

Q ss_pred             CcccccccccCC-CCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccCCHHHHHHHHHHH
Q 048114           46 TSFICDICVEPK-STDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNAL  124 (234)
Q Consensus        46 ~~~~C~iC~~~~-~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~  124 (234)
                      +..+|.||+.+. ....++....|+|.||.+|+++|++++.. ....++||...|...++.+....+|++++.++|++.+
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~-~~~~~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~~  223 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLL-SGTVIRCPHDGCESRLTLESCRKLLTPKLREMWEQRL  223 (384)
T ss_pred             ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhc-cCCCccCCCCCCCccCCHHHHhhhcCHHHHHHHHHHH
Confidence            467899999444 44466777799999999999999999943 4568999999999999999999999999999999999


Q ss_pred             HHHHHhCCCeecCCCCCCCCceecCCC---CccCcccCccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHH
Q 048114          125 CEAVILGAQKFYCPFKDCSALLIDDGG---EAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTL  201 (234)
Q Consensus       125 ~~~~~~~~~~~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~  201 (234)
                      .+.++...+.+|||.++|...+...+.   .......|+.|+..||..|+.+||.+.+|++|+++..+... .+..+..+
T Consensus       224 ~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~-d~~~~~~l  302 (384)
T KOG1812|consen  224 KEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYV-DDITLKYL  302 (384)
T ss_pred             HHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccc-cHHHHHHH
Confidence            998888777779999999988876542   33445679999999999999999999999999999864432 23333333


Q ss_pred             HhcCCcccCCCCCceeeeccCCCceEecCCCCC
Q 048114          202 AQKENWRRCPNCKIFVEKKEGCRYMRCSSNPQL  234 (234)
Q Consensus       202 ~~~~~~k~CP~C~~~i~k~~GCnhm~C~C~~~F  234 (234)
                      +  .+|+.||+|+.+|++++|||||+|+||++|
T Consensus       303 a--~~wr~CpkC~~~ie~~~GCnhm~CrC~~~f  333 (384)
T KOG1812|consen  303 A--KRWRQCPKCKFMIELSEGCNHMTCRCGHQF  333 (384)
T ss_pred             H--HhcCcCcccceeeeecCCcceEEeeccccc
Confidence            3  899999999999999999999999999998

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

Probab=100.00  E-value=1.7e-34  Score=233.70  Aligned_cols=190  Identities=26%  Similarity=0.669  Sum_probs=155.4

Q ss_pred             hcCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcC-CccccCCCCCCCCCCCHHHHhccCCHHHHHHHH
Q 048114           43 RIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQEN-ITSINCPVADCKGVLEPEYCRDILPEDVFNRWG  121 (234)
Q Consensus        43 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~-~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~  121 (234)
                      .+...+.|.|||++..+...+.+++|+|.||+.|++.|+...|.+| +..++||.+.|+..-.+..++.++..+++++|+
T Consensus       180 F~~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe  259 (445)
T KOG1814|consen  180 FVNSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARYE  259 (445)
T ss_pred             HHhhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHHH
Confidence            3567899999999998888888899999999999999999999998 678999999999999999999999999999999


Q ss_pred             HHHHHHHHh-CCCeecCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCCCChhhH--------HHhhhccCC
Q 048114          122 NALCEAVIL-GAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEF--------QKLHKDERE  192 (234)
Q Consensus       122 ~~~~~~~~~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~--------~~~~~~~~~  192 (234)
                      +++.+..+. ..+.+|||++.|+.....+++  ...+.|.+|+..||..|+..||+...|.--        ..+.....+
T Consensus       260 ~l~lqk~l~~msdv~yCPr~~Cq~p~~~d~~--~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a  337 (445)
T KOG1814|consen  260 KLMLQKTLELMSDVVYCPRACCQLPVKQDPG--RALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADEA  337 (445)
T ss_pred             HHHHHHHHHhhcccccCChhhccCccccCch--hhhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCHH
Confidence            998876664 678899999999998854433  456899999999999999999999999532        112111100


Q ss_pred             -h-----------HH----HHHHHHHhcCCcccCCCCCceeeeccCCCceEec-CCCCC
Q 048114          193 -P-----------ED----IMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRCS-SNPQL  234 (234)
Q Consensus       193 -~-----------~~----~~l~~~~~~~~~k~CP~C~~~i~k~~GCnhm~C~-C~~~F  234 (234)
                       +           .+    ..+++-+...+.|+||+|+++|+|++|||||+|. ||+-|
T Consensus       338 ~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~f  396 (445)
T KOG1814|consen  338 RKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCTKCGTYF  396 (445)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeeccccccc
Confidence             0           01    1122233456789999999999999999999995 88755

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

Probab=99.95  E-value=8.5e-29  Score=213.02  Aligned_cols=225  Identities=21%  Similarity=0.443  Sum_probs=177.6

Q ss_pred             ccccccCCCCCCcccCCCCCcccccccccCCCCcccchh--h--hcCCcccccccccCCCCCCceeeCCCCChhhHHHHH
Q 048114            3 ILNFVPQNTPFGKAKKPFSSRSVTEKGQCSNSKNEVTIE--E--RIETSFICDICVEPKSTDESFSIKGCSHSYCTECMT   78 (234)
Q Consensus         3 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~--~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~   78 (234)
                      +|.+++..+.+++..+.|+...+.+.....+...-....  .  ......+|.||++.+..  ......|+|.||..||.
T Consensus        22 ~ls~~~~~~~~ll~~~~W~~~kl~~~~~~~~~~~~~~~g~~~~~~~~~~~~c~ic~~~~~~--~~~~~~c~H~~c~~cw~   99 (444)
T KOG1815|consen   22 ILSLSHAVARILLAHFCWNVEKLLEEWVEDEETGCFFVGLLLWPKKKGDVQCGICVESYDG--EIIGLGCGHPFCPPCWT   99 (444)
T ss_pred             hhcCCHHHHHHHHHhcCcchHHHHHHHHhcCcchhhhccccccCCCCccccCCcccCCCcc--hhhhcCCCcHHHHHHHH
Confidence            577788888899999999998887666544443211111  0  12345899999998865  34456999999999999


Q ss_pred             HHHHHHHhcCCc-cccCCCCCCCCCCCHHHHhccCCH-HHHHHHHHHHHHHHHhCCC-eecCCCCCCCCceecCCCCccC
Q 048114           79 KYVASKLQENIT-SINCPVADCKGVLEPEYCRDILPE-DVFNRWGNALCEAVILGAQ-KFYCPFKDCSALLIDDGGEAIR  155 (234)
Q Consensus        79 ~~~~~~i~~~~~-~i~CP~~~C~~~l~~~~i~~~l~~-~~~~~~~~~~~~~~~~~~~-~~~Cp~~~C~~~~~~~~~~~~~  155 (234)
                      .|+...|.++.. .|+||...|...+..+.|..++++ +..++|.+.+..+++.... ..|||.|+|+..+... .....
T Consensus       100 ~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~~i~~syve~~~~lkwCP~~~C~~av~~~-~~~~~  178 (444)
T KOG1815|consen  100 GYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQRYILRSYVEDNVPLKWCPAPGCGLAVKFG-SLESV  178 (444)
T ss_pred             HHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHHHHHHHHHHhcCCccccCCCCCCCceeecc-CCCcc
Confidence            999999988633 399999999999999999999888 5999999999998887544 5799999999987753 23345


Q ss_pred             cccCccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHHHhcCCcccCCCCCceeeeccCCCceEec---CCC
Q 048114          156 ESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRCS---SNP  232 (234)
Q Consensus       156 ~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~~i~k~~GCnhm~C~---C~~  232 (234)
                      .+.|. |++.||+.|+.+||.+.+|..+..|........+ .+.  ....++++||+|.++|+|++|||||+|.   |++
T Consensus       179 ~v~C~-~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se-~~~--wi~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~  254 (444)
T KOG1815|consen  179 EVDCG-CGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSE-TIN--WILANTKECPKCKVPIEKDGGCNHMTCKSASCKH  254 (444)
T ss_pred             ceeCC-CCchhHhhccccccCCCcccchHHHHHhhhhhhh-hhh--hhhccCccCCCcccchhccCCccccccccCCcCC
Confidence            58895 6779999999999999999999988764332211 111  3467889999999999999999999995   999


Q ss_pred             CC
Q 048114          233 QL  234 (234)
Q Consensus       233 ~F  234 (234)
                      +|
T Consensus       255 ~F  256 (444)
T KOG1815|consen  255 EF  256 (444)
T ss_pred             ee
Confidence            88

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

Probab=99.92  E-value=1.5e-25  Score=176.19  Aligned_cols=182  Identities=25%  Similarity=0.573  Sum_probs=139.6

Q ss_pred             cCCcccccccccCCCCCCceeeCCCC--ChhhHHHHHHHHHHHHhcCC--------ccccCCCCCCCCCCCHHH-HhccC
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCS--HSYCTECMTKYVASKLQENI--------TSINCPVADCKGVLEPEY-CRDIL  112 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~~--------~~i~CP~~~C~~~l~~~~-i~~~l  112 (234)
                      +....+|..|-+.-   +.+..++|.  |..|.+|++.|..+.+++..        ..+.||. +|...+-.+. -..+|
T Consensus       218 N~~ni~C~~Ctdv~---~~vlvf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~il  293 (446)
T KOG0006|consen  218 NSRNITCITCTDVR---SPVLVFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFRIL  293 (446)
T ss_pred             ccccceeEEecCCc---cceEEEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhheec
Confidence            46688999997743   556667997  99999999999999987632        4678886 7876654332 23488


Q ss_pred             CHHHHHHHHHHHHHHHHhCCCeecCCCCCCCCceecCCCCccCcccCcc-ccccccccCCCCCCCCCChhhHHH------
Q 048114          113 PEDVFNRWGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPD-CNRMFCAQCKVPWHAGIRCAEFQK------  185 (234)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~-C~~~~C~~C~~~~H~~~~C~~~~~------  185 (234)
                      ..+.+.+|++...+..+...+.+.||+|+|++.+...+  +..++.|+. |++.||..|+..+|.| .|.+.-.      
T Consensus       294 g~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EP--D~rkvtC~~gCgf~FCR~C~e~yh~g-eC~~~~~as~t~t  370 (446)
T KOG0006|consen  294 GEEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEP--DQRKVTCEGGCGFAFCRECKEAYHEG-ECSAVFEASGTTT  370 (446)
T ss_pred             chhHHHHHHHhhhhhheeecCCEecCCCCCCcccccCC--CCCcccCCCCchhHhHHHHHhhhccc-cceeeeccccccc
Confidence            99999999999999988888899999999999888765  356699987 9999999999999998 3432111      


Q ss_pred             ------hhhccCChHHHHHHHHHhcCCcccCCCCCceeeeccCCCceEec---CCCC
Q 048114          186 ------LHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKKEGCRYMRCS---SNPQ  233 (234)
Q Consensus       186 ------~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~~i~k~~GCnhm~C~---C~~~  233 (234)
                            ....++..+++.. +...+..+|+||+|+++.||+|||.||.|.   ||.+
T Consensus       371 c~y~vde~~a~~arwd~as-~~TIk~tTkpCPkChvptErnGGCmHm~Ct~~~Cg~e  426 (446)
T KOG0006|consen  371 CAYRVDERAAEQARWDAAS-KETIKKTTKPCPKCHVPTERNGGCMHMKCTQPQCGLE  426 (446)
T ss_pred             eeeecChhhhhhhhhhhhh-hhhhhhccCCCCCccCccccCCceEEeecCCCCCCce
Confidence                  1112222333332 334467889999999999999999999994   8865

>smart00647 IBR In Between Ring fingers

Probab=99.34  E-value=1.8e-12  Score=81.99  Aligned_cols=63  Identities=35%  Similarity=0.835  Sum_probs=53.0

Q ss_pred             HHHHHHHHHHHHhC-CCeecCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCCCCh
Q 048114          118 NRWGNALCEAVILG-AQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRC  180 (234)
Q Consensus       118 ~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C  180 (234)
                      ++|++++.+.++.. ++.+|||+++|+.++..........+.|+.|+..||+.|+.+||.+.+|
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            36888888888775 5778999999999888764334567999999999999999999999987

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=99.26  E-value=1.1e-12  Score=82.94  Aligned_cols=63  Identities=29%  Similarity=0.774  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHHHhC-CCeecCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCCCCh
Q 048114          118 NRWGNALCEAVILG-AQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRC  180 (234)
Q Consensus       118 ~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C  180 (234)
                      ++|++++.+.++.. .+.+|||+++|+.++..+.......+.|+.|+..||+.|+.+||.+.+|
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            35666666655543 4557999999999999876655445999999999999999999999987

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=98.88  E-value=4.6e-10  Score=64.15  Aligned_cols=40  Identities=28%  Similarity=0.845  Sum_probs=28.0

Q ss_pred             ccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114           50 CDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCP   95 (234)
Q Consensus        50 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP   95 (234)
                      |+||++.+.  +++++ +|||+||..|+.+++...   +...+.||
T Consensus         1 CpiC~~~~~--~Pv~l-~CGH~FC~~Cl~~~~~~~---~~~~~~CP   40 (42)
T PF15227_consen    1 CPICLDLFK--DPVSL-PCGHSFCRSCLERLWKEP---SGSGFSCP   40 (42)
T ss_dssp             ETTTTSB-S--SEEE--SSSSEEEHHHHHHHHCCS---SSST---S
T ss_pred             CCccchhhC--Ccccc-CCcCHHHHHHHHHHHHcc---CCcCCCCc
Confidence            899999986  66665 999999999999999643   12237888

>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=98.77  E-value=7e-09  Score=59.19  Aligned_cols=39  Identities=36%  Similarity=1.044  Sum_probs=32.4

Q ss_pred             ccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114           50 CDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCP   95 (234)
Q Consensus        50 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP   95 (234)
                      |+||++.+.  +...+++|||.||.+|+.++++.     ...++||
T Consensus         1 C~iC~~~~~--~~~~~~~C~H~fC~~C~~~~~~~-----~~~~~CP   39 (41)
T PF00097_consen    1 CPICLEPFE--DPVILLPCGHSFCRDCLRKWLEN-----SGSVKCP   39 (41)
T ss_dssp             ETTTSSBCS--SEEEETTTSEEEEHHHHHHHHHH-----TSSSBTT
T ss_pred             CCcCCcccc--CCCEEecCCCcchHHHHHHHHHh-----cCCccCC
Confidence            799999876  44557799999999999999986     3466788

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 ....

>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=98.74  E-value=5.1e-09  Score=59.04  Aligned_cols=37  Identities=35%  Similarity=1.055  Sum_probs=29.2

Q ss_pred             ccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114           50 CDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCP   95 (234)
Q Consensus        50 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP   95 (234)
                      |+||++.+.  +++.+++|||.||.+|+.+|++.       ..+||
T Consensus         1 C~iC~~~~~--~~~~~~~CGH~fC~~C~~~~~~~-------~~~CP   37 (39)
T PF13923_consen    1 CPICLDELR--DPVVVTPCGHSFCKECIEKYLEK-------NPKCP   37 (39)
T ss_dssp             ETTTTSB-S--SEEEECTTSEEEEHHHHHHHHHC-------TSB-T
T ss_pred             CCCCCCccc--CcCEECCCCCchhHHHHHHHHHC-------cCCCc
Confidence            899999876  56567899999999999999863       25788

>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=98.74  E-value=2.9e-09  Score=61.79  Aligned_cols=40  Identities=25%  Similarity=0.682  Sum_probs=32.2

Q ss_pred             cccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114           49 ICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCP   95 (234)
Q Consensus        49 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP   95 (234)
                      +|+||++++..++.+..++|+|.||.+|+.+|++..       .+||
T Consensus         2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~-------~~CP   41 (44)
T PF13639_consen    2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN-------NSCP   41 (44)
T ss_dssp             CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS-------SB-T
T ss_pred             CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC-------CcCC
Confidence            599999999655666666899999999999999653       2888

...

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

Probab=98.74  E-value=1.4e-08  Score=74.67  Aligned_cols=58  Identities=24%  Similarity=0.704  Sum_probs=45.7

Q ss_pred             hcCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114           43 RIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD  110 (234)
Q Consensus        43 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  110 (234)
                      ..+..+.|+||++.+....++.. .|||.||+.|++..+.       ...+||  .|...++..++..
T Consensus       127 ~~~~~~~CPiCl~~~sek~~vsT-kCGHvFC~~Cik~alk-------~~~~CP--~C~kkIt~k~~~r  184 (187)
T KOG0320|consen  127 RKEGTYKCPICLDSVSEKVPVST-KCGHVFCSQCIKDALK-------NTNKCP--TCRKKITHKQFHR  184 (187)
T ss_pred             ccccccCCCceecchhhcccccc-ccchhHHHHHHHHHHH-------hCCCCC--Ccccccchhhhee
Confidence            34667899999999986565554 9999999999998885       345899  7877888776654

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.70  E-value=2.2e-08  Score=57.98  Aligned_cols=43  Identities=33%  Similarity=0.877  Sum_probs=35.8

Q ss_pred             cccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCC
Q 048114           49 ICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCK  100 (234)
Q Consensus        49 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~  100 (234)
                      .|+||++.+.....+.+++|||+||..|+.+..       ...+.||  .|+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-------~~~~~CP--~C~   43 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-------GKSVKCP--ICR   43 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-------CCCCCCc--CCC
Confidence            499999999656678888999999999998887       3567899  665

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

Probab=98.68  E-value=1.3e-08  Score=58.10  Aligned_cols=43  Identities=26%  Similarity=0.709  Sum_probs=24.1

Q ss_pred             ccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114           50 CDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCP   95 (234)
Q Consensus        50 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP   95 (234)
                      |+||.+.....+.+.+++|||.||.+|++++.....   ...++||
T Consensus         1 CpIc~e~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~---~~~~kCP   43 (43)
T PF13445_consen    1 CPICKEFSTEENPPMVLPCGHVFCKDCLQKLSKKSD---RNRFKCP   43 (43)
T ss_dssp             -TTT----TTSS-EEE-SSS-EEEHHHHHHHHHH-S----S-B--T
T ss_pred             CCccccccCCCCCCEEEeCccHHHHHHHHHHHhcCC---CCeeeCc
Confidence            899999334455666679999999999999997432   3567887

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=98.63  E-value=3.6e-08  Score=74.38  Aligned_cols=64  Identities=22%  Similarity=0.527  Sum_probs=47.9

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHH---------hcCCccccCCCCCCCCCCCHHHHhccCC
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKL---------QENITSINCPVADCKGVLEPEYCRDILP  113 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i---------~~~~~~i~CP~~~C~~~l~~~~i~~~l~  113 (234)
                      ...++|+||++.+.  +++. +.|||.||..|+.+|+...-         ........||  .|+..++...+..+..
T Consensus        16 ~~~~~CpICld~~~--dPVv-T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CP--vCR~~Is~~~LvPiyg   88 (193)
T PLN03208         16 GGDFDCNICLDQVR--DPVV-TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCP--VCKSDVSEATLVPIYG   88 (193)
T ss_pred             CCccCCccCCCcCC--CcEE-cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCC--CCCCcCChhcEEEeec
Confidence            45788999999874  5444 59999999999999976421         1123467999  9999999877766543

>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=98.49  E-value=1.8e-07  Score=54.08  Aligned_cols=44  Identities=32%  Similarity=0.823  Sum_probs=34.6

Q ss_pred             cccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCC
Q 048114           49 ICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGV  102 (234)
Q Consensus        49 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~  102 (234)
                      +|+||++.+.  +.+.+.+|+|.||..|+..|+..      ....||  .|+..
T Consensus         1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~------~~~~Cp--~C~~~   44 (45)
T cd00162           1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKS------GKNTCP--LCRTP   44 (45)
T ss_pred             CCCcCchhhh--CceEecCCCChhcHHHHHHHHHh------CcCCCC--CCCCc
Confidence            4999999873  55666679999999999999874      346799  77654

>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=98.40  E-value=2.3e-07  Score=55.24  Aligned_cols=46  Identities=28%  Similarity=0.764  Sum_probs=35.3

Q ss_pred             cccccccccCCCCCCceeeCCCCCh-hhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           47 SFICDICVEPKSTDESFSIKGCSHS-YCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ...|.||++...  + +.+.+|||. ||.+|+.+++.       ...+||  .|+..+.
T Consensus         2 ~~~C~iC~~~~~--~-~~~~pCgH~~~C~~C~~~~~~-------~~~~CP--~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPR--D-VVLLPCGHLCFCEECAERLLK-------RKKKCP--ICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBS--S-EEEETTCEEEEEHHHHHHHHH-------TTSBBT--TTTBB-S
T ss_pred             cCCCccCCccCC--c-eEEeCCCChHHHHHHhHHhcc-------cCCCCC--cCChhhc
Confidence            457999999763  3 555699999 99999999997       356899  8887654

...

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

Probab=98.18  E-value=2.7e-06  Score=70.43  Aligned_cols=111  Identities=18%  Similarity=0.472  Sum_probs=67.9

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccCCHHHHHHHHHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNA  123 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~  123 (234)
                      ....++|+||++.+...   .+++|+|.||..|+...+.       ..+.||  .|.. ...    .+............
T Consensus        10 ~~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~-------~~~~Cp--~cr~-~~~----~~~~n~~l~~~~~~   72 (386)
T KOG2177|consen   10 LQEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE-------GPLSCP--VCRP-PSR----NLRPNVLLANLVER   72 (386)
T ss_pred             ccccccChhhHHHhhcC---ccccccchHhHHHHHHhcC-------CCcCCc--ccCC-chh----ccCccHHHHHHHHH
Confidence            45688999999999733   5669999999999999997       458999  7773 221    22222222222222


Q ss_pred             HHHHHHhCC-Ce--ecCCCCCCCCceecCCCCccCcccCccccccccccCC-CCCCCCCChhh
Q 048114          124 LCEAVILGA-QK--FYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCK-VPWHAGIRCAE  182 (234)
Q Consensus       124 ~~~~~~~~~-~~--~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~-~~~H~~~~C~~  182 (234)
                      ......... ..  ..|+           .......+.|..|+..+|..|. ...|.++.-..
T Consensus        73 ~~~~~~~~~~~~~~~~c~-----------~~~~~~~~~c~~~~~~~c~~c~~~~~h~~h~~~~  124 (386)
T KOG2177|consen   73 LRQLRLSRPLGSKEELCE-----------KHGEELKLFCEEDEKLLCVLCRESGEHRGHPVLP  124 (386)
T ss_pred             HHhcCCcccccccchhhh-----------hcCCcceEEecccccccCCCCCCcccccCCcccc
Confidence            221111100 00  0233           1111144889999999999998 56787766543

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

Probab=98.17  E-value=1e-06  Score=69.93  Aligned_cols=52  Identities=29%  Similarity=0.775  Sum_probs=41.1

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHH
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYC  108 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  108 (234)
                      +....|.+|++...   .++.++|||.||..|+..|...+-       .||  -|...+.+..+
T Consensus       237 ~a~~kC~LCLe~~~---~pSaTpCGHiFCWsCI~~w~~ek~-------eCP--lCR~~~~pskv  288 (293)
T KOG0317|consen  237 EATRKCSLCLENRS---NPSATPCGHIFCWSCILEWCSEKA-------ECP--LCREKFQPSKV  288 (293)
T ss_pred             CCCCceEEEecCCC---CCCcCcCcchHHHHHHHHHHcccc-------CCC--cccccCCCcce
Confidence            45688999999763   455679999999999999997442       299  89888877654

>smart00184 RING Ring finger

Probab=98.17  E-value=2.7e-06  Score=47.25  Aligned_cols=37  Identities=30%  Similarity=0.889  Sum_probs=28.3

Q ss_pred             ccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114           50 CDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCP   95 (234)
Q Consensus        50 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP   95 (234)
                      |+||++..   ....+++|+|.||..|+..|+.      .....||
T Consensus         1 C~iC~~~~---~~~~~~~C~H~~c~~C~~~~~~------~~~~~CP   37 (39)
T smart00184        1 CPICLEEL---KDPVVLPCGHTFCRSCIRKWLK------SGNNTCP   37 (39)
T ss_pred             CCcCccCC---CCcEEecCCChHHHHHHHHHHH------hCcCCCC
Confidence            78999873   3444569999999999999987      1245677

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)

>PHA02926 zinc finger-like protein; Provisional

Probab=98.17  E-value=2.8e-06  Score=65.11  Aligned_cols=58  Identities=24%  Similarity=0.580  Sum_probs=41.3

Q ss_pred             cCCcccccccccCCCC-----C-CceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           44 IETSFICDICVEPKST-----D-ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~-----~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      .++..+|+||+|..-.     . ..-.+.+|+|.||..|++.|....-..+ ..-.||  .|+..+.
T Consensus       167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~-~~rsCP--iCR~~f~  230 (242)
T PHA02926        167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETG-ASDNCP--ICRTRFR  230 (242)
T ss_pred             ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccC-cCCcCC--CCcceee
Confidence            4567899999997621     1 1234679999999999999998653222 345799  7876543

>smart00504 Ubox Modified RING finger domain

Probab=98.11  E-value=4.4e-06  Score=52.22  Aligned_cols=51  Identities=20%  Similarity=0.249  Sum_probs=40.0

Q ss_pred             ccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114           48 FICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD  110 (234)
Q Consensus        48 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  110 (234)
                      +.|+||++.+.  +++. .+|||.||+.|+.+|+..       ...||  .|+..++.+++..
T Consensus         2 ~~Cpi~~~~~~--~Pv~-~~~G~v~~~~~i~~~~~~-------~~~cP--~~~~~~~~~~l~~   52 (63)
T smart00504        2 FLCPISLEVMK--DPVI-LPSGQTYERRAIEKWLLS-------HGTDP--VTGQPLTHEDLIP   52 (63)
T ss_pred             cCCcCCCCcCC--CCEE-CCCCCEEeHHHHHHHHHH-------CCCCC--CCcCCCChhhcee
Confidence            56999999875  5554 599999999999999964       24789  7888887665443

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

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

Probab=98.08  E-value=3e-06  Score=65.30  Aligned_cols=59  Identities=22%  Similarity=0.639  Sum_probs=45.9

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccC
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDIL  112 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l  112 (234)
                      ...++|.||+|.-.  +++ +..|||.||..||-+|+..+..    .-.||  .|+..++.+.+-.+.
T Consensus        45 ~~~FdCNICLd~ak--dPV-vTlCGHLFCWpClyqWl~~~~~----~~~cP--VCK~~Vs~~~vvPlY  103 (230)
T KOG0823|consen   45 GGFFDCNICLDLAK--DPV-VTLCGHLFCWPCLYQWLQTRPN----SKECP--VCKAEVSIDTVVPLY  103 (230)
T ss_pred             CCceeeeeeccccC--CCE-EeecccceehHHHHHHHhhcCC----CeeCC--ccccccccceEEeee
Confidence            56899999999653  544 4589999999999999986633    33578  899888887766554

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

Probab=98.08  E-value=2.3e-06  Score=72.96  Aligned_cols=59  Identities=24%  Similarity=0.589  Sum_probs=46.9

Q ss_pred             cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccC
Q 048114           47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDIL  112 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l  112 (234)
                      ...||||+++.+   ...++.|||.||..||.+|+....  ....-.||  -|...+.+.++..+.
T Consensus       186 ~~~CPICL~~~~---~p~~t~CGHiFC~~CiLqy~~~s~--~~~~~~CP--iC~s~I~~kdl~pv~  244 (513)
T KOG2164|consen  186 DMQCPICLEPPS---VPVRTNCGHIFCGPCILQYWNYSA--IKGPCSCP--ICRSTITLKDLLPVF  244 (513)
T ss_pred             CCcCCcccCCCC---cccccccCceeeHHHHHHHHhhhc--ccCCccCC--chhhhccccceeeee
Confidence            789999999875   233457999999999999998772  23467899  899999887777654

>PHA02929 N1R/p28-like protein; Provisional

Probab=98.07  E-value=4.3e-06  Score=65.92  Aligned_cols=51  Identities=25%  Similarity=0.626  Sum_probs=37.8

Q ss_pred             CCcccccccccCCCCCC-----ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           45 ETSFICDICVEPKSTDE-----SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~-----~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      .+..+|+||++.+....     ...+++|+|.||.+|+..|...       .-.||  .|+..+.
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            44678999999875322     1345689999999999999852       23799  7876554

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.07  E-value=3.9e-06  Score=70.89  Aligned_cols=68  Identities=24%  Similarity=0.633  Sum_probs=49.0

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHh-ccCCHHHHHHHHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR-DILPEDVFNRWGN  122 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~-~~l~~~~~~~~~~  122 (234)
                      ++..+.|+||++.+.  +++ +++|+|.||..|+..|+..       ...||  .|...+....+. +.+-.++++.|..
T Consensus        23 Le~~l~C~IC~d~~~--~Pv-itpCgH~FCs~CI~~~l~~-------~~~CP--~Cr~~~~~~~Lr~N~~L~~iVe~~~~   90 (397)
T TIGR00599        23 LDTSLRCHICKDFFD--VPV-LTSCSHTFCSLCIRRCLSN-------QPKCP--LCRAEDQESKLRSNWLVSEIVESFKN   90 (397)
T ss_pred             cccccCCCcCchhhh--Ccc-CCCCCCchhHHHHHHHHhC-------CCCCC--CCCCccccccCccchHHHHHHHHHHH
Confidence            566889999999885  444 4699999999999999853       23799  898887654433 3444556666654


Q ss_pred             H
Q 048114          123 A  123 (234)
Q Consensus       123 ~  123 (234)
                      .
T Consensus        91 ~   91 (397)
T TIGR00599        91 L   91 (397)
T ss_pred             h
Confidence            3

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

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

Probab=98.01  E-value=3.1e-06  Score=68.49  Aligned_cols=66  Identities=23%  Similarity=0.592  Sum_probs=51.1

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc-cCCHHHHHHHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD-ILPEDVFNRWG  121 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~-~l~~~~~~~~~  121 (234)
                      ++..+.|.||++.|.   .+.+.+|+|.||.-|++.|+.       ..-.||  .|...+....++. .+-.++++.|.
T Consensus        20 lD~lLRC~IC~eyf~---ip~itpCsHtfCSlCIR~~L~-------~~p~CP--~C~~~~~Es~Lr~n~il~Eiv~S~~   86 (442)
T KOG0287|consen   20 LDDLLRCGICFEYFN---IPMITPCSHTFCSLCIRKFLS-------YKPQCP--TCCVTVTESDLRNNRILDEIVKSLN   86 (442)
T ss_pred             hHHHHHHhHHHHHhc---CceeccccchHHHHHHHHHhc-------cCCCCC--ceecccchhhhhhhhHHHHHHHHHH
Confidence            455778999999984   455669999999999999996       345799  8988888888775 45566666664

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=97.85  E-value=5.2e-05  Score=61.68  Aligned_cols=56  Identities=25%  Similarity=0.564  Sum_probs=39.8

Q ss_pred             cccccccccCCCCCCc--eeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114           47 SFICDICVEPKSTDES--FSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD  110 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  110 (234)
                      ...||+|..+...+..  +.+.+|||.||..|+...+.    .+  +..||  .|+..+....++.
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~----~~--~~~CP--~C~~~lrk~~fr~   60 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV----RG--SGSCP--ECDTPLRKNNFRV   60 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhc----CC--CCCCC--CCCCccchhhccc
Confidence            3569999986432222  22227999999999999873    22  35899  9998888876554

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).

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

Probab=97.69  E-value=3.7e-05  Score=61.50  Aligned_cols=54  Identities=22%  Similarity=0.667  Sum_probs=45.0

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      .....+|.||++.+...+.+..++|.|.|...|+.+|+.     | ...+||  .|...+++
T Consensus       320 a~~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~-----~-y~~~CP--vCrt~iPP  373 (374)
T COG5540         320 ADKGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLL-----G-YSNKCP--VCRTAIPP  373 (374)
T ss_pred             cCCCceEEEEhhhhcccceEEEeccCceechhHHHHHHh-----h-hcccCC--ccCCCCCC
Confidence            456789999999998777777889999999999999995     2 356899  89887764

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

Probab=97.50  E-value=7.2e-06  Score=50.24  Aligned_cols=51  Identities=25%  Similarity=0.712  Sum_probs=24.8

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY  107 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  107 (234)
                      ++....|++|.+.+.  .++.+..|.|.||..|+...+.         -.||  .|..+--..+
T Consensus         4 le~lLrCs~C~~~l~--~pv~l~~CeH~fCs~Ci~~~~~---------~~CP--vC~~Paw~qD   54 (65)
T PF14835_consen    4 LEELLRCSICFDILK--EPVCLGGCEHIFCSSCIRDCIG---------SECP--VCHTPAWIQD   54 (65)
T ss_dssp             HHHTTS-SSS-S--S--S-B---SSS--B-TTTGGGGTT---------TB-S--SS--B-S-SS
T ss_pred             HHHhcCCcHHHHHhc--CCceeccCccHHHHHHhHHhcC---------CCCC--CcCChHHHHH
Confidence            445678999999875  7777789999999999966431         2499  7876544333

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

Probab=97.49  E-value=8.1e-05  Score=61.59  Aligned_cols=46  Identities=28%  Similarity=0.726  Sum_probs=39.3

Q ss_pred             ccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCC
Q 048114           48 FICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKG  101 (234)
Q Consensus        48 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~  101 (234)
                      .+|.||+|++..++.+..++|+|.|...|+..|+...      .=.||  .|+.
T Consensus       230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~------r~~CP--vCK~  275 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT------RTFCP--VCKR  275 (348)
T ss_pred             ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc------CccCC--CCCC
Confidence            6899999999988888889999999999999999744      23599  6665

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

Probab=97.40  E-value=0.00012  Score=44.59  Aligned_cols=47  Identities=32%  Similarity=0.731  Sum_probs=33.1

Q ss_pred             cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCC
Q 048114           47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCK  100 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~  100 (234)
                      .+.|||-+..+.  +++....|+|.|-++-+.+|+     .+...+.||..+|.
T Consensus        11 ~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i-----~~~~~~~CPv~GC~   57 (57)
T PF11789_consen   11 SLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYI-----QRNGSKRCPVAGCN   57 (57)
T ss_dssp             -SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHC-----TTTS-EE-SCCC-S
T ss_pred             ccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHH-----HhcCCCCCCCCCCC
Confidence            678999999886  888878999999999999999     33467899988884

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

Probab=97.34  E-value=0.00024  Score=56.00  Aligned_cols=54  Identities=24%  Similarity=0.555  Sum_probs=40.2

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHH
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYC  108 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  108 (234)
                      ...+.|.||++...   .+..++|||.||..|+...++.+     ..-.||  .|.....+..+
T Consensus       213 ~~d~kC~lC~e~~~---~ps~t~CgHlFC~~Cl~~~~t~~-----k~~~Cp--lCRak~~pk~v  266 (271)
T COG5574         213 LADYKCFLCLEEPE---VPSCTPCGHLFCLSCLLISWTKK-----KYEFCP--LCRAKVYPKKV  266 (271)
T ss_pred             ccccceeeeecccC---CcccccccchhhHHHHHHHHHhh-----ccccCc--hhhhhccchhh
Confidence            34788999999763   45556999999999999854322     244699  88888777665

>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=97.32  E-value=0.00012  Score=47.06  Aligned_cols=40  Identities=25%  Similarity=0.710  Sum_probs=28.9

Q ss_pred             cccccccCCCC----------CCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114           49 ICDICVEPKST----------DESFSIKGCSHSYCTECMTKYVASKLQENITSINCP   95 (234)
Q Consensus        49 ~C~iC~~~~~~----------~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP   95 (234)
                      .|.||++++..          .-.+....|||.|...||.+|++.+       -.||
T Consensus        21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~-------~~CP   70 (73)
T PF12678_consen   21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN-------NTCP   70 (73)
T ss_dssp             BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS-------SB-T
T ss_pred             cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC-------CcCC
Confidence            49999999921          1234456899999999999999532       2888

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 ....

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

Probab=97.22  E-value=0.00014  Score=65.16  Aligned_cols=57  Identities=21%  Similarity=0.620  Sum_probs=45.1

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhcc
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDI  111 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~  111 (234)
                      .....+|++|.+..   +...+..|+|.||..|++..+...      .=+||  .|...|+..+|..+
T Consensus       640 yK~~LkCs~Cn~R~---Kd~vI~kC~H~FC~~Cvq~r~etR------qRKCP--~Cn~aFganDv~~I  696 (698)
T KOG0978|consen  640 YKELLKCSVCNTRW---KDAVITKCGHVFCEECVQTRYETR------QRKCP--KCNAAFGANDVHRI  696 (698)
T ss_pred             HHhceeCCCccCch---hhHHHHhcchHHHHHHHHHHHHHh------cCCCC--CCCCCCCccccccc
Confidence            46688999998543   344456999999999999988654      34899  99999999888754

>smart00647 IBR In Between Ring fingers

Probab=97.22  E-value=0.00054  Score=42.69  Aligned_cols=30  Identities=23%  Similarity=0.698  Sum_probs=26.6

Q ss_pred             CCcccCC--CCCceeeecc--CCCceEe-cCCCCC
Q 048114          205 ENWRRCP--NCKIFVEKKE--GCRYMRC-SSNPQL  234 (234)
Q Consensus       205 ~~~k~CP--~C~~~i~k~~--GCnhm~C-~C~~~F  234 (234)
                      .+++.||  +|+..|+..+  |.++|+| .||+.|
T Consensus        16 ~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~f   50 (64)
T smart00647       16 PDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSF   50 (64)
T ss_pred             CCccCCCCCCCcceEEecCCCCCCeeECCCCCCeE
Confidence            5789999  9999999964  9999999 699887

the domains occurs between pairs og RING fingers

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

Probab=97.06  E-value=0.00031  Score=60.43  Aligned_cols=56  Identities=27%  Similarity=0.730  Sum_probs=42.3

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPE  106 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  106 (234)
                      .....+|.+|-++-.  +.+. ..|.|.||+-|++.|+..... +. .+.||  .|...|+.+
T Consensus       533 nk~~~~C~lc~d~ae--d~i~-s~ChH~FCrlCi~eyv~~f~~-~~-nvtCP--~C~i~LsiD  588 (791)
T KOG1002|consen  533 NKGEVECGLCHDPAE--DYIE-SSCHHKFCRLCIKEYVESFME-NN-NVTCP--VCHIGLSID  588 (791)
T ss_pred             ccCceeecccCChhh--hhHh-hhhhHHHHHHHHHHHHHhhhc-cc-CCCCc--ccccccccc
Confidence            355778999988643  4444 599999999999999976643 32 49999  887776665

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

Probab=97.02  E-value=0.00043  Score=55.20  Aligned_cols=67  Identities=18%  Similarity=0.418  Sum_probs=45.7

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc-cCCHHHHHHHHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD-ILPEDVFNRWGN  122 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~-~l~~~~~~~~~~  122 (234)
                      ++....|.||-+.+.   .+...+|||.||.-|++.|+..       .-.||  .|....-...++. .+..+..+.|..
T Consensus        22 LDs~lrC~IC~~~i~---ip~~TtCgHtFCslCIR~hL~~-------qp~CP--~Cr~~~~esrlr~~s~~~ei~es~~~   89 (391)
T COG5432          22 LDSMLRCRICDCRIS---IPCETTCGHTFCSLCIRRHLGT-------QPFCP--VCREDPCESRLRGSSGSREINESHAR   89 (391)
T ss_pred             chhHHHhhhhhheee---cceecccccchhHHHHHHHhcC-------CCCCc--cccccHHhhhcccchhHHHHHHhhhh
Confidence            455677999988774   4556799999999999999952       23588  7766544444443 344555555543

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

Probab=97.00  E-value=0.00032  Score=44.68  Aligned_cols=57  Identities=18%  Similarity=0.457  Sum_probs=26.5

Q ss_pred             cccccccccCCC-CCCcee-e---CCCCChhhHHHHHHHHHHHHhcC--Ccc--ccCCCCCCCCCCCH
Q 048114           47 SFICDICVEPKS-TDESFS-I---KGCSHSYCTECMTKYVASKLQEN--ITS--INCPVADCKGVLEP  105 (234)
Q Consensus        47 ~~~C~iC~~~~~-~~~~~~-~---~~C~H~fC~~Cl~~~~~~~i~~~--~~~--i~CP~~~C~~~l~~  105 (234)
                      ..+|+||++.+. .+.... .   ..|+..|...||.+|+...-...  ..+  =.||  .|...|+.
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP--~C~~~i~~   67 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECP--YCSSPISW   67 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-T--TT-SEEEG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCc--CCCCeeeE
Confidence            457999999865 222221 1   37899999999999998764432  222  2699  89887654

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

Probab=97.00  E-value=0.00039  Score=44.75  Aligned_cols=51  Identities=16%  Similarity=0.296  Sum_probs=36.3

Q ss_pred             CcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHH
Q 048114           46 TSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY  107 (234)
Q Consensus        46 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  107 (234)
                      ..+.|+|+.+-+.  +++.+ ++||+|.+.++.+|+..      ....||  .++..++..+
T Consensus         3 ~~f~CpIt~~lM~--dPVi~-~~G~tyer~~I~~~l~~------~~~~~P--~t~~~l~~~~   53 (73)
T PF04564_consen    3 DEFLCPITGELMR--DPVIL-PSGHTYERSAIERWLEQ------NGGTDP--FTRQPLSESD   53 (73)
T ss_dssp             GGGB-TTTSSB-S--SEEEE-TTSEEEEHHHHHHHHCT------TSSB-T--TT-SB-SGGG
T ss_pred             cccCCcCcCcHhh--CceeC-CcCCEEcHHHHHHHHHc------CCCCCC--CCCCcCCccc
Confidence            4788999999875  66665 89999999999999964      345788  6777777653

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 ....

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

Probab=96.67  E-value=0.0021  Score=51.06  Aligned_cols=51  Identities=29%  Similarity=0.650  Sum_probs=38.8

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ....+|++|.+.-.  .+....+|+|.||..|+..-....     ..+.||  .|+....
T Consensus       237 t~~~~C~~Cg~~Pt--iP~~~~~C~HiyCY~Ci~ts~~~~-----asf~Cp--~Cg~~~~  287 (298)
T KOG2879|consen  237 TSDTECPVCGEPPT--IPHVIGKCGHIYCYYCIATSRLWD-----ASFTCP--LCGENVE  287 (298)
T ss_pred             cCCceeeccCCCCC--CCeeeccccceeehhhhhhhhcch-----hhcccC--ccCCCCc
Confidence            34778999988643  566666899999999998776432     358999  8887655

>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=96.55  E-value=0.00073  Score=42.06  Aligned_cols=31  Identities=35%  Similarity=0.948  Sum_probs=20.0

Q ss_pred             cCCcccCCC--CCceeeeccCCCc--eEec-CCCCC
Q 048114          204 KENWRRCPN--CKIFVEKKEGCRY--MRCS-SNPQL  234 (234)
Q Consensus       204 ~~~~k~CP~--C~~~i~k~~GCnh--m~C~-C~~~F  234 (234)
                      ...++.||+  |...|++.+|.++  |+|. |+++|
T Consensus        15 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f   50 (64)
T PF01485_consen   15 DPNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEF   50 (64)
T ss_dssp             ---CC--TTSST---ECS-SSTTS--CCTTSCCSEE
T ss_pred             CCCccCCCCCCCcccEEecCCCCCCeeECCCCCCcC
Confidence            345689987  9999999999999  9997 99876

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.

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

Probab=96.33  E-value=0.004  Score=51.58  Aligned_cols=53  Identities=19%  Similarity=0.519  Sum_probs=38.4

Q ss_pred             CCcccccccccCC-CCC---------CceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHH
Q 048114           45 ETSFICDICVEPK-STD---------ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPE  106 (234)
Q Consensus        45 ~~~~~C~iC~~~~-~~~---------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  106 (234)
                      .....|.||+|+. ..+         ..+..++|||.+...|++.|++.+       -.||  .|+.++-.+
T Consensus       285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq-------QTCP--ICr~p~ifd  347 (491)
T COG5243         285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ-------QTCP--ICRRPVIFD  347 (491)
T ss_pred             CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc-------cCCC--cccCccccc
Confidence            4467899999994 322         123456999999999999999733       4799  788764443

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

Probab=96.32  E-value=0.0033  Score=52.41  Aligned_cols=57  Identities=28%  Similarity=0.588  Sum_probs=40.3

Q ss_pred             CCcccccccccCCCCCC-----ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCC
Q 048114           45 ETSFICDICVEPKSTDE-----SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVL  103 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~-----~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l  103 (234)
                      ....+|.||++......     .-.+++|.|.||..|++.|-...-.+....-.||  .|....
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP--~CRv~s  220 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCP--FCRVPS  220 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCC--cccCcc
Confidence            45789999999885333     2234689999999999999855433333456899  776543

>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=96.22  E-value=0.0023  Score=32.17  Aligned_cols=23  Identities=22%  Similarity=0.548  Sum_probs=17.4

Q ss_pred             ccCCCCCceeeeccCCCceEec-CCCCC
Q 048114          208 RRCPNCKIFVEKKEGCRYMRCS-SNPQL  234 (234)
Q Consensus       208 k~CP~C~~~i~k~~GCnhm~C~-C~~~F  234 (234)
                      |.||.|+..|..+    -+.|. |||.|
T Consensus         1 K~CP~C~~~V~~~----~~~Cp~CG~~F   24 (26)
T PF10571_consen    1 KTCPECGAEVPES----AKFCPHCGYDF   24 (26)
T ss_pred             CcCCCCcCCchhh----cCcCCCCCCCC
Confidence            5799999988543    46775 99887

Several members are annotated as putative helicases.

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

Probab=96.01  E-value=0.0035  Score=51.14  Aligned_cols=51  Identities=27%  Similarity=0.764  Sum_probs=39.4

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      +.+-.+|.+|-..+.  +...+..|-|+||++||-.|++.       ...||  .|...+..
T Consensus        12 ~n~~itC~LC~GYli--DATTI~eCLHTFCkSCivk~l~~-------~~~CP--~C~i~ih~   62 (331)
T KOG2660|consen   12 LNPHITCRLCGGYLI--DATTITECLHTFCKSCIVKYLEE-------SKYCP--TCDIVIHK   62 (331)
T ss_pred             cccceehhhccceee--cchhHHHHHHHHHHHHHHHHHHH-------hccCC--ccceeccC
Confidence            355789999998876  44455699999999999999975       45799  77655444

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

Probab=95.75  E-value=0.024  Score=33.31  Aligned_cols=41  Identities=20%  Similarity=0.636  Sum_probs=29.1

Q ss_pred             cccccccCCCCCCceeeCCCC-----ChhhHHHHHHHHHHHHhcCCccccCC
Q 048114           49 ICDICVEPKSTDESFSIKGCS-----HSYCTECMTKYVASKLQENITSINCP   95 (234)
Q Consensus        49 ~C~iC~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~i~CP   95 (234)
                      .|-||++.....+.. ..+|.     |.+..+||.+|+...-     ..+||
T Consensus         1 ~CrIC~~~~~~~~~l-~~PC~C~G~~~~vH~~Cl~~W~~~~~-----~~~C~   46 (49)
T smart00744        1 ICRICHDEGDEGDPL-VSPCRCKGSLKYVHQECLERWINESG-----NKTCE   46 (49)
T ss_pred             CccCCCCCCCCCCee-EeccccCCchhHHHHHHHHHHHHHcC-----CCcCC
Confidence            388999844444444 45885     7899999999997552     34787

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

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

Probab=95.69  E-value=0.0083  Score=50.76  Aligned_cols=35  Identities=26%  Similarity=0.610  Sum_probs=27.9

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHH
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVA   82 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~   82 (234)
                      ++.+.|+||..-+.  +++. ++|+|..|+.|.+....
T Consensus         2 eeelkc~vc~~f~~--epii-l~c~h~lc~~ca~~~~~   36 (699)
T KOG4367|consen    2 EEELKCPVCGSFYR--EPII-LPCSHNLCQACARNILV   36 (699)
T ss_pred             cccccCceehhhcc--CceE-eecccHHHHHHHHhhcc
Confidence            45677999998875  5555 49999999999987654

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

Probab=95.46  E-value=0.036  Score=45.72  Aligned_cols=122  Identities=18%  Similarity=0.375  Sum_probs=64.2

Q ss_pred             cccccccccCCCCC---CceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCC--CCHHHHhccCCHHHHHHHH
Q 048114           47 SFICDICVEPKSTD---ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGV--LEPEYCRDILPEDVFNRWG  121 (234)
Q Consensus        47 ~~~C~iC~~~~~~~---~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~--l~~~~i~~~l~~~~~~~~~  121 (234)
                      ...|.||-++++..   ..+..+.|||.+|..|+...+.      ...+.||  .|...  +....++.+-..-..-...
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 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLG------NSRILCP--FCRETTEIPDGDVKSLQKNFALLQAI   74 (296)
T ss_pred             CCceeecCccccccCcccCCcccccCceehHhHHHHHhc------Cceeecc--CCCCcccCCchhHhhhhhhHHHHHHH
Confidence            45799999999643   3455679999999999988774      2356777  78777  4444554433222221111


Q ss_pred             HHHHHHHHhCCCeecCCCCCCCCceecCCCCccCcccCccccccccccCCCC-CCCC
Q 048114          122 NALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVP-WHAG  177 (234)
Q Consensus       122 ~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~-~H~~  177 (234)
                      .......+.......+| +.|..............-.|......+|..|... .|.+
T Consensus        75 ~~~~~~~~~~~~~~~~~-~~c~~~~~nl~~~vc~~~~~~~~~~~~c~t~~~~~~~~~  130 (296)
T KOG4185|consen   75 EHMKKTTVEEKGEADSP-PKCKEHPYNLAEFVCVEPDCSSKDKLMCRTCEEFGIHKG  130 (296)
T ss_pred             HHHhcccccccCcccCC-cccccCcccccceeecCCCcchhhhhhhhhccchhhhhh
Confidence            11111111111122233 1255332221111111224566667788888764 3444

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=95.31  E-value=0.012  Score=34.99  Aligned_cols=27  Identities=26%  Similarity=0.500  Sum_probs=21.0

Q ss_pred             ccCCCCCceeeecc--CCCceEec-CCCCC
Q 048114          208 RRCPNCKIFVEKKE--GCRYMRCS-SNPQL  234 (234)
Q Consensus       208 k~CP~C~~~i~k~~--GCnhm~C~-C~~~F  234 (234)
                      +.||.|+.++...+  +-+++.|. |||+|
T Consensus         1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~   30 (52)
T smart00661        1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE   30 (52)
T ss_pred             CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence            46999999887654  35699996 99975

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

Probab=95.29  E-value=0.014  Score=50.25  Aligned_cols=53  Identities=21%  Similarity=0.651  Sum_probs=38.8

Q ss_pred             cCCcccccccccCCCCCC--------------ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           44 IETSFICDICVEPKSTDE--------------SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~--------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ++.+..|.||+.+++.-.              ...+.+|.|.|.+.|+++|+.     + ..+.||  .|...|+
T Consensus       568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd-----~-ykl~CP--vCR~pLP  634 (636)
T KOG0828|consen  568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMD-----T-YKLICP--VCRCPLP  634 (636)
T ss_pred             hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHh-----h-hcccCC--ccCCCCC
Confidence            466788999999885211              123569999999999999995     2 257899  6665554

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

Probab=95.24  E-value=0.016  Score=51.93  Aligned_cols=48  Identities=21%  Similarity=0.600  Sum_probs=36.2

Q ss_pred             CCcccccccccCCCCCCc--eeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCC
Q 048114           45 ETSFICDICVEPKSTDES--FSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKG  101 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~  101 (234)
                      .....|.||.|++.....  ...++|+|.|+..|+++|++.       .-.||  .|..
T Consensus       289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er-------~qtCP--~CR~  338 (543)
T KOG0802|consen  289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER-------QQTCP--TCRT  338 (543)
T ss_pred             hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHH-------hCcCC--cchh
Confidence            447789999999863221  455699999999999999986       23688  5554

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

Probab=95.22  E-value=0.004  Score=53.12  Aligned_cols=105  Identities=19%  Similarity=0.430  Sum_probs=62.7

Q ss_pred             CcccccccccCCCCC---Cc--eeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccCCHHHHHHH
Q 048114           46 TSFICDICVEPKSTD---ES--FSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRW  120 (234)
Q Consensus        46 ~~~~C~iC~~~~~~~---~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~  120 (234)
                      +...|+.++......   +.  .....|+-.||.+|-..|-.                   .++-++++.+.++..... 
T Consensus       237 p~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~-------------------~~sC~eykk~~~~~~~d~-  296 (384)
T KOG1812|consen  237 PYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHA-------------------NLSCEEYKKLNPEEYVDD-  296 (384)
T ss_pred             CCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCC-------------------CCCHHHHHHhCCcccccH-
Confidence            455677776654321   11  11236666677777654431                   144456666554332221 


Q ss_pred             HHHHHHHHHhCCCeecCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCCCC
Q 048114          121 GNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIR  179 (234)
Q Consensus       121 ~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~  179 (234)
                         .....+. ...+.||  .|...+....+  .+.+.|. |++.||+.|+..|+.+..
T Consensus       297 ---~~~~~la-~~wr~Cp--kC~~~ie~~~G--Cnhm~Cr-C~~~fcy~C~~~~~~~~~  346 (384)
T KOG1812|consen  297 ---ITLKYLA-KRWRQCP--KCKFMIELSEG--CNHMTCR-CGHQFCYMCGGDWKTHNG  346 (384)
T ss_pred             ---HHHHHHH-HhcCcCc--ccceeeeecCC--cceEEee-ccccchhhcCcchhhCCc
Confidence               1112222 4567899  99988876554  6779998 999999999999866543

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

Probab=95.19  E-value=0.023  Score=33.02  Aligned_cols=46  Identities=24%  Similarity=0.636  Sum_probs=21.1

Q ss_pred             ccccccCCCCCC-ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCC
Q 048114           50 CDICVEPKSTDE-SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVL  103 (234)
Q Consensus        50 C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l  103 (234)
                      |++|.+++...+ .+.--+|+..+|+.|+.+...     + ..=+||  .|+...
T Consensus         1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~-----~-~~g~CP--gCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILE-----N-EGGRCP--GCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SSTTS----HHHHHHHTT-----S-S-SB-T--TT--B-
T ss_pred             CCCcccccccCCCccccCcCCCcHHHHHHHHHHh-----c-cCCCCC--CCCCCC
Confidence            789999884333 333347899999999977664     1 133789  887653

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

Probab=95.17  E-value=0.027  Score=36.92  Aligned_cols=52  Identities=23%  Similarity=0.611  Sum_probs=35.5

Q ss_pred             cccccccccCCCCC---------C-ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           47 SFICDICVEPKSTD---------E-SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        47 ~~~C~iC~~~~~~~---------~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ...|+||...|+..         + ++..-.|+|.|..-|+.+|+.++-.    .=.||  -|.+.+.
T Consensus        21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~----~~~CP--mCR~~w~   82 (85)
T PF12861_consen   21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSS----KGQCP--MCRQPWK   82 (85)
T ss_pred             CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccC----CCCCC--CcCCeee
Confidence            44588887777521         1 3344589999999999999986521    23799  6776543

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

Probab=95.15  E-value=0.0028  Score=52.10  Aligned_cols=52  Identities=27%  Similarity=0.746  Sum_probs=37.9

Q ss_pred             hhcCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCC
Q 048114           42 ERIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVL  103 (234)
Q Consensus        42 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l  103 (234)
                      ..+...+.|+||++-+.  .......|.|.||.+|+..-+.    .+  .=.||  .|...+
T Consensus        38 ~~~~~~v~c~icl~llk--~tmttkeClhrfc~~ci~~a~r----~g--n~ecp--tcRk~l   89 (381)
T KOG0311|consen   38 AMFDIQVICPICLSLLK--KTMTTKECLHRFCFDCIWKALR----SG--NNECP--TCRKKL   89 (381)
T ss_pred             HHhhhhhccHHHHHHHH--hhcccHHHHHHHHHHHHHHHHH----hc--CCCCc--hHHhhc
Confidence            34677889999999875  4445569999999999977664    33  22588  776543

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

Probab=95.13  E-value=0.029  Score=45.61  Aligned_cols=94  Identities=22%  Similarity=0.588  Sum_probs=55.9

Q ss_pred             CCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccCCHHHHHHHHHHHHHHHHhCCCeecCCCCCCCCce
Q 048114           67 GCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALL  146 (234)
Q Consensus        67 ~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~  146 (234)
                      .||-.||++|++.|-...-..+... . -...|...+++...       ...+|..+..+.+  .....-||  .|....
T Consensus       341 gCgf~FCR~C~e~yh~geC~~~~~a-s-~t~tc~y~vde~~a-------~~arwd~as~~TI--k~tTkpCP--kChvpt  407 (446)
T KOG0006|consen  341 GCGFAFCRECKEAYHEGECSAVFEA-S-GTTTCAYRVDERAA-------EQARWDAASKETI--KKTTKPCP--KCHVPT  407 (446)
T ss_pred             CchhHhHHHHHhhhccccceeeecc-c-cccceeeecChhhh-------hhhhhhhhhhhhh--hhccCCCC--CccCcc
Confidence            4889999999998875332221100 0 00135544444322       2345555544322  22345688  898777


Q ss_pred             ecCCCCccCcccCcc--ccccccccCCCCCC
Q 048114          147 IDDGGEAIRESVCPD--CNRMFCAQCKVPWH  175 (234)
Q Consensus       147 ~~~~~~~~~~~~C~~--C~~~~C~~C~~~~H  175 (234)
                      .+++.  ...+.|+.  |+..+|+.|+-+|.
T Consensus       408 ErnGG--CmHm~Ct~~~Cg~eWCw~C~tEW~  436 (446)
T KOG0006|consen  408 ERNGG--CMHMKCTQPQCGLEWCWNCGTEWN  436 (446)
T ss_pred             ccCCc--eEEeecCCCCCCceeEeccCChhh
Confidence            66543  34578865  99999999999884

>PHA00626 hypothetical protein

Probab=95.13  E-value=0.017  Score=34.23  Aligned_cols=26  Identities=23%  Similarity=0.464  Sum_probs=21.6

Q ss_pred             cCCCCCc-eeeeccCCCc----eEec-CCCCC
Q 048114          209 RCPNCKI-FVEKKEGCRY----MRCS-SNPQL  234 (234)
Q Consensus       209 ~CP~C~~-~i~k~~GCnh----m~C~-C~~~F  234 (234)
                      .||+|+. -|.|.+-|+.    -.|. |||.|
T Consensus         2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f   33 (59)
T PHA00626          2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND   33 (59)
T ss_pred             CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence            5999999 5889887765    7895 99987

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

Probab=95.11  E-value=0.027  Score=46.67  Aligned_cols=49  Identities=31%  Similarity=0.663  Sum_probs=36.2

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCCh-hhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHS-YCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      .+...+|.||+++..   ...+++|.|. .|.+|.+...-   ..+    .||  .|...+.
T Consensus       287 ~~~gkeCVIClse~r---dt~vLPCRHLCLCs~Ca~~Lr~---q~n----~CP--ICRqpi~  336 (349)
T KOG4265|consen  287 SESGKECVICLSESR---DTVVLPCRHLCLCSGCAKSLRY---QTN----NCP--ICRQPIE  336 (349)
T ss_pred             ccCCCeeEEEecCCc---ceEEecchhhehhHhHHHHHHH---hhc----CCC--ccccchH
Confidence            366889999999863   4556699999 99999987652   122    589  8877654

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

Probab=94.85  E-value=0.049  Score=45.94  Aligned_cols=112  Identities=21%  Similarity=0.497  Sum_probs=68.3

Q ss_pred             CCcccccc--cccCC---CCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccC-----C-
Q 048114           45 ETSFICDI--CVEPK---STDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDIL-----P-  113 (234)
Q Consensus        45 ~~~~~C~i--C~~~~---~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l-----~-  113 (234)
                      .....||-  |..+.   +...+.....|.-+||..|...|-      |..       .|+...+ +.++-++     + 
T Consensus       271 sdv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~H------G~s-------~Ck~~~~-~~~~l~~~~~~~d~  336 (445)
T KOG1814|consen  271 SDVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWH------GVS-------PCKVKAE-KLIELYLEYLEADE  336 (445)
T ss_pred             cccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhc------CCC-------cccCchH-HHHHHHHHHhhcCH
Confidence            44567887  55442   122344456889999999998876      221       3544322 2222111     1 


Q ss_pred             ---HHHHHHHHHHHHHHHHh--------CCCeecCCCCCCCCceecCCCCccCcccCccccccccccCCCCC
Q 048114          114 ---EDVFNRWGNALCEAVIL--------GAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPW  174 (234)
Q Consensus       114 ---~~~~~~~~~~~~~~~~~--------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~  174 (234)
                         .++..+|-+++.+..+.        ..+...||  .|...+.+.++  .+++.|..|++.||+.|....
T Consensus       337 a~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP--~C~v~IEr~eG--CnKM~C~~c~~~fc~~c~~~l  404 (445)
T KOG1814|consen  337 ARKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCP--KCKVVIERSEG--CNKMHCTKCGTYFCWICAELL  404 (445)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCC--cccceeecCCC--ccceeeccccccceeehhhhc
Confidence               23445565444333222        23445899  99999887654  566999999999999998754

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

Probab=94.76  E-value=0.044  Score=53.23  Aligned_cols=69  Identities=20%  Similarity=0.441  Sum_probs=53.6

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcC---CccccCCCCCCCCCCCHHHHhccCCH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQEN---ITSINCPVADCKGVLEPEYCRDILPE  114 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~---~~~i~CP~~~C~~~l~~~~i~~~l~~  114 (234)
                      .+..-.|.|||.+-....+...+.|+|.|...|.+..++..-..-   ...|.||  .|..++..-.++++|++
T Consensus      3483 QD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCP--iC~n~InH~~LkDLldP 3554 (3738)
T KOG1428|consen 3483 QDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCP--ICKNKINHIVLKDLLDP 3554 (3738)
T ss_pred             cccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecc--cccchhhhHHHHHHHHH
Confidence            355678999998765555555569999999999998887654331   2468999  99999999888888874

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

Probab=94.71  E-value=0.034  Score=47.69  Aligned_cols=52  Identities=21%  Similarity=0.750  Sum_probs=38.3

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPE  106 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  106 (234)
                      ++..+.|++|...+.  +++....|||.||..|+..+...       ...||  .|...+...
T Consensus        18 ~~~~l~C~~C~~vl~--~p~~~~~cgh~fC~~C~~~~~~~-------~~~cp--~~~~~~~~~   69 (391)
T KOG0297|consen   18 LDENLLCPICMSVLR--DPVQTTTCGHRFCAGCLLESLSN-------HQKCP--VCRQELTQA   69 (391)
T ss_pred             CcccccCcccccccc--CCCCCCCCCCcccccccchhhcc-------CcCCc--ccccccchh
Confidence            466889999999886  55543599999999999988864       45677  565444433

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

Probab=94.62  E-value=0.036  Score=47.31  Aligned_cols=49  Identities=29%  Similarity=0.767  Sum_probs=36.7

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      +...++|.||+..+.  .++.. +|||+||..|+.+-.    .   ....||  .|...+.
T Consensus        81 ~~sef~c~vc~~~l~--~pv~t-pcghs~c~~Cl~r~l----d---~~~~cp--~Cr~~l~  129 (398)
T KOG4159|consen   81 IRSEFECCVCSRALY--PPVVT-PCGHSFCLECLDRSL----D---QETECP--LCRDELV  129 (398)
T ss_pred             ccchhhhhhhHhhcC--CCccc-cccccccHHHHHHHh----c---cCCCCc--ccccccc
Confidence            366899999998875  55555 999999999977722    2   345788  6877666

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

Probab=94.55  E-value=0.022  Score=46.02  Aligned_cols=52  Identities=17%  Similarity=0.353  Sum_probs=37.6

Q ss_pred             cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHh
Q 048114           47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR  109 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~  109 (234)
                      ..+|.||+.+-.  .+ +.+.|+|.||.-|++.-+..      ....|+  -|...++...+.
T Consensus         7 ~~eC~IC~nt~n--~P-v~l~C~HkFCyiCiKGsy~n------dk~~Ca--vCR~pids~i~~   58 (324)
T KOG0824|consen    7 KKECLICYNTGN--CP-VNLYCFHKFCYICIKGSYKN------DKKTCA--VCRFPIDSTIDF   58 (324)
T ss_pred             CCcceeeeccCC--cC-ccccccchhhhhhhcchhhc------CCCCCc--eecCCCCcchhc
Confidence            557999998753  33 45699999999999876541      234588  888887765443

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

Probab=94.35  E-value=0.022  Score=43.13  Aligned_cols=33  Identities=27%  Similarity=0.826  Sum_probs=26.4

Q ss_pred             CcccccccccCCCCCCceeeCCCCChhhHHHHHHHH
Q 048114           46 TSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYV   81 (234)
Q Consensus        46 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~   81 (234)
                      -.+.|.||-.++.  .++ ...|||.||..|...-+
T Consensus       195 IPF~C~iCKkdy~--spv-vt~CGH~FC~~Cai~~y  227 (259)
T COG5152         195 IPFLCGICKKDYE--SPV-VTECGHSFCSLCAIRKY  227 (259)
T ss_pred             Cceeehhchhhcc--chh-hhhcchhHHHHHHHHHh
Confidence            3678999999985  444 45999999999986655

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

Probab=94.25  E-value=0.049  Score=45.78  Aligned_cols=61  Identities=18%  Similarity=0.384  Sum_probs=49.6

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD  110 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  110 (234)
                      .-.-|.|||=-+.-+.++++..+.|||.++++=+.+..+    +|...++||  .|+..-..+..++
T Consensus       331 fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~----ng~~sfKCP--YCP~e~~~~~~kq  391 (394)
T KOG2817|consen  331 FHSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSK----NGSQSFKCP--YCPVEQLASDTKQ  391 (394)
T ss_pred             ccceeecccchhhccCCCCCeeeeccceecHHHHHHHhh----CCCeeeeCC--CCCcccCHHhccc
Confidence            455789999988888888888889999999998877765    555689999  9998777766554

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

Probab=94.11  E-value=0.018  Score=45.21  Aligned_cols=49  Identities=24%  Similarity=0.611  Sum_probs=35.9

Q ss_pred             cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHH
Q 048114           47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY  107 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  107 (234)
                      -..|..|+---+ .+.+.++.|.|.||..|...-.         +-.||  .|+..+....
T Consensus         3 ~VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~---------~~~C~--lCkk~ir~i~   51 (233)
T KOG4739|consen    3 FVHCNKCFRFPS-QDPFFLTACRHVFCEPCLKASS---------PDVCP--LCKKSIRIIQ   51 (233)
T ss_pred             eEEeccccccCC-CCceeeeechhhhhhhhcccCC---------ccccc--cccceeeeee
Confidence            356888987655 6778888999999999985432         12799  8987765543

>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=94.07  E-value=0.033  Score=39.79  Aligned_cols=37  Identities=14%  Similarity=0.515  Sum_probs=28.4

Q ss_pred             CcccccccccCCCCCCceeeCCCC------ChhhHHHHHHHHH
Q 048114           46 TSFICDICVEPKSTDESFSIKGCS------HSYCTECMTKYVA   82 (234)
Q Consensus        46 ~~~~C~iC~~~~~~~~~~~~~~C~------H~fC~~Cl~~~~~   82 (234)
                      ...+|.||++.+...+.+...+|+      |.||.+|+++|-.
T Consensus        25 ~~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   25 CTVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             cCeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHh
Confidence            378999999999763444444675      7799999999953

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.

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=93.85  E-value=0.034  Score=32.78  Aligned_cols=27  Identities=19%  Similarity=0.449  Sum_probs=20.1

Q ss_pred             CcccCCCCCc-eeeeccCCCceEec-CCCCC
Q 048114          206 NWRRCPNCKI-FVEKKEGCRYMRCS-SNPQL  234 (234)
Q Consensus       206 ~~k~CP~C~~-~i~k~~GCnhm~C~-C~~~F  234 (234)
                      ..+.||+|+. .+....  +.++|. ||+++
T Consensus        19 ~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~   47 (50)
T PRK00432         19 KNKFCPRCGSGFMAEHL--DRWHCGKCGYTE   47 (50)
T ss_pred             ccCcCcCCCcchheccC--CcEECCCcCCEE
Confidence            4579999998 444444  799995 99864

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

Probab=93.82  E-value=0.044  Score=29.68  Aligned_cols=27  Identities=22%  Similarity=0.528  Sum_probs=17.1

Q ss_pred             ccCCCCCceee-eccCCCceEec-CCCCC
Q 048114          208 RRCPNCKIFVE-KKEGCRYMRCS-SNPQL  234 (234)
Q Consensus       208 k~CP~C~~~i~-k~~GCnhm~C~-C~~~F  234 (234)
                      +-||.|+.++. +.++=..+.|+ |+|++
T Consensus         2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y~~   30 (35)
T PF02150_consen    2 RFCPECGNLLYPKEDKEKRVACRTCGYEE   30 (35)
T ss_dssp             -BETTTTSBEEEEEETTTTEEESSSS-EE
T ss_pred             eeCCCCCccceEcCCCccCcCCCCCCCcc
Confidence            57999999554 44444444995 99864

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 ....

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

Probab=93.77  E-value=0.098  Score=44.14  Aligned_cols=56  Identities=21%  Similarity=0.605  Sum_probs=41.0

Q ss_pred             CcccccccccCCC--CCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHH
Q 048114           46 TSFICDICVEPKS--TDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYC  108 (234)
Q Consensus        46 ~~~~C~iC~~~~~--~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  108 (234)
                      -..+|+||++.+.  .+.....+.|||.|=.+|+++|+.     ....+.||  .|..+-....|
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-----k~~~~~cp--~c~~katkr~i   60 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-----KKTKMQCP--LCSGKATKRQI   60 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHh-----hhhhhhCc--ccCChhHHHHH
Confidence            3568999999874  333444569999999999999993     33577899  78765444443

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=93.65  E-value=0.05  Score=29.86  Aligned_cols=31  Identities=26%  Similarity=0.690  Sum_probs=23.1

Q ss_pred             eecCCCCCCCCceecCCC---CccCcccCccccccc
Q 048114          134 KFYCPFKDCSALLIDDGG---EAIRESVCPDCNRMF  166 (234)
Q Consensus       134 ~~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~~  166 (234)
                      .+.||  .|+..+..+++   .....++|+.|+..|
T Consensus         2 ~i~CP--~C~~~f~v~~~~l~~~~~~vrC~~C~~~f   35 (37)
T PF13719_consen    2 IITCP--NCQTRFRVPDDKLPAGGRKVRCPKCGHVF   35 (37)
T ss_pred             EEECC--CCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence            35799  99988877653   345579999998765

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

Probab=93.47  E-value=0.091  Score=48.31  Aligned_cols=55  Identities=25%  Similarity=0.620  Sum_probs=43.6

Q ss_pred             cCCcccccccccCCCCCC-ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCC
Q 048114           44 IETSFICDICVEPKSTDE-SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCK  100 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~  100 (234)
                      ....++|.||++.+.... +.+...|-|.|...|++.|....-.++...-+||  .|.
T Consensus       188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP--~Cq  243 (950)
T KOG1952|consen  188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCP--ACQ  243 (950)
T ss_pred             hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCC--ccc
Confidence            466889999999986443 4566689999999999999998544456677999  676

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

Probab=93.11  E-value=0.025  Score=44.95  Aligned_cols=56  Identities=16%  Similarity=0.431  Sum_probs=41.5

Q ss_pred             cccccccccCCCCCC-------ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHh
Q 048114           47 SFICDICVEPKSTDE-------SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR  109 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~-------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~  109 (234)
                      ...|.||...+..+.       ....++|+|.|.-.|++.|...    | ..-.||  -|++.++....-
T Consensus       224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWciv----G-KkqtCP--YCKekVdl~rmf  286 (328)
T KOG1734|consen  224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIV----G-KKQTCP--YCKEKVDLKRMF  286 (328)
T ss_pred             cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheee----c-CCCCCc--hHHHHhhHhhhc
Confidence            456999998875433       3334599999999999999853    3 245899  999988876543

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

Probab=93.05  E-value=0.052  Score=44.86  Aligned_cols=35  Identities=26%  Similarity=0.585  Sum_probs=26.4

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHH
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVA   82 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~   82 (234)
                      .+...|+||+..-.  . ..+.+|+|.-|.+|+.+|+-
T Consensus       420 sEd~lCpICyA~pi--~-Avf~PC~H~SC~~CI~qHlm  454 (489)
T KOG4692|consen  420 SEDNLCPICYAGPI--N-AVFAPCSHRSCYGCITQHLM  454 (489)
T ss_pred             cccccCcceecccc--h-hhccCCCCchHHHHHHHHHh
Confidence            44668999987421  2 23459999999999999984

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.93  E-value=0.12  Score=40.64  Aligned_cols=57  Identities=14%  Similarity=0.285  Sum_probs=44.0

Q ss_pred             CCcccccccccCCCCCC-ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114           45 ETSFICDICVEPKSTDE-SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD  110 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  110 (234)
                      +..+.|+||-+.+...- ...+.+|||.||.+|++.+|.       ..+.||  .++.++...+|-.
T Consensus       219 s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir-------~D~v~p--v~d~plkdrdiI~  276 (303)
T KOG3039|consen  219 SKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR-------KDMVDP--VTDKPLKDRDIIG  276 (303)
T ss_pred             ccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc-------cccccc--CCCCcCcccceEe
Confidence            56899999999986332 345779999999999999985       345678  7888887776543

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

Probab=92.27  E-value=0.083  Score=44.43  Aligned_cols=47  Identities=34%  Similarity=0.844  Sum_probs=34.5

Q ss_pred             CcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCC
Q 048114           46 TSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCK  100 (234)
Q Consensus        46 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~  100 (234)
                      ....|-||-|.-   +.+.+.+|||..|..|+..|-.+.  +   .-.||.+.|.
T Consensus       368 TFeLCKICaend---KdvkIEPCGHLlCt~CLa~WQ~sd--~---gq~CPFCRcE  414 (563)
T KOG1785|consen  368 TFELCKICAEND---KDVKIEPCGHLLCTSCLAAWQDSD--E---GQTCPFCRCE  414 (563)
T ss_pred             hHHHHHHhhccC---CCcccccccchHHHHHHHhhcccC--C---CCCCCceeeE
Confidence            345799998753   667788999999999999887432  1   3468865553

>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=91.95  E-value=0.055  Score=42.28  Aligned_cols=52  Identities=19%  Similarity=0.602  Sum_probs=37.1

Q ss_pred             cccccccccCCCCCCcee---eCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           47 SFICDICVEPKSTDESFS---IKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~~~---~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ...||||..+.-.+-.+.   .+.|-|.+|-+|+.+.++    .  .+-.||-.+|+.+|.
T Consensus        10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs----~--GpAqCP~~gC~kILR   64 (314)
T COG5220          10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFS----R--GPAQCPYKGCGKILR   64 (314)
T ss_pred             cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhc----C--CCCCCCCccHHHHHH
Confidence            346999997763322222   235999999999998885    2  367899999986544

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=91.91  E-value=0.13  Score=27.99  Aligned_cols=31  Identities=29%  Similarity=0.633  Sum_probs=22.3

Q ss_pred             eecCCCCCCCCceecCCC---CccCcccCccccccc
Q 048114          134 KFYCPFKDCSALLIDDGG---EAIRESVCPDCNRMF  166 (234)
Q Consensus       134 ~~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~~  166 (234)
                      .+.||  .|+..+..++.   .....+.|+.|+..|
T Consensus         2 ~i~Cp--~C~~~y~i~d~~ip~~g~~v~C~~C~~~f   35 (36)
T PF13717_consen    2 IITCP--NCQAKYEIDDEKIPPKGRKVRCSKCGHVF   35 (36)
T ss_pred             EEECC--CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence            35788  89988777643   344568999998764

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

Probab=91.68  E-value=0.16  Score=42.64  Aligned_cols=48  Identities=25%  Similarity=0.705  Sum_probs=32.6

Q ss_pred             cccccccccCCCCCCceeeC-CCCChhhHHHHHHHHHHHHhcCCccccCCCCCCC
Q 048114           47 SFICDICVEPKSTDESFSIK-GCSHSYCTECMTKYVASKLQENITSINCPVADCK  100 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~~~~~-~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~  100 (234)
                      .-.|.||-+-++.+...... .|||.|...|+.+|+...-+    .-.||  .|+
T Consensus         4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps----~R~cp--ic~   52 (465)
T KOG0827|consen    4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPS----NRGCP--ICQ   52 (465)
T ss_pred             cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCc----cCCCC--cee
Confidence            34699995555544444333 49999999999999964322    24688  665

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

Probab=91.66  E-value=0.17  Score=41.03  Aligned_cols=40  Identities=20%  Similarity=0.551  Sum_probs=34.2

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHH
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASK   84 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~   84 (234)
                      -+.-.|.||+--|..+..|....|.|+|...||.+|++..
T Consensus       113 ~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~  152 (368)
T KOG4445|consen  113 HPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTEC  152 (368)
T ss_pred             CCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHH
Confidence            4566899999888777778888999999999999999654

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

Probab=91.46  E-value=0.082  Score=45.15  Aligned_cols=49  Identities=22%  Similarity=0.569  Sum_probs=35.4

Q ss_pred             CCcccccccccCCCCCC-ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           45 ETSFICDICVEPKSTDE-SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      -+..+|+||+|....+- .+....|.|+|...|+..|.         ...||  .|.....
T Consensus       173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~---------~~scp--vcR~~q~  222 (493)
T KOG0804|consen  173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW---------DSSCP--VCRYCQS  222 (493)
T ss_pred             ccCCCcchhHhhcCccccceeeeecccccchHHHhhcc---------cCcCh--hhhhhcC
Confidence            44679999999886432 33445999999999998876         45788  5654433

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

Probab=91.41  E-value=0.24  Score=40.12  Aligned_cols=44  Identities=23%  Similarity=0.776  Sum_probs=33.3

Q ss_pred             ccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCC
Q 048114           48 FICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKG  101 (234)
Q Consensus        48 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~  101 (234)
                      +.|+.|.--+.  +......|+|.||.+|+..-+..      ..+.||  .|..
T Consensus       275 LkCplc~~Llr--np~kT~cC~~~fc~eci~~al~d------sDf~Cp--nC~r  318 (427)
T COG5222         275 LKCPLCHCLLR--NPMKTPCCGHTFCDECIGTALLD------SDFKCP--NCSR  318 (427)
T ss_pred             ccCcchhhhhh--CcccCccccchHHHHHHhhhhhh------ccccCC--Cccc
Confidence            78999987654  55666789999999999876642      267899  6754

>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding

Probab=91.41  E-value=0.1  Score=29.36  Aligned_cols=27  Identities=26%  Similarity=0.709  Sum_probs=20.6

Q ss_pred             cCCcccCCCCCceeeeccCCCceEec---CCCCC
Q 048114          204 KENWRRCPNCKIFVEKKEGCRYMRCS---SNPQL  234 (234)
Q Consensus       204 ~~~~k~CP~C~~~i~k~~GCnhm~C~---C~~~F  234 (234)
                      ..++++||+|+++-    |+--+.|+   |++.|
T Consensus         8 lRGirkCp~CGt~N----G~R~~~CKN~~C~~~~   37 (44)
T PF14952_consen    8 LRGIRKCPKCGTYN----GTRGLSCKNKSCPQVF   37 (44)
T ss_pred             HhccccCCcCcCcc----CcccccccCCccchhh
Confidence            46789999999975    66667784   77655

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

Probab=91.34  E-value=0.069  Score=31.57  Aligned_cols=44  Identities=27%  Similarity=0.598  Sum_probs=31.1

Q ss_pred             ccccccccCCCCCCceeeCCCCCh-hhHHHHHHHHHHHHhcCCccccCCCCCCCCC
Q 048114           48 FICDICVEPKSTDESFSIKGCSHS-YCTECMTKYVASKLQENITSINCPVADCKGV  102 (234)
Q Consensus        48 ~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~  102 (234)
                      -+|.||+|.-.  +.+ +-.|||. +|.+|-.+.++.      ..=.||  .|..+
T Consensus         8 dECTICye~pv--dsV-lYtCGHMCmCy~Cg~rl~~~------~~g~CP--iCRap   52 (62)
T KOG4172|consen    8 DECTICYEHPV--DSV-LYTCGHMCMCYACGLRLKKA------LHGCCP--ICRAP   52 (62)
T ss_pred             cceeeeccCcc--hHH-HHHcchHHhHHHHHHHHHHc------cCCcCc--chhhH
Confidence            56999998542  333 3489999 999999887753      233688  67654

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

Probab=90.77  E-value=0.25  Score=28.47  Aligned_cols=26  Identities=27%  Similarity=0.424  Sum_probs=16.6

Q ss_pred             ccCCCCCceeeeccCCCceEec-CCCC
Q 048114          208 RRCPNCKIFVEKKEGCRYMRCS-SNPQ  233 (234)
Q Consensus       208 k~CP~C~~~i~k~~GCnhm~C~-C~~~  233 (234)
                      -.||+|+..++-.++=..++|. ||..
T Consensus         4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~   30 (46)
T PRK00398          4 YKCARCGREVELDEYGTGVRCPYCGYR   30 (46)
T ss_pred             EECCCCCCEEEECCCCCceECCCCCCe
Confidence            4677888777654433367774 7764

>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=90.50  E-value=0.071  Score=31.45  Aligned_cols=37  Identities=27%  Similarity=0.625  Sum_probs=17.5

Q ss_pred             CCCCceecCCC--CccCcccCccccccccccCCCCCCCC
Q 048114          141 DCSALLIDDGG--EAIRESVCPDCNRMFCAQCKVPWHAG  177 (234)
Q Consensus       141 ~C~~~~~~~~~--~~~~~~~C~~C~~~~C~~C~~~~H~~  177 (234)
                      +|...+.....  .......|+.|+..||..|..-.|..
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            45554443321  11345899999999999887765643

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.

>PF04641 Rtf2: Rtf2 RING-finger

Probab=90.42  E-value=0.37  Score=39.06  Aligned_cols=71  Identities=15%  Similarity=0.358  Sum_probs=51.1

Q ss_pred             cCCcccccccccCCCCC-CceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccCCH-HHHHHHH
Q 048114           44 IETSFICDICVEPKSTD-ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPE-DVFNRWG  121 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~-~~~~~~~  121 (234)
                      ....+.|||...++... ..+.+.+|||.|...++++.-        ..-.||  .|+..+...+|-.+-+. +.++.+.
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k--------~~~~Cp--~c~~~f~~~DiI~Lnp~~ee~~~l~  179 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK--------KSKKCP--VCGKPFTEEDIIPLNPPEEELEKLR  179 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc--------cccccc--ccCCccccCCEEEecCCccHHHHHH
Confidence            36688999999998643 456677999999999998772        123499  99999998877666543 3444444


Q ss_pred             HHH
Q 048114          122 NAL  124 (234)
Q Consensus       122 ~~~  124 (234)
                      ..+
T Consensus       180 ~~~  182 (260)
T PF04641_consen  180 ERM  182 (260)
T ss_pred             HHH
Confidence            333

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=89.93  E-value=0.092  Score=31.30  Aligned_cols=47  Identities=21%  Similarity=0.458  Sum_probs=31.6

Q ss_pred             CcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHH
Q 048114           46 TSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPE  106 (234)
Q Consensus        46 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  106 (234)
                      +...|-.|...-.  . -.+++|+|.+|..||         .+..--.||  -|+..++..
T Consensus         6 ~~~~~~~~~~~~~--~-~~~~pCgH~I~~~~f---------~~~rYngCP--fC~~~~~~~   52 (55)
T PF14447_consen    6 PEQPCVFCGFVGT--K-GTVLPCGHLICDNCF---------PGERYNGCP--FCGTPFEFD   52 (55)
T ss_pred             cceeEEEcccccc--c-cccccccceeecccc---------ChhhccCCC--CCCCcccCC
Confidence            3455777755432  3 334699999999999         433344699  898887654

>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=89.89  E-value=0.12  Score=35.64  Aligned_cols=34  Identities=26%  Similarity=0.617  Sum_probs=27.6

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMT   78 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~   78 (234)
                      +++...|++|...+.. ..+...+|||.|...|++
T Consensus        75 i~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   75 ITESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             ECCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence            3567789999999865 556667999999999975

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 [].

>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=89.75  E-value=0.75  Score=37.24  Aligned_cols=51  Identities=22%  Similarity=0.674  Sum_probs=35.2

Q ss_pred             cccccccCCCCC--CceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHH
Q 048114           49 ICDICVEPKSTD--ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY  107 (234)
Q Consensus        49 ~C~iC~~~~~~~--~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  107 (234)
                      .|++|-.+.-..  -...+-+|+|..|-+|+...+.      ..+-.||  .|..++...-
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~------~g~~~Cp--eC~~iLRk~n   54 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFS------LGPAQCP--ECMVILRKNN   54 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHh------cCCCCCC--cccchhhhcc
Confidence            489998765322  1222349999999999988874      2355799  9988766543

>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed

Probab=89.37  E-value=0.096  Score=42.90  Aligned_cols=30  Identities=27%  Similarity=0.463  Sum_probs=24.7

Q ss_pred             CCcccCCCCCceeeecc-CCCceEec-CCCCC
Q 048114          205 ENWRRCPNCKIFVEKKE-GCRYMRCS-SNPQL  234 (234)
Q Consensus       205 ~~~k~CP~C~~~i~k~~-GCnhm~C~-C~~~F  234 (234)
                      ..|.+||+|+..|.+.+ .=|.++|. |||||
T Consensus        36 ~lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~   67 (296)
T CHL00174         36 HLWVQCENCYGLNYKKFLKSKMNICEQCGYHL   67 (296)
T ss_pred             CCeeECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence            45899999999888644 67889995 99997

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

Probab=89.25  E-value=0.43  Score=30.54  Aligned_cols=57  Identities=23%  Similarity=0.482  Sum_probs=20.2

Q ss_pred             CCCCceecCCCCccCcccCccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHHHhcCCcccCCCCCceeeec
Q 048114          141 DCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKIFVEKK  220 (234)
Q Consensus       141 ~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~~i~k~  220 (234)
                      -|+.-+-..... ...+.|..|+...|..|          -+|.+                  +...+-||+|+....+.
T Consensus        14 iCGD~VGl~~~G-e~FVAC~eC~fPvCr~C----------yEYEr------------------keg~q~CpqCkt~ykr~   64 (80)
T PF14569_consen   14 ICGDDVGLTENG-EVFVACHECAFPVCRPC----------YEYER------------------KEGNQVCPQCKTRYKRH   64 (80)
T ss_dssp             SS--B--B-SSS-SB--S-SSS-----HHH----------HHHHH------------------HTS-SB-TTT--B----
T ss_pred             cccCccccCCCC-CEEEEEcccCCccchhH----------HHHHh------------------hcCcccccccCCCcccc
Confidence            565444333322 34488999999999844          44333                  56779999999998887


Q ss_pred             cCCCce
Q 048114          221 EGCRYM  226 (234)
Q Consensus       221 ~GCnhm  226 (234)
                      .|+..|
T Consensus        65 kgsp~V   70 (80)
T PF14569_consen   65 KGSPRV   70 (80)
T ss_dssp             TT----
T ss_pred             cCCCCC
Confidence            777543

>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains

Probab=89.20  E-value=0.35  Score=25.42  Aligned_cols=27  Identities=22%  Similarity=0.411  Sum_probs=17.6

Q ss_pred             cccCCCCCceeeeccCCCceEec-CCCC
Q 048114          207 WRRCPNCKIFVEKKEGCRYMRCS-SNPQ  233 (234)
Q Consensus       207 ~k~CP~C~~~i~k~~GCnhm~C~-C~~~  233 (234)
                      .+.||.|+.......|=--|.|. ||.+
T Consensus         3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~   30 (32)
T PF09297_consen    3 HRFCGRCGAPTKPAPGGWARRCPSCGHE   30 (32)
T ss_dssp             TSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred             CcccCcCCccccCCCCcCEeECCCCcCE
Confidence            47899999999998887789995 8875

; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=89.20  E-value=0.32  Score=28.65  Aligned_cols=28  Identities=36%  Similarity=0.913  Sum_probs=19.6

Q ss_pred             cCCCCCCCCceecCCCCccCcccCcccccc
Q 048114          136 YCPFKDCSALLIDDGGEAIRESVCPDCNRM  165 (234)
Q Consensus       136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~  165 (234)
                      +||  .|+..+............|+.|++.
T Consensus         2 FCp--~Cg~~l~~~~~~~~~~~vC~~Cg~~   29 (52)
T smart00661        2 FCP--KCGNMLIPKEGKEKRRFVCRKCGYE   29 (52)
T ss_pred             CCC--CCCCccccccCCCCCEEECCcCCCe
Confidence            688  9998877765433345788888764

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

Probab=89.15  E-value=0.36  Score=42.27  Aligned_cols=40  Identities=30%  Similarity=0.766  Sum_probs=28.4

Q ss_pred             CeecCCCCCCCCceecCCCCccCcccCcc--ccccccccCCCCC--CC
Q 048114          133 QKFYCPFKDCSALLIDDGGEAIRESVCPD--CNRMFCAQCKVPW--HA  176 (234)
Q Consensus       133 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~--H~  176 (234)
                      +...||  .|...+..+..  .+.+.|..  |++.||+.|...|  |.
T Consensus       225 ntk~CP--~c~~~iek~~g--c~~~~~~~~~c~~~FCw~Cl~~~~~h~  268 (444)
T KOG1815|consen  225 NTKECP--KCKVPIEKDGG--CNHMTCKSASCKHEFCWVCLASLSDHG  268 (444)
T ss_pred             cCccCC--CcccchhccCC--ccccccccCCcCCeeceeeeccccccc
Confidence            334588  89888776543  33356655  9999999997776  64

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

Probab=89.09  E-value=0.23  Score=45.64  Aligned_cols=52  Identities=33%  Similarity=0.829  Sum_probs=38.1

Q ss_pred             ccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114           48 FICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD  110 (234)
Q Consensus        48 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  110 (234)
                      +.|.+|.+   . +.+.+..|+|.||.+|+...+...     ....||  .|...+....+..
T Consensus       455 ~~c~ic~~---~-~~~~it~c~h~~c~~c~~~~i~~~-----~~~~~~--~cr~~l~~~~l~s  506 (674)
T KOG1001|consen  455 HWCHICCD---L-DSFFITRCGHDFCVECLKKSIQQS-----ENAPCP--LCRNVLKEKKLLS  506 (674)
T ss_pred             cccccccc---c-ccceeecccchHHHHHHHhccccc-----cCCCCc--HHHHHHHHHHHhh
Confidence            89999999   2 334445999999999999999533     223677  8887776665544

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

Probab=88.71  E-value=0.17  Score=27.38  Aligned_cols=28  Identities=29%  Similarity=0.743  Sum_probs=19.1

Q ss_pred             ecCCCCCCCCceecCCCCccCcccCcccccc
Q 048114          135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRM  165 (234)
Q Consensus       135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~  165 (234)
                      .+||  .|++.+....+..... .|+.|++.
T Consensus         2 ~FCp--~C~nlL~p~~~~~~~~-~C~~C~Y~   29 (35)
T PF02150_consen    2 RFCP--ECGNLLYPKEDKEKRV-ACRTCGYE   29 (35)
T ss_dssp             -BET--TTTSBEEEEEETTTTE-EESSSS-E
T ss_pred             eeCC--CCCccceEcCCCccCc-CCCCCCCc
Confidence            4789  9999988776554443 78888764

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 ....

>PHA03096 p28-like protein; Provisional

Probab=88.66  E-value=0.3  Score=39.92  Aligned_cols=39  Identities=21%  Similarity=0.401  Sum_probs=30.6

Q ss_pred             ccccccccCCCCC-----CceeeCCCCChhhHHHHHHHHHHHHh
Q 048114           48 FICDICVEPKSTD-----ESFSIKGCSHSYCTECMTKYVASKLQ   86 (234)
Q Consensus        48 ~~C~iC~~~~~~~-----~~~~~~~C~H~fC~~Cl~~~~~~~i~   86 (234)
                      ..|.||++.....     ..-.+..|.|.||..|++.|......
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            7899999987532     12235699999999999999987753

>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]

Probab=88.54  E-value=0.32  Score=28.21  Aligned_cols=29  Identities=21%  Similarity=0.261  Sum_probs=19.2

Q ss_pred             CCcccCCCCCceeeeccCCCceEe-cCCCC
Q 048114          205 ENWRRCPNCKIFVEKKEGCRYMRC-SSNPQ  233 (234)
Q Consensus       205 ~~~k~CP~C~~~i~k~~GCnhm~C-~C~~~  233 (234)
                      ...+.||+|+--+....-=+...| +|||.
T Consensus        17 rk~~~CPrCG~gvfmA~H~dR~~CGkCgyT   46 (51)
T COG1998          17 RKNRFCPRCGPGVFMADHKDRWACGKCGYT   46 (51)
T ss_pred             EccccCCCCCCcchhhhcCceeEeccccce
Confidence            345799999964444333348889 69873

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

Probab=88.09  E-value=0.4  Score=25.71  Aligned_cols=25  Identities=20%  Similarity=0.545  Sum_probs=14.1

Q ss_pred             ccCCCCCceeeec----cCCCceEec-CCC
Q 048114          208 RRCPNCKIFVEKK----EGCRYMRCS-SNP  232 (234)
Q Consensus       208 k~CP~C~~~i~k~----~GCnhm~C~-C~~  232 (234)
                      |.||.|+..++..    ++=..+.|. ||+
T Consensus         1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~   30 (34)
T PF14803_consen    1 KFCPQCGGPLERRIPEGDDRERLVCPACGF   30 (34)
T ss_dssp             -B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred             CccccccChhhhhcCCCCCccceECCCCCC
Confidence            5799999988862    567779995 885

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

Probab=87.13  E-value=0.42  Score=44.46  Aligned_cols=41  Identities=29%  Similarity=0.614  Sum_probs=34.0

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKL   85 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i   85 (234)
                      +++...|.+|.-.+.. ++|.+.+|||.|.++|+.+++....
T Consensus       814 ~ep~d~C~~C~~~ll~-~pF~vf~CgH~FH~~Cl~~~v~~~~  854 (911)
T KOG2034|consen  814 LEPQDSCDHCGRPLLI-KPFYVFPCGHCFHRDCLIRHVLSLL  854 (911)
T ss_pred             ecCccchHHhcchhhc-CcceeeeccchHHHHHHHHHHHccc
Confidence            4778899999988854 5677779999999999999986543

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

Probab=86.84  E-value=0.48  Score=38.18  Aligned_cols=54  Identities=19%  Similarity=0.516  Sum_probs=39.7

Q ss_pred             CCcccccccccCCCCCCceeeCCC-CChhhHHHHHHHHHHHHhcCCccccCCCC-CCC
Q 048114           45 ETSFICDICVEPKSTDESFSIKGC-SHSYCTECMTKYVASKLQENITSINCPVA-DCK  100 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C-~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~-~C~  100 (234)
                      ...+-|.+|.|.++...+++..+= .|.||.-|-++.|+.+-.  ...+.||.. .|.
T Consensus       266 ~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~--sgevYCPSGdkCP  321 (352)
T KOG3579|consen  266 SAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGA--SGEVYCPSGDKCP  321 (352)
T ss_pred             CCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcC--CCceeCCCCCcCc
Confidence            445899999999976665543221 799999999999988743  347899963 454

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=86.79  E-value=0.37  Score=26.36  Aligned_cols=30  Identities=17%  Similarity=0.506  Sum_probs=20.3

Q ss_pred             ecCCCCCCCCceecCCC---CccCcccCccccccc
Q 048114          135 FYCPFKDCSALLIDDGG---EAIRESVCPDCNRMF  166 (234)
Q Consensus       135 ~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~~  166 (234)
                      +.||  .|+..+..+.+   .....+.|+.|+..|
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  89987766532   123358999998764

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.

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=86.23  E-value=0.41  Score=23.17  Aligned_cols=22  Identities=45%  Similarity=1.224  Sum_probs=14.1

Q ss_pred             cCCCCCCCCceecCCCCccCcccCcccccc
Q 048114          136 YCPFKDCSALLIDDGGEAIRESVCPDCNRM  165 (234)
Q Consensus       136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~  165 (234)
                      +||  .|+..+..+      ..+|+.||+.
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            477  788766422      2568888764

>PLN03086 PRLI-interacting factor K; Provisional

Probab=86.14  E-value=1.4  Score=39.59  Aligned_cols=59  Identities=17%  Similarity=0.472  Sum_probs=36.4

Q ss_pred             CccccCCCCCCCCCCCHHHHhccCCHHHHHHHHHHHHHHHHhCCCeecCCCCCCCCceecCCCCccCcccCccccccc
Q 048114           89 ITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMF  166 (234)
Q Consensus        89 ~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~  166 (234)
                      ...+.||  .|...+....+..++.               .=....+.||..+|+..+.....  ...+.|+.|+..|
T Consensus       405 ~~~V~C~--NC~~~i~l~~l~lHe~---------------~C~r~~V~Cp~~~Cg~v~~r~el--~~H~~C~~Cgk~f  463 (567)
T PLN03086        405 VDTVECR--NCKHYIPSRSIALHEA---------------YCSRHNVVCPHDGCGIVLRVEEA--KNHVHCEKCGQAF  463 (567)
T ss_pred             CCeEECC--CCCCccchhHHHHHHh---------------hCCCcceeCCcccccceeecccc--ccCccCCCCCCcc
Confidence            4567899  5988877666542210               01123456887679988765433  2346888887765

>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)

Probab=86.08  E-value=0.79  Score=25.70  Aligned_cols=23  Identities=26%  Similarity=0.692  Sum_probs=18.1

Q ss_pred             cccCCCCCceeee-ccCCCceEec-CC
Q 048114          207 WRRCPNCKIFVEK-KEGCRYMRCS-SN  231 (234)
Q Consensus       207 ~k~CP~C~~~i~k-~~GCnhm~C~-C~  231 (234)
                      ...||.|+.++.+ .+|  .+.|. |+
T Consensus        17 ~~~Cp~C~~PL~~~k~g--~~~Cv~C~   41 (41)
T PF06677_consen   17 DEHCPDCGTPLMRDKDG--KIYCVSCG   41 (41)
T ss_pred             cCccCCCCCeeEEecCC--CEECCCCC
Confidence            3799999998888 556  68885 74

It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=85.88  E-value=1.4  Score=36.47  Aligned_cols=55  Identities=25%  Similarity=0.600  Sum_probs=37.9

Q ss_pred             cccccccccCCCCC-CceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHh
Q 048114           47 SFICDICVEPKSTD-ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR  109 (234)
Q Consensus        47 ~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~  109 (234)
                      .-.|++|++++... +.|.-.+||-.+|+-||...-     ++ ..=+||  .|....+.+.++
T Consensus        14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~ir-----q~-lngrcp--acrr~y~denv~   69 (480)
T COG5175          14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIR-----QN-LNGRCP--ACRRKYDDENVR   69 (480)
T ss_pred             cccCcccccccccccCCcccCCcccHHHHHHHHHHH-----hh-ccCCCh--Hhhhhcccccee
Confidence            44599999998643 334344889999999995432     33 234799  898887776555

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

Probab=85.34  E-value=0.37  Score=40.58  Aligned_cols=50  Identities=28%  Similarity=0.697  Sum_probs=37.7

Q ss_pred             CCcccccccccCCCCC-CceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCC
Q 048114           45 ETSFICDICVEPKSTD-ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKG  101 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~  101 (234)
                      +-.+.|..|.+-+... +....++|.|+|...|+..++.     +..+-.||  .|..
T Consensus       363 e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~-----~n~~rsCP--~Crk  413 (518)
T KOG1941|consen  363 ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILE-----NNGTRSCP--NCRK  413 (518)
T ss_pred             HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHH-----hCCCCCCc--cHHH
Confidence            4467899999988432 3445679999999999999983     33466899  7763

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

Probab=84.63  E-value=0.74  Score=38.00  Aligned_cols=46  Identities=28%  Similarity=0.592  Sum_probs=32.6

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ...++||||++.+...- ++ .+=||..|.+|-.          ...-+||  .|...+.
T Consensus        46 ~~lleCPvC~~~l~~Pi-~Q-C~nGHlaCssC~~----------~~~~~CP--~Cr~~~g   91 (299)
T KOG3002|consen   46 LDLLDCPVCFNPLSPPI-FQ-CDNGHLACSSCRT----------KVSNKCP--TCRLPIG   91 (299)
T ss_pred             hhhccCchhhccCcccc-ee-cCCCcEehhhhhh----------hhcccCC--ccccccc
Confidence            44788999999985211 22 1448999999985          1345899  6887777

>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=84.26  E-value=1.2  Score=22.72  Aligned_cols=21  Identities=33%  Similarity=0.751  Sum_probs=13.9

Q ss_pred             cCCCCCceeeeccCCCceEec
Q 048114          209 RCPNCKIFVEKKEGCRYMRCS  229 (234)
Q Consensus       209 ~CP~C~~~i~k~~GCnhm~C~  229 (234)
                      .||.|+..+.+.+|=-...|.
T Consensus         1 ~CP~C~s~l~~~~~ev~~~C~   21 (28)
T PF03119_consen    1 TCPVCGSKLVREEGEVDIRCP   21 (28)
T ss_dssp             B-TTT--BEEE-CCTTCEEE-
T ss_pred             CcCCCCCEeEcCCCCEeEECC
Confidence            599999999999887788874

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.

>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated

Probab=84.06  E-value=0.62  Score=43.56  Aligned_cols=24  Identities=33%  Similarity=0.858  Sum_probs=21.3

Q ss_pred             ccCCCCCceeeeccCCCceEec-CCCC
Q 048114          208 RRCPNCKIFVEKKEGCRYMRCS-SNPQ  233 (234)
Q Consensus       208 k~CP~C~~~i~k~~GCnhm~C~-C~~~  233 (234)
                      ..||.|+..+...+||.  +|+ |||.
T Consensus       725 ~~Cp~Cg~~l~~~~GC~--~C~~CG~s  749 (752)
T PRK08665        725 GACPECGSILEHEEGCV--VCHSCGYS  749 (752)
T ss_pred             CCCCCCCcccEECCCCC--cCCCCCCC
Confidence            36999999999999998  996 9984

>PF12773 DZR: Double zinc ribbon

Probab=84.03  E-value=0.9  Score=26.46  Aligned_cols=26  Identities=27%  Similarity=0.844  Sum_probs=12.7

Q ss_pred             eecCCCCCCCCceecCCCCccCcccCccccc
Q 048114          134 KFYCPFKDCSALLIDDGGEAIRESVCPDCNR  164 (234)
Q Consensus       134 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~  164 (234)
                      ..+||  .|+..+..   .....+.|+.|++
T Consensus        12 ~~fC~--~CG~~l~~---~~~~~~~C~~Cg~   37 (50)
T PF12773_consen   12 AKFCP--HCGTPLPP---PDQSKKICPNCGA   37 (50)
T ss_pred             ccCCh--hhcCChhh---ccCCCCCCcCCcC
Confidence            34666  66665541   1122255665544

>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]

Probab=83.98  E-value=0.65  Score=33.14  Aligned_cols=26  Identities=23%  Similarity=0.542  Sum_probs=21.4

Q ss_pred             CcccCCCCCceeeeccCCCceEec-CCCC
Q 048114          206 NWRRCPNCKIFVEKKEGCRYMRCS-SNPQ  233 (234)
Q Consensus       206 ~~k~CP~C~~~i~k~~GCnhm~C~-C~~~  233 (234)
                      ..+.||.||.+.++.+|  .++|. ||+.
T Consensus        27 L~~hCp~Cg~PLF~KdG--~v~CPvC~~~   53 (131)
T COG1645          27 LAKHCPKCGTPLFRKDG--EVFCPVCGYR   53 (131)
T ss_pred             HHhhCcccCCcceeeCC--eEECCCCCce
Confidence            34899999999998776  79994 9864

>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=83.72  E-value=0.97  Score=26.12  Aligned_cols=27  Identities=22%  Similarity=0.288  Sum_probs=20.3

Q ss_pred             CcccCC--CCCceeeeccCCCceEe-cCCC
Q 048114          206 NWRRCP--NCKIFVEKKEGCRYMRC-SSNP  232 (234)
Q Consensus       206 ~~k~CP--~C~~~i~k~~GCnhm~C-~C~~  232 (234)
                      .-+.||  +|+.-+.-..--+..+| +||+
T Consensus        17 ~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~   46 (47)
T PF01599_consen   17 LRKECPSPRCGAGVFMAEHKDRHYCGKCGY   46 (47)
T ss_dssp             SSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred             hhhcCCCcccCCceEeeecCCCccCCCccc
Confidence            358999  99997777666789999 6986

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.

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

Probab=83.68  E-value=0.15  Score=41.72  Aligned_cols=82  Identities=21%  Similarity=0.491  Sum_probs=44.5

Q ss_pred             hhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccCCHHHHHHHHHHHHHH----H--HhCCCeecCCCCCCCC
Q 048114           71 SYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNALCEA----V--ILGAQKFYCPFKDCSA  144 (234)
Q Consensus        71 ~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~~~~----~--~~~~~~~~Cp~~~C~~  144 (234)
                      .||..|-..+..       .|+.||  .|...|       ++++.+...|..+.--.    .  ........|-  .|+.
T Consensus       277 y~CP~CkakvCs-------LP~eCp--iC~ltL-------Vss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf--~C~~  338 (378)
T KOG2807|consen  277 YFCPQCKAKVCS-------LPIECP--ICSLTL-------VSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCF--ACQG  338 (378)
T ss_pred             eeCCcccCeeec-------CCccCC--ccceeE-------ecchHHHHHHHhhcCCcchhhccccccCCCccee--eecc
Confidence            455555443332       678888  675432       23344444454443111    0  1122334576  6632


Q ss_pred             ceecCCCCccCcccCccccccccccCCCCCC
Q 048114          145 LLIDDGGEAIRESVCPDCNRMFCAQCKVPWH  175 (234)
Q Consensus       145 ~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H  175 (234)
                      .     .......+|..|+..||..|..-.|
T Consensus       339 ~-----~~~~~~y~C~~Ck~~FCldCDv~iH  364 (378)
T KOG2807|consen  339 E-----LLSSGRYRCESCKNVFCLDCDVFIH  364 (378)
T ss_pred             c-----cCCCCcEEchhccceeeccchHHHH
Confidence            2     2223448999999999999977555

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=83.59  E-value=0.62  Score=23.21  Aligned_cols=23  Identities=30%  Similarity=1.003  Sum_probs=14.4

Q ss_pred             ecCCCCCCCCceecCCCCccCcccCcccccc
Q 048114          135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRM  165 (234)
Q Consensus       135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~  165 (234)
                      +.||  .|+..+.. +     ..+|+.||+.
T Consensus         3 ~~Cp--~Cg~~~~~-~-----~~fC~~CG~~   25 (26)
T PF13248_consen    3 MFCP--NCGAEIDP-D-----AKFCPNCGAK   25 (26)
T ss_pred             CCCc--ccCCcCCc-c-----cccChhhCCC
Confidence            4688  88874322 1     2678888764

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

Probab=83.57  E-value=0.36  Score=39.11  Aligned_cols=33  Identities=27%  Similarity=0.571  Sum_probs=26.9

Q ss_pred             cccccccccCCCCCCceeeCCCCChhhHHHHHHHHH
Q 048114           47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVA   82 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~   82 (234)
                      .+-|.||-.++.  +++. ..|+|+||..|....++
T Consensus       241 Pf~c~icr~~f~--~pVv-t~c~h~fc~~ca~~~~q  273 (313)
T KOG1813|consen  241 PFKCFICRKYFY--RPVV-TKCGHYFCEVCALKPYQ  273 (313)
T ss_pred             Cccccccccccc--cchh-hcCCceeehhhhccccc
Confidence            567999999985  4454 59999999999977764

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=83.53  E-value=1.2  Score=43.33  Aligned_cols=29  Identities=31%  Similarity=0.903  Sum_probs=21.1

Q ss_pred             ecCCCCCCCCceecCCCCccCcccCccccccc-----cccCCCC
Q 048114          135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRMF-----CAQCKVP  173 (234)
Q Consensus       135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~-----C~~C~~~  173 (234)
                      +.||  .|+.....        .+|+.||...     |..|+..
T Consensus       668 rkCP--kCG~~t~~--------~fCP~CGs~te~vy~CPsCGae  701 (1337)
T PRK14714        668 RRCP--SCGTETYE--------NRCPDCGTHTEPVYVCPDCGAE  701 (1337)
T ss_pred             EECC--CCCCcccc--------ccCcccCCcCCCceeCccCCCc
Confidence            6899  89875321        4899998775     8888774

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=82.92  E-value=1.6  Score=26.00  Aligned_cols=33  Identities=21%  Similarity=0.528  Sum_probs=27.5

Q ss_pred             cccccccccCCC-CCCceeeCCCCChhhHHHHHH
Q 048114           47 SFICDICVEPKS-TDESFSIKGCSHSYCTECMTK   79 (234)
Q Consensus        47 ~~~C~iC~~~~~-~~~~~~~~~C~H~fC~~Cl~~   79 (234)
                      .-.|++|.+.|. .++.+....|+-.+.++||..
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            456999999996 556777789999999999964

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

Probab=82.64  E-value=1.4  Score=26.68  Aligned_cols=32  Identities=19%  Similarity=0.575  Sum_probs=20.8

Q ss_pred             cCCCCCCCCceecCCCCccCcccCccccccccccCC
Q 048114          136 YCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCK  171 (234)
Q Consensus       136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~  171 (234)
                      .|.  +|+..+...+  ....+.||.||...=++|.
T Consensus        11 ~Ct--SCg~~i~p~e--~~v~F~CPnCGe~~I~Rc~   42 (61)
T COG2888          11 VCT--SCGREIAPGE--TAVKFPCPNCGEVEIYRCA   42 (61)
T ss_pred             eec--cCCCEeccCC--ceeEeeCCCCCceeeehhh
Confidence            566  7877764332  2345899999977666554

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=82.62  E-value=0.86  Score=41.77  Aligned_cols=14  Identities=29%  Similarity=0.567  Sum_probs=8.7

Q ss_pred             CCcccCCCCCceee
Q 048114          205 ENWRRCPNCKIFVE  218 (234)
Q Consensus       205 ~~~k~CP~C~~~i~  218 (234)
                      .+.+.||+||....
T Consensus        39 ~~~~fC~~CG~~~~   52 (645)
T PRK14559         39 VDEAHCPNCGAETG   52 (645)
T ss_pred             cccccccccCCccc
Confidence            34567777776543

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

Probab=82.53  E-value=0.98  Score=36.66  Aligned_cols=46  Identities=28%  Similarity=0.649  Sum_probs=34.6

Q ss_pred             cccccccccCCCCC-CceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCC
Q 048114           47 SFICDICVEPKSTD-ESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKG  101 (234)
Q Consensus        47 ~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~  101 (234)
                      ...||||.+.+... ..+..++|||..-..|++.++.    ++   .+||  .|..
T Consensus       158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~----~~---y~CP--~C~~  204 (276)
T KOG1940|consen  158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMIC----EG---YTCP--ICSK  204 (276)
T ss_pred             cCCCchhHHHhccccccCCccCcccchHHHHHHHHhc----cC---CCCC--cccc
Confidence            44599999987433 3344569999999999998884    22   7899  7876

>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]

Probab=81.47  E-value=2.4  Score=27.89  Aligned_cols=31  Identities=16%  Similarity=0.382  Sum_probs=26.3

Q ss_pred             cCCcccCCCCCceeeeccCCCceEec-CCCCC
Q 048114          204 KENWRRCPNCKIFVEKKEGCRYMRCS-SNPQL  234 (234)
Q Consensus       204 ~~~~k~CP~C~~~i~k~~GCnhm~C~-C~~~F  234 (234)
                      ......||.|+....|..+=---.|. ||+.|
T Consensus        32 ~~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~f   63 (89)
T COG1997          32 QRAKHVCPFCGRTTVKRIATGIWKCRKCGAKF   63 (89)
T ss_pred             HhcCCcCCCCCCcceeeeccCeEEcCCCCCee
Confidence            45567999999999998888888995 99987

>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family

Probab=81.17  E-value=1.4  Score=26.12  Aligned_cols=27  Identities=19%  Similarity=0.255  Sum_probs=18.2

Q ss_pred             cccCCCCCceee------eccCCCceE-ec-CCCC
Q 048114          207 WRRCPNCKIFVE------KKEGCRYMR-CS-SNPQ  233 (234)
Q Consensus       207 ~k~CP~C~~~i~------k~~GCnhm~-C~-C~~~  233 (234)
                      .|+||-|+-.-+      .+.+..++. |. ||++
T Consensus         1 LkPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~   35 (53)
T TIGR03655         1 LKPCPFCGGADVYLRRGFDPLDLSHYFECSTCGAS   35 (53)
T ss_pred             CCCCCCCCCcceeeEeccCCCCCEEEEECCCCCCC
Confidence            379999998444      233566664 85 9875

Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.

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

Probab=81.15  E-value=1.1  Score=25.96  Aligned_cols=33  Identities=24%  Similarity=0.693  Sum_probs=21.8

Q ss_pred             ccccccCCCCCCceeeCCCCC-----hhhHHHHHHHHHH
Q 048114           50 CDICVEPKSTDESFSIKGCSH-----SYCTECMTKYVAS   83 (234)
Q Consensus        50 C~iC~~~~~~~~~~~~~~C~H-----~fC~~Cl~~~~~~   83 (234)
                      |-||++....+.... .+|..     .+..+||.+|+..
T Consensus         1 CrIC~~~~~~~~~li-~pC~C~Gs~~~vH~~CL~~W~~~   38 (47)
T PF12906_consen    1 CRICLEGEEEDEPLI-SPCRCKGSMKYVHRSCLERWIRE   38 (47)
T ss_dssp             ETTTTEE-SSSS-EE--SSS-SSCCGSEECCHHHHHHHH
T ss_pred             CeEeCCcCCCCCcee-cccccCCCcchhHHHHHHHHHHh
Confidence            668998876555333 46743     4789999999987

>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=80.28  E-value=1.9  Score=24.33  Aligned_cols=24  Identities=21%  Similarity=0.459  Sum_probs=13.7

Q ss_pred             cCCCCCce-eeeccCCCceEec-CCC
Q 048114          209 RCPNCKIF-VEKKEGCRYMRCS-SNP  232 (234)
Q Consensus       209 ~CP~C~~~-i~k~~GCnhm~C~-C~~  232 (234)
                      .||.|+.. +.-+..=..+.|. ||.
T Consensus         2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~   27 (43)
T PF08271_consen    2 KCPNCGSKEIVFDPERGELVCPNCGL   27 (43)
T ss_dssp             SBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred             CCcCCcCCceEEcCCCCeEECCCCCC
Confidence            47777773 3444555566774 764

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 zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.

---

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	234
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	2e-14
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	6e-08
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	3e-05

>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 = 65.6 bits (160), Expect = 2e-14
 Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 3/85 (3%)

Query: 45  ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQE-NITSINCPVADC--KG 101
             S  C +C+     ++  +I  C   +CT C+ +YV   ++E   T+I+CP A C  +G
Sbjct: 3   SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQG 62

Query: 102 VLEPEYCRDILPEDVFNRWGNALCE 126
            L+      ++  ++  R+     E
Sbjct: 63  HLQENEIECMVAAEIMQRYKKLQFE 87

>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 = 48.1 bits (114), Expect = 6e-08
 Identities = 24/84 (28%), Positives = 35/84 (41%), Gaps = 9/84 (10%)

Query: 115 DVFNRWGNALCEAVILGAQKF-YCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVP 173
                +   L E V++   KF +C    CS   I +  +   E+ CP C++ FC +CK  
Sbjct: 5   SSGALFHKKLTEGVLMRDPKFLWCA--QCSFGFIYEREQ--LEATCPQCHQTFCVRCKRQ 60

Query: 174 W---HAGIRCAEFQKLHKDEREPE 194
           W   H G  C +FQ   K      
Sbjct: 61  WEEQHRGRSCEDFQNW-KRMNSGP 83

>1wd2_A Ariadne-1 protein homolog; ring, IBR, triad, zinc finger, ligase; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 60

 Score = 39.7 bits (93), Expect = 3e-05
 Identities = 10/27 (37%), Positives = 15/27 (55%)

Query: 204 KENWRRCPNCKIFVEKKEGCRYMRCSS 230
             N + CP C + +EK  GC +M C +
Sbjct: 3   AANTKECPKCHVTIEKDGGCNHMVCRN 29

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	234
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.75
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	99.37
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	99.33
2jmo_A	80	Parkin; IBR, E3 ligase, zinc binding domain, RBR;	99.29
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.17
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.1
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	98.94
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	98.94
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	98.91
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.9
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	98.89
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	98.89
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.89
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	98.89
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	98.87
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	98.86
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	98.84
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	98.83
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	98.83
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	98.82
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	98.8
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	98.8
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	98.8
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	98.79
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	98.76
2ect_A	78	Ring finger protein 126; metal binding protein, st	98.76
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	98.73
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	98.72
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	98.72
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	98.71
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	98.7
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	98.69
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	98.68
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	98.68
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	98.67
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	98.66
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.65
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	98.65
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	98.64
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.63
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	98.63
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	98.58
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.55
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	98.54
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	98.53
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.51
1z6u_A	150	NP95-like ring finger protein isoform B; structura	98.48
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	98.47
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.44
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.4
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	98.38
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.36
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	98.36
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.33
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.3
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.24
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	98.2
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	98.01
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	97.98
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	97.97
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	97.95
2ea5_A	68	Cell growth regulator with ring finger domain prot	97.92
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	97.91
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	97.91
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	97.84
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	97.83
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	97.82
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	97.5
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	97.25
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	97.18
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	96.83
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	96.4
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	96.2
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	95.97
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	95.75
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	95.7
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	95.62
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	93.26
3nw0_A	238	Non-structural maintenance of chromosomes element	92.78
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	92.13
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	91.7
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	91.67
2jmo_A	80	Parkin; IBR, E3 ligase, zinc binding domain, RBR;	91.08
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	90.58
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	90.2
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	89.72
2jr6_A	68	UPF0434 protein NMA0874; solution, structural geno	83.6
1z60_A	59	TFIIH basal transcription factor complex P44 subun	82.16
2jne_A	101	Hypothetical protein YFGJ; zinc fingers, two zinc,	81.99
2d8v_A	67	Zinc finger FYVE domain-containing protein 19; zfy	81.52
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	81.44

>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=99.75  E-value=1.2e-18  Score=118.21  Aligned_cols=86  Identities=23%  Similarity=0.506  Sum_probs=75.1

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCC-ccccCCCCCCCCC--CCHHHHhccCCHHHHHHHH
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENI-TSINCPVADCKGV--LEPEYCRDILPEDVFNRWG  121 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~-~~i~CP~~~C~~~--l~~~~i~~~l~~~~~~~~~  121 (234)
                      ...++|+||++++...+++.+.+|||.||.+||++|+..+|.+|. .+++||...|...  ++++.++.+++++++++|+
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            347889999999876666777689999999999999999998874 6899998889999  9999999999999999999


Q ss_pred             HHHHHHHHh
Q 048114          122 NALCEAVIL  130 (234)
Q Consensus       122 ~~~~~~~~~  130 (234)
                      +++.+.++.
T Consensus        83 ~~~~~~~v~   91 (94)
T 1wim_A           83 KLQFERSGP   91 (94)
T ss_dssp             HHHHHSSCS
T ss_pred             HHHHHhhhc
Confidence            987765543

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

Probab=99.37  E-value=9.4e-14  Score=84.79  Aligned_cols=31  Identities=32%  Similarity=0.862  Sum_probs=29.0

Q ss_pred             cCCcccCCCCCceeeeccCCCceEec---CCCCC
Q 048114          204 KENWRRCPNCKIFVEKKEGCRYMRCS---SNPQL  234 (234)
Q Consensus       204 ~~~~k~CP~C~~~i~k~~GCnhm~C~---C~~~F  234 (234)
                      ..++|+||+|+++|||++|||||+|+   |+++|
T Consensus         3 ~~~~k~CP~C~~~Iek~~GCnhmtC~~~~C~~~F   36 (60)
T 1wd2_A            3 AANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEF   36 (60)
T ss_dssp             CCCCCCCTTTCCCCSSCCSCCSSSCCSSGGGSCC
T ss_pred             cccceECcCCCCeeEeCCCCCcEEECCCCcCCEE
Confidence            46789999999999999999999996   99998

>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=99.33  E-value=2.6e-14  Score=94.55  Aligned_cols=72  Identities=29%  Similarity=0.710  Sum_probs=58.7

Q ss_pred             HHHHHHHHHHHHHHHHh-CCCeecCCCCCCCCceecCCCCccCcccCccccccccccCCCCC---CCCCChhhHHHhhhc
Q 048114          114 EDVFNRWGNALCEAVIL-GAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPW---HAGIRCAEFQKLHKD  189 (234)
Q Consensus       114 ~~~~~~~~~~~~~~~~~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~---H~~~~C~~~~~~~~~  189 (234)
                      ++++++|++++.+.++. ++..+|||  +|+++++.+..  ...+.|+.|+..||+.|+.+|   |.+.+|+++++|..+
T Consensus         4 ~~~~e~y~~~l~e~~v~~~~~~~wCP--~C~~~~~~~~~--~~~v~C~~C~~~FC~~C~~~w~~~H~~~sC~~~~~w~~~   79 (86)
T 2ct7_A            4 GSSGALFHKKLTEGVLMRDPKFLWCA--QCSFGFIYERE--QLEATCPQCHQTFCVRCKRQWEEQHRGRSCEDFQNWKRM   79 (86)
T ss_dssp             CCCCCSSSSCCCCSCCCSCCCEECCS--SSCCCEECCCS--CSCEECTTTCCEECSSSCSBCCTTTTTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCEeECc--CCCchheecCC--CCceEeCCCCCccccccCCchhhcCCCCChHHHHHHHHh
Confidence            34567777777776664 45567999  99998887643  455999999999999999999   999999999998764

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

Probab=99.29  E-value=2.3e-14  Score=93.32  Aligned_cols=69  Identities=28%  Similarity=0.617  Sum_probs=59.0

Q ss_pred             cCCHHHHHHHHHHHHHHHHhCCCeecCCCCCCCCceecCCCCccCcccCc-----cccccccccCCCCCCCCCChhh
Q 048114          111 ILPEDVFNRWGNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCP-----DCNRMFCAQCKVPWHAGIRCAE  182 (234)
Q Consensus       111 ~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~-----~C~~~~C~~C~~~~H~~~~C~~  182 (234)
                      +|+++++++|++++.+.++.....+|||+|+|++++..+.  ....+.|+     .|+..||+.|+..||. .+|..
T Consensus         2 ~l~~~~~~rY~~~~~e~~v~~~~~~~CP~p~C~~~v~~~~--~~~~v~C~~~~~~~C~~~FC~~C~~~wH~-~~C~~   75 (80)
T 2jmo_A            2 HMGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEP--DQRKVTCEGGNGLGCGFAFCRECKEAYHE-GECSA   75 (80)
T ss_dssp             CCCCCCCCSCCCSSSCCSSCCCSSCCCCSSSCCCCCCCCS--CTTSBCTTSSSTTCCSCCEETTTTEECCS-SCSSS
T ss_pred             CCCHHHHHHHHHHHHHHHhhhCCcEECCCCCCCcccEECC--CCCcCCCCCCCCCCCCCeeccccCccccC-Ccccc
Confidence            5677888899988888777766689999999999988765  34559998     9999999999999999 99975

>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=99.17  E-value=1.5e-11  Score=92.09  Aligned_cols=132  Identities=23%  Similarity=0.487  Sum_probs=81.7

Q ss_pred             hcCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccCCHHHHHHHHH
Q 048114           43 RIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGN  122 (234)
Q Consensus        43 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~  122 (234)
                      .++..+.|+||++.+.  +++. ++|||+||..|+.+|+...      ...||  .|...+....+.   ....++    
T Consensus        14 ~~~~~~~C~IC~~~~~--~pv~-~~CgH~fC~~Ci~~~~~~~------~~~CP--~Cr~~~~~~~~~---~~~~~~----   75 (170)
T 3hcs_A           14 PLESKYECPICLMALR--EAVQ-TPCGHRFCKACIIKSIRDA------GHKCP--VDNEILLENQLF---PDNFAK----   75 (170)
T ss_dssp             CCCGGGBCTTTCSBCS--SEEE-CTTSCEEEHHHHHHHHHHH------CSBCT--TTCCBCCGGGCE---ECHHHH----
T ss_pred             CCCCCCCCCCCChhhc--CcEE-CCCCCHHHHHHHHHHHHhC------CCCCC--CCccCcchhhhh---hhHHHH----
Confidence            4566889999999885  5555 5999999999999999754      23899  898888775432   211111    


Q ss_pred             HHHHHHHhCCCeecCCCCCCCCceecCCCC------ccCcccCccccccccccCCCCCCCCCChhhHHHhhhccCChHHH
Q 048114          123 ALCEAVILGAQKFYCPFKDCSALLIDDGGE------AIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDI  196 (234)
Q Consensus       123 ~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~------~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~  196 (234)
                          ..+. .-.++||+.+|...+......      ....+.|+.|+..+- .....+|....|                
T Consensus        76 ----~~i~-~l~v~C~n~GC~~~~~~~~l~~H~~~C~~~~v~C~~C~~~~~-r~~l~~H~~~~C----------------  133 (170)
T 3hcs_A           76 ----REIL-SLMVKCPNEGCLHKMELRHLEDHQAHCEFALMDCPQCQRPFQ-KFHINIHILKDC----------------  133 (170)
T ss_dssp             ----HHHH-TSEEECCSTTCCCEEEGGGHHHHHTTCTTSEEECTTTCCEEE-GGGHHHHHHHTC----------------
T ss_pred             ----HHHh-hcccCCCCCCCCceecHhHHHHHHhcCCceeeECCCCChHHH-HHHHHHHhhhhC----------------
Confidence                1111 245799999999887765321      112345555554431 111112222222                


Q ss_pred             HHHHHHhcCCcccCCCCCceeeecc
Q 048114          197 MLMTLAQKENWRRCPNCKIFVEKKE  221 (234)
Q Consensus       197 ~l~~~~~~~~~k~CP~C~~~i~k~~  221 (234)
                             ......||.|+..+....
T Consensus       134 -------~~r~~~C~~C~~~~~~~~  151 (170)
T 3hcs_A          134 -------PRRQVSCDNCAASMAFED  151 (170)
T ss_dssp             -------TTCEEECTTTCCEEEGGG
T ss_pred             -------CCCCeECCCCCCccCHHH
Confidence                   245578999998887643

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

Probab=99.10  E-value=1.4e-12  Score=93.69  Aligned_cols=118  Identities=24%  Similarity=0.586  Sum_probs=78.6

Q ss_pred             CCcccccccccCCCC----CCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccCCHHHHHHH
Q 048114           45 ETSFICDICVEPKST----DESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRW  120 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~----~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~  120 (234)
                      ...++|+||++.+..    .+.+..++|||.||.+|+.+|+..       ...||  .|+..+....+..+.        
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-------~~~CP--~Cr~~~~~~~l~~l~--------   67 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-------ANTCP--TCRKKINHKRYHPIY--------   67 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTT-------CSBCT--TTCCBCTTTCEEECB--------
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHh-------CCCCC--CCCCcCccccccccc--------
Confidence            347789999998852    122355699999999999999852       23899  899988776654431        


Q ss_pred             HHHHHHHHHhCCCeecCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHH
Q 048114          121 GNALCEAVILGAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMT  200 (234)
Q Consensus       121 ~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~  200 (234)
                               ...+...|+  -|...+..... .........||..||..|...|..                        
T Consensus        68 ---------i~~~~~~C~--iC~~~~~~~~~-~~~~~~~~~CgH~fc~~Ci~~~~~------------------------  111 (133)
T 4ap4_A           68 ---------IGSGTVSCP--ICMDGYSEIVQ-NGRLIVSTECGHVFCSQCLRDSLK------------------------  111 (133)
T ss_dssp             ---------CSSSSCBCT--TTCCBHHHHHH-TTCCEEEETTSBEEEHHHHHHHHH------------------------
T ss_pred             ---------cCCCCCCCC--CCCCccccccc-cCcceEeCCCCChhhHHHHHHHHH------------------------
Confidence                     123445788  77765543210 111134457999999988654310                        


Q ss_pred             HHhcCCcccCCCCCceeeec
Q 048114          201 LAQKENWRRCPNCKIFVEKK  220 (234)
Q Consensus       201 ~~~~~~~k~CP~C~~~i~k~  220 (234)
                           ..+.||.|+..+.++
T Consensus       112 -----~~~~CP~Cr~~~~~~  126 (133)
T 4ap4_A          112 -----NANTCPTCRKKINHK  126 (133)
T ss_dssp             -----HCSBCTTTCCBCCGG
T ss_pred             -----cCCCCCCCCCcCChh
Confidence                 126999999998865

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

Probab=98.94  E-value=3.2e-10  Score=72.40  Aligned_cols=56  Identities=23%  Similarity=0.591  Sum_probs=44.2

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD  110 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  110 (234)
                      ++..++|+||++.+.  +++.+.+|+|.||..|+.+|+..       ...||  .|+..+...++..
T Consensus        12 ~~~~~~C~IC~~~~~--~p~~~~~CgH~fC~~Ci~~~~~~-------~~~CP--~Cr~~~~~~~~~~   67 (72)
T 2djb_A           12 LTPYILCSICKGYLI--DATTITECLHTFCKSCIVRHFYY-------SNRCP--KCNIVVHQTQPLS   67 (72)
T ss_dssp             CCGGGSCTTTSSCCS--SCEECSSSCCEECHHHHHHHHHH-------CSSCT--TTCCCCCSSCSCC
T ss_pred             cCCCCCCCCCChHHH--CcCEECCCCCHHHHHHHHHHHHc-------CCcCC--CcCcccCcccccc
Confidence            355788999999886  55665699999999999999964       35899  8998887655433

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

Probab=98.94  E-value=4.5e-10  Score=74.51  Aligned_cols=61  Identities=25%  Similarity=0.629  Sum_probs=46.7

Q ss_pred             cCCcccccccccCCCCCCc-eeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114           44 IETSFICDICVEPKSTDES-FSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD  110 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  110 (234)
                      ++..++|+||++.+...+. +.+++|||.||..|+.+|+...    .....||  .|+..+....+..
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~----~~~~~CP--~Cr~~~~~~~i~~   73 (88)
T 2ct2_A           12 LREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASS----INGVRCP--FCSKITRITSLTQ   73 (88)
T ss_dssp             CCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHC----SSCBCCT--TTCCCBCCSSTTT
T ss_pred             ccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcC----CCCcCCC--CCCCcccchhHHH
Confidence            3557889999999864332 4556999999999999999743    2467999  8998877665544

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

Probab=98.91  E-value=5.1e-10  Score=73.69  Aligned_cols=59  Identities=27%  Similarity=0.705  Sum_probs=46.4

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYC  108 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  108 (234)
                      +...++|+||++.+.  +++. ++|||.||..|+..|+..+...+ ....||  .|+..+..+.+
T Consensus        16 ~~~~~~C~IC~~~~~--~p~~-~~CgH~fC~~Ci~~~~~~~~~~~-~~~~CP--~Cr~~~~~~~~   74 (85)
T 2ecv_A           16 VKEEVTCPICLELLT--QPLS-LDCGHSFCQACLTANHKKSMLDK-GESSCP--VCRISYQPENI   74 (85)
T ss_dssp             CCCCCCCTTTCSCCS--SCBC-CSSSCCBCTTHHHHHHHHHHHTT-SCCCCT--TTCCSSCSSSC
T ss_pred             ccCCCCCCCCCcccC--Ccee-CCCCCHHHHHHHHHHHHHhhcCC-CCCcCC--CCCCccCHHhc
Confidence            456789999999885  4444 49999999999999998765544 367999  89988876543

>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=98.90  E-value=9e-10  Score=77.06  Aligned_cols=83  Identities=22%  Similarity=0.502  Sum_probs=58.1

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccCCHHHHHHHHHHH
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGNAL  124 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~~~  124 (234)
                      ...+.|+||++.+.  +++. ++|||.||..|+.+|+...      ...||  .|...+....+...+ ..+    .+.+
T Consensus        21 ~~~~~C~IC~~~~~--~p~~-~~CgH~fC~~Ci~~~~~~~------~~~CP--~Cr~~~~~~~~~~~~-~~l----~~~i   84 (116)
T 1rmd_A           21 VKSISCQICEHILA--DPVE-TSCKHLFCRICILRCLKVM------GSYCP--SCRYPCFPTDLESPV-KSF----LNIL   84 (116)
T ss_dssp             HHHTBCTTTCSBCS--SEEE-CTTSCEEEHHHHHHHHHHT------CSBCT--TTCCBCCGGGCBCCC-HHH----HHHH
T ss_pred             cCCCCCCCCCcHhc--CcEE-cCCCCcccHHHHHHHHhHC------cCcCC--CCCCCCCHhhccccH-HHH----HHHH
Confidence            34678999999885  5555 5999999999999999742      35799  899998876654331 111    1111


Q ss_pred             HHHHHhCCCeecCCCCCCCCceecC
Q 048114          125 CEAVILGAQKFYCPFKDCSALLIDD  149 (234)
Q Consensus       125 ~~~~~~~~~~~~Cp~~~C~~~~~~~  149 (234)
                            ..-.++||+.+|...+...
T Consensus        85 ------~~l~v~C~~~gC~~~~~~~  103 (116)
T 1rmd_A           85 ------NSLMVKCPAQDCNEEVSLE  103 (116)
T ss_dssp             ------HHCEEECCSTTCCCEEEHH
T ss_pred             ------HHhcCCCCCCCCcchhhHh
Confidence                  1235689988898776543

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

Probab=98.89  E-value=3.4e-10  Score=72.42  Aligned_cols=55  Identities=25%  Similarity=0.710  Sum_probs=42.7

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY  107 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  107 (234)
                      ++..++|+||++.+.  +++.+ +|||.||..|+..|+.    .......||  .|+..+..++
T Consensus        17 ~~~~~~C~IC~~~~~--~~~~~-~CgH~fC~~Ci~~~~~----~~~~~~~CP--~Cr~~~~~~~   71 (73)
T 2ysl_A           17 LQEEVICPICLDILQ--KPVTI-DCGHNFCLKCITQIGE----TSCGFFKCP--LCKTSVRKNA   71 (73)
T ss_dssp             CCCCCBCTTTCSBCS--SEEEC-TTCCEEEHHHHHHHCS----SSCSCCCCS--SSCCCCCCCC
T ss_pred             CccCCEeccCCcccC--CeEEc-CCCChhhHHHHHHHHH----cCCCCCCCC--CCCCcCCccc
Confidence            456789999999885  55554 9999999999999985    223467899  8988876543

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

Probab=98.89  E-value=7.3e-10  Score=72.92  Aligned_cols=60  Identities=28%  Similarity=0.554  Sum_probs=45.7

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHh
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR  109 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~  109 (234)
                      ++..++|+||++.+.  +++ +++|+|.||..|+..|+..... +.....||  .|+..+..+.+.
T Consensus        16 ~~~~~~C~IC~~~~~--~p~-~~~CgH~fC~~Ci~~~~~~~~~-~~~~~~CP--~Cr~~~~~~~~~   75 (85)
T 2ecw_A           16 IKEEVTCPICLELLK--EPV-SADCNHSFCRACITLNYESNRN-TDGKGNCP--VCRVPYPFGNLK   75 (85)
T ss_dssp             CCTTTSCTTTCSCCS--SCE-ECTTSCCBCHHHHHHHHHHSBC-TTSCBCCT--TTCCCCCTTCCE
T ss_pred             CccCCCCcCCChhhC--cce-eCCCCCHHHHHHHHHHHHhccC-CCCCCCCC--CCCCcCCHHhCC
Confidence            355788999999885  444 4599999999999999976532 22467999  899888765443

>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=98.89  E-value=1.6e-10  Score=83.61  Aligned_cols=94  Identities=20%  Similarity=0.430  Sum_probs=57.9

Q ss_pred             hhcCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccCCHHHHHHHH
Q 048114           42 ERIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWG  121 (234)
Q Consensus        42 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~  121 (234)
                      +.++..++|+||++.+.  +++. ++|||.||..|+..|+..      ....||  .|...+.......+++...  .|.
T Consensus        26 ~~l~~~~~C~IC~~~~~--~pv~-~~CgH~FC~~Ci~~~~~~------~~~~CP--~Cr~~~~~~~~~~~l~~~~--~~~   92 (141)
T 3knv_A           26 TKLEAKYLCSACRNVLR--RPFQ-AQCGHRYCSFCLASILSS------GPQNCA--ACVHEGIYEEGISILESSS--AFP   92 (141)
T ss_dssp             GGCCGGGBCTTTCSBCS--SEEE-CTTSCEEEHHHHHHHGGG------SCEECH--HHHHTTCCCTTTTEECGGG--CEE
T ss_pred             ccCCcCcCCCCCChhhc--CcEE-CCCCCccCHHHHHHHHhc------CCCCCC--CCCCcccccccccccchhh--hcc
Confidence            45677899999999885  5555 499999999999999841      245899  7876554332222221110  000


Q ss_pred             HHHHHHHHhCCCeecCCCCCCCCceecC
Q 048114          122 NALCEAVILGAQKFYCPFKDCSALLIDD  149 (234)
Q Consensus       122 ~~~~~~~~~~~~~~~Cp~~~C~~~~~~~  149 (234)
                      ....+..+. .-.++||+.+|...+...
T Consensus        93 d~~~~~~i~-~L~v~Cpn~GC~~~~~l~  119 (141)
T 3knv_A           93 DNAARREVE-SLPAVCPSDGCTWKGTLK  119 (141)
T ss_dssp             CHHHHHHHH-TSEEECCSTTCCCEEEHH
T ss_pred             cHHHHHHHc-ccccccCCCCCCCEeEHH
Confidence            011111122 346799988898776543

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

Probab=98.89  E-value=1.9e-09  Score=66.76  Aligned_cols=45  Identities=27%  Similarity=0.814  Sum_probs=35.9

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCP   95 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP   95 (234)
                      ++..++|+||++.+.  +++.+ +|||.||..|+.+|+..    ......||
T Consensus        17 ~~~~~~C~IC~~~~~--~p~~~-~CgH~fC~~Ci~~~~~~----~~~~~~CP   61 (63)
T 2ysj_A           17 LQEEVICPICLDILQ--KPVTI-DCGHNFCLKCITQIGET----SCGFFKCP   61 (63)
T ss_dssp             CCCCCBCTTTCSBCS--SCEEC-TTSSEECHHHHHHHHHH----CSSCCCCS
T ss_pred             CccCCCCCcCCchhC--CeEEe-CCCCcchHHHHHHHHHc----CCCCCcCc
Confidence            466889999999886  55555 99999999999999974    22356888

>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=98.87  E-value=2.8e-09  Score=74.78  Aligned_cols=85  Identities=24%  Similarity=0.552  Sum_probs=59.4

Q ss_pred             hcCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhccCCHHHHHHHHH
Q 048114           43 RIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDILPEDVFNRWGN  122 (234)
Q Consensus        43 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~l~~~~~~~~~~  122 (234)
                      .++..+.|+||++.+.  +++. ++|||.||..|+..|+...      ...||  .|+..+....+   .....+++   
T Consensus        14 ~~~~~~~C~IC~~~~~--~p~~-~~CgH~fC~~Ci~~~~~~~------~~~CP--~Cr~~~~~~~~---~~~~~l~~---   76 (118)
T 3hct_A           14 PLESKYECPICLMALR--EAVQ-TPCGHRFCKACIIKSIRDA------GHKCP--VDNEILLENQL---FPDNFAKR---   76 (118)
T ss_dssp             CCCGGGBCTTTCSBCS--SEEE-CTTSCEEEHHHHHHHHHHH------CSBCT--TTCCBCCGGGC---EECHHHHH---
T ss_pred             CCCCCCCCCcCChhhc--CeEE-CCcCChhhHHHHHHHHhhC------CCCCC--CCCCCcCHHhc---ccCHHHHH---
Confidence            3466789999999885  5555 4999999999999999754      23899  89988876432   22222111   


Q ss_pred             HHHHHHHhCCCeecCCCCCCCCceecCC
Q 048114          123 ALCEAVILGAQKFYCPFKDCSALLIDDG  150 (234)
Q Consensus       123 ~~~~~~~~~~~~~~Cp~~~C~~~~~~~~  150 (234)
                           .+. .-.++||+.+|...+....
T Consensus        77 -----~i~-~l~v~C~n~gC~~~~~~~~   98 (118)
T 3hct_A           77 -----EIL-SLMVKCPNEGCLHKMELRH   98 (118)
T ss_dssp             -----HHH-TSEEECSSTTCCCEEEGGG
T ss_pred             -----HHc-cceeECCCCCCCCEEeeHH
Confidence                 112 2457999999998777653

>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=98.86  E-value=1.2e-09  Score=74.29  Aligned_cols=61  Identities=25%  Similarity=0.579  Sum_probs=48.3

Q ss_pred             hhhcCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhcc
Q 048114           41 EERIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDI  111 (234)
Q Consensus        41 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~  111 (234)
                      ...++..++|+||++.+.  +++.+++|||.||..|+..|+...      ...||  .|...+....+...
T Consensus        16 ~~~l~~~~~C~IC~~~~~--~p~~~~~CgH~FC~~Ci~~~~~~~------~~~CP--~Cr~~~~~~~l~~~   76 (100)
T 3lrq_A           16 VESIAEVFRCFICMEKLR--DARLCPHCSKLCCFSCIRRWLTEQ------RAQCP--HCRAPLQLRELVNC   76 (100)
T ss_dssp             HHHHHHHTBCTTTCSBCS--SEEECTTTCCEEEHHHHHHHHHHT------CSBCT--TTCCBCCGGGCEEC
T ss_pred             cccCCCCCCCccCCcccc--CccccCCCCChhhHHHHHHHHHHC------cCCCC--CCCCcCCHHHhHhh
Confidence            344566889999999986  566647999999999999999743      26899  89999987766543

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

Probab=98.84  E-value=7.3e-10  Score=69.40  Aligned_cols=53  Identities=21%  Similarity=0.619  Sum_probs=41.6

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY  107 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  107 (234)
                      ++..++|+||++.+.  +++. ++|||.||..|+.+|+.      .....||  .|+..+..++
T Consensus        12 ~~~~~~C~IC~~~~~--~p~~-~~CgH~fC~~Ci~~~~~------~~~~~CP--~Cr~~~~~~~   64 (66)
T 2ecy_A           12 VEDKYKCEKCHLVLC--SPKQ-TECGHRFCESCMAALLS------SSSPKCT--ACQESIVKDK   64 (66)
T ss_dssp             CCCCEECTTTCCEES--SCCC-CSSSCCCCHHHHHHHHT------TSSCCCT--TTCCCCCTTT
T ss_pred             CCcCCCCCCCChHhc--CeeE-CCCCCHHHHHHHHHHHH------hCcCCCC--CCCcCCChhh
Confidence            355788999999885  4444 59999999999999985      1356899  8988877543

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

Probab=98.83  E-value=2.9e-09  Score=72.23  Aligned_cols=54  Identities=30%  Similarity=0.697  Sum_probs=43.1

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYC  108 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  108 (234)
                      ++..++|+||++.+.  +++.+.+|||.||..|+..|+..       ...||  .|+..+....+
T Consensus        19 ~~~~~~C~IC~~~~~--~p~~~~~CgH~fC~~Ci~~~~~~-------~~~CP--~Cr~~~~~~~l   72 (99)
T 2y43_A           19 IDDLLRCGICFEYFN--IAMIIPQCSHNYCSLCIRKFLSY-------KTQCP--TCCVTVTEPDL   72 (99)
T ss_dssp             HHHHTBCTTTCSBCS--SEEECTTTCCEEEHHHHHHHHTT-------CCBCT--TTCCBCCGGGC
T ss_pred             CCCCCCcccCChhhC--CcCEECCCCCHhhHHHHHHHHHC-------CCCCC--CCCCcCChhhC
Confidence            455788999999886  55555599999999999999962       35899  89998887543

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

Probab=98.83  E-value=1.7e-09  Score=70.05  Aligned_cols=67  Identities=15%  Similarity=0.358  Sum_probs=48.6

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHh-ccCCHHHHHHHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR-DILPEDVFNRWG  121 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~-~~l~~~~~~~~~  121 (234)
                      +...+.|+||++.+.  +++.+ +|||+||..|+.+|+..      ....||  .|+..+....+. +..-.++++.|.
T Consensus         5 ~~~~~~C~IC~~~~~--~Pv~~-~CgH~fc~~Ci~~~~~~------~~~~CP--~C~~~~~~~~l~~n~~l~~~i~~~~   72 (78)
T 1t1h_A            5 FPEYFRCPISLELMK--DPVIV-STGQTYERSSIQKWLDA------GHKTCP--KSQETLLHAGLTPNYVLKSLIALWC   72 (78)
T ss_dssp             CSSSSSCTTTSCCCS--SEEEE-TTTEEEEHHHHHHHHTT------TCCBCT--TTCCBCSSCCCEECTTTHHHHHHHH
T ss_pred             CcccCCCCCcccccc--CCEEc-CCCCeecHHHHHHHHHH------CcCCCC--CCcCCCChhhCccCHHHHHHHHHHH
Confidence            355889999999885  66665 99999999999999952      256899  899888765443 333345555543

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

Probab=98.82  E-value=1.4e-10  Score=75.36  Aligned_cols=61  Identities=26%  Similarity=0.510  Sum_probs=46.1

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHh
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR  109 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~  109 (234)
                      ++..++|+||++.+.  +++. ++|||.||..|+.+|+............||  .|+..+....+.
T Consensus         9 ~~~~~~C~IC~~~~~--~p~~-l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP--~Cr~~~~~~~l~   69 (79)
T 2egp_A            9 VQEEVTCPICLELLT--EPLS-LDCGHSLCRACITVSNKEAVTSMGGKSSCP--VCGISYSFEHLQ   69 (79)
T ss_dssp             CCCCCEETTTTEECS--SCCC-CSSSCCCCHHHHSCCCCCCSSSCCCCCCCS--SSCCCCCSSGGG
T ss_pred             cccCCCCcCCCcccC--CeeE-CCCCCHHHHHHHHHHHHhcccCCCCCCcCC--CCCCcCCHhhCC
Confidence            356788999999985  4444 499999999999999865433333478999  899888765543

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

Probab=98.80  E-value=1e-09  Score=73.45  Aligned_cols=50  Identities=28%  Similarity=0.724  Sum_probs=40.2

Q ss_pred             cCCcccccccccCCCCCCceeeCC-CCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCC
Q 048114           44 IETSFICDICVEPKSTDESFSIKG-CSHSYCTECMTKYVASKLQENITSINCPVADCKGVL  103 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l  103 (234)
                      ++..++|+||++.+.  +++.+ + |||+||..|+..|+...     ....||  .|...+
T Consensus        10 ~~~~~~C~IC~~~~~--~p~~~-~~CgH~fC~~Ci~~~~~~~-----~~~~CP--~Cr~~~   60 (92)
T 3ztg_A           10 IPDELLCLICKDIMT--DAVVI-PCCGNSYCDECIRTALLES-----DEHTCP--TCHQND   60 (92)
T ss_dssp             CCTTTEETTTTEECS--SCEEC-TTTCCEECHHHHHHHHHHC-----TTCCCT--TTCCSS
T ss_pred             CCcCCCCCCCChhhc--CceEC-CCCCCHHHHHHHHHHHHhc-----CCCcCc--CCCCcC
Confidence            456889999999886  55655 7 99999999999998632     247899  888876

>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=98.80  E-value=3.9e-09  Score=63.44  Aligned_cols=50  Identities=26%  Similarity=0.499  Sum_probs=39.5

Q ss_pred             CcccccccccCCCC-CCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           46 TSFICDICVEPKST-DESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        46 ~~~~C~iC~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ...+|+||++.+.. .+.+.+++|+|.||..|+.+|+...       ..||  .|...++
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~-------~~CP--~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEG-------YRCP--LCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHT-------CCCT--TSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcC-------CcCC--CCCCcCC
Confidence            36779999999843 3446667999999999999999743       6799  7887664

>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=98.80  E-value=6e-09  Score=65.75  Aligned_cols=51  Identities=24%  Similarity=0.576  Sum_probs=40.6

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      +...+|+||++.+.....+..++|+|.||..|+..|+...       ..||  .|...+.
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~-------~~CP--~Cr~~~~   62 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITN-------KKCP--ICRVDIE   62 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHC-------SBCT--TTCSBSC
T ss_pred             CCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcC-------CCCc--CcCcccc
Confidence            4467899999998765566667999999999999999642       2599  8887665

>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=98.79  E-value=3.3e-09  Score=73.59  Aligned_cols=74  Identities=24%  Similarity=0.540  Sum_probs=53.8

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc-cCCHHHHHHHHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD-ILPEDVFNRWGN  122 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~-~l~~~~~~~~~~  122 (234)
                      +...++|+||++.+.  +++. ++|||.||..|+..|+...    .....||  .|...+....+.. ....++++.+.+
T Consensus        18 ~~~~~~C~IC~~~~~--~p~~-~~CgH~fC~~Ci~~~~~~~----~~~~~CP--~Cr~~~~~~~~~~~~~l~~~~~~~~~   88 (112)
T 1jm7_A           18 MQKILECPICLELIK--EPVS-TKCDHIFCKFCMLKLLNQK----KGPSQCP--LCKNDITKRSLQESTRFSQLVEELLK   88 (112)
T ss_dssp             HHHHTSCSSSCCCCS--SCCB-CTTSCCCCSHHHHHHHHSS----SSSCCCT--TTSCCCCTTTCBCCCSSSHHHHHHHH
T ss_pred             ccCCCCCcccChhhc--CeEE-CCCCCHHHHHHHHHHHHhC----CCCCCCc--CCCCcCCHhhcCccHHHHHHHHHHHH
Confidence            445778999999875  4444 5999999999999999632    2357899  8999888876654 333456666665


Q ss_pred             HHHH
Q 048114          123 ALCE  126 (234)
Q Consensus       123 ~~~~  126 (234)
                      .+..
T Consensus        89 ~~~~   92 (112)
T 1jm7_A           89 IICA   92 (112)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5544

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

Probab=98.76  E-value=3e-09  Score=63.94  Aligned_cols=52  Identities=21%  Similarity=0.621  Sum_probs=39.6

Q ss_pred             cCCcccccccccCCCCCCceeeCC-CCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           44 IETSFICDICVEPKSTDESFSIKG-CSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ++...+|+||++++...+.+..++ |+|.||.+|+.+|+..       ...||  .|+..+.
T Consensus         2 ~~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~-------~~~CP--~Cr~~~~   54 (55)
T 1iym_A            2 MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGS-------HSTCP--LCRLTVV   54 (55)
T ss_dssp             CCCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTT-------CCSCS--SSCCCSC
T ss_pred             CCCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHc-------CCcCc--CCCCEeE
Confidence            355778999999997655454455 9999999999999842       34799  7877654

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

Probab=98.76  E-value=3.9e-09  Score=68.29  Aligned_cols=55  Identities=22%  Similarity=0.558  Sum_probs=43.7

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHH
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYC  108 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  108 (234)
                      ....+|+||++.+.....+..++|+|.||..|+.+|+..       ...||  .|+..+....+
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~-------~~~CP--~Cr~~~~~~~~   67 (78)
T 2ect_A           13 GSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQ-------HDSCP--VCRKSLTGQNT   67 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTT-------TCSCT--TTCCCCCCSCS
T ss_pred             CCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHc-------CCcCc--CcCCccCCccc
Confidence            457789999999976666666799999999999999852       24899  89888776543

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

Probab=98.73  E-value=4.9e-09  Score=67.71  Aligned_cols=55  Identities=22%  Similarity=0.507  Sum_probs=40.6

Q ss_pred             CCcccccccccCCCCCCceee-CCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHH
Q 048114           45 ETSFICDICVEPKSTDESFSI-KGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY  107 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~-~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  107 (234)
                      +..++|+||++.+...+...+ ++|||.||..|+.+++..      ....||  .|...+....
T Consensus         9 ~~~~~CpICle~~~~~d~~~~p~~CGH~fC~~Cl~~~~~~------~~~~CP--~CR~~~~~~~   64 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTD------ENGLCP--ACRKPYPEDP   64 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTTTCCSSTTSCCCCHHHHHHHTTS------SCSBCT--TTCCBCSSCS
T ss_pred             ccCCcCCccCccCccccccccccCCCCCcCHHHHHHHHhc------CCCCCC--CCCCccCCCc
Confidence            557889999998864433322 249999999999988742      356899  8988877543

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

Probab=98.72  E-value=1.4e-09  Score=69.02  Aligned_cols=57  Identities=19%  Similarity=0.613  Sum_probs=43.3

Q ss_pred             CCcccccccccCCCC----CCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114           45 ETSFICDICVEPKST----DESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD  110 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~----~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  110 (234)
                      +...+|+||++.+..    .+.+..++|||.||..|+.+|+...       ..||  .|...+....+..
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~-------~~CP--~Cr~~~~~~~~~~   68 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA-------NTCP--TCRKKINHKRYHP   68 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHC-------SBCT--TTCCBCCCCSCCC
T ss_pred             CCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcC-------CCCC--CCCCccChhheee
Confidence            457789999998742    2334567999999999999999632       4899  8998887665543

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

Probab=98.72  E-value=6.6e-09  Score=66.53  Aligned_cols=50  Identities=28%  Similarity=0.724  Sum_probs=39.5

Q ss_pred             cCCcccccccccCCCCCCceeeCC-CCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCC
Q 048114           44 IETSFICDICVEPKSTDESFSIKG-CSHSYCTECMTKYVASKLQENITSINCPVADCKGVL  103 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l  103 (234)
                      +...++|+||++.+.  +++.+ + |||.||..|+..|+...     ....||  .|+..+
T Consensus        12 ~~~~~~C~IC~~~~~--~p~~~-~~CgH~fC~~Ci~~~~~~~-----~~~~CP--~Cr~~~   62 (74)
T 2yur_A           12 IPDELLCLICKDIMT--DAVVI-PCCGNSYCDECIRTALLES-----DEHTCP--TCHQND   62 (74)
T ss_dssp             SCGGGSCSSSCCCCT--TCEEC-SSSCCEECTTHHHHHHHHS-----SSSCCS--SSCCSS
T ss_pred             CCCCCCCcCCChHHh--CCeEc-CCCCCHHHHHHHHHHHHhc-----CCCcCC--CCCCcC
Confidence            355788999999886  55655 6 99999999999999742     246899  888753

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

Probab=98.71  E-value=3.9e-09  Score=67.06  Aligned_cols=54  Identities=20%  Similarity=0.499  Sum_probs=43.3

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD  110 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  110 (234)
                      ...++|+||++.+.  +.+.+ +|+|.||..|+..|+..       ...||  .|+..+....+..
T Consensus        13 ~~~~~C~IC~~~~~--~~~~~-~CgH~fC~~Ci~~~~~~-------~~~CP--~Cr~~~~~~~~~~   66 (71)
T 2d8t_A           13 LTVPECAICLQTCV--HPVSL-PCKHVFCYLCVKGASWL-------GKRCA--LCRQEIPEDFLDS   66 (71)
T ss_dssp             SSCCBCSSSSSBCS--SEEEE-TTTEEEEHHHHHHCTTC-------SSBCS--SSCCBCCHHHHSC
T ss_pred             CCCCCCccCCcccC--CCEEc-cCCCHHHHHHHHHHHHC-------CCcCc--CcCchhCHhhccC
Confidence            44678999999875  55555 89999999999998842       25899  8999999877654

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

Probab=98.70  E-value=1.1e-08  Score=65.45  Aligned_cols=51  Identities=22%  Similarity=0.622  Sum_probs=40.7

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      +...+|+||++.+.....+..++|+|.||..|+.+|+...       ..||  .|...+.
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~-------~~CP--~Cr~~~~   63 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVR-------KVCP--LCNMPVL   63 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHC-------SBCT--TTCCBCS
T ss_pred             CCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcC-------CcCC--CcCcccc
Confidence            4467899999999766656566999999999999999642       2799  8887654

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

Probab=98.69  E-value=1.9e-09  Score=66.88  Aligned_cols=55  Identities=20%  Similarity=0.632  Sum_probs=42.2

Q ss_pred             cccccccccCCCC----CCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114           47 SFICDICVEPKST----DESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD  110 (234)
Q Consensus        47 ~~~C~iC~~~~~~----~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  110 (234)
                      ..+|+||++.+..    .+.+.+++|||.||.+|+.+|+..       ...||  .|...+...++..
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-------~~~CP--~Cr~~~~~~~~~~   61 (64)
T 2xeu_A            3 MVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-------ANTCP--TCRKKINHKRYHP   61 (64)
T ss_dssp             CCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHH-------CSBCT--TTCCBCTTTCEEE
T ss_pred             CCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHc-------CCCCC--CCCccCCccceee
Confidence            5689999998742    133355699999999999999964       34899  8998887765543

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

Probab=98.68  E-value=5.8e-09  Score=64.99  Aligned_cols=56  Identities=21%  Similarity=0.501  Sum_probs=41.6

Q ss_pred             ccccccccc-CCCCCC-ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114           47 SFICDICVE-PKSTDE-SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD  110 (234)
Q Consensus        47 ~~~C~iC~~-~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  110 (234)
                      .++|+||++ .+.... .+.+++|||.||..|+.+++..      ....||  .|+..+....++.
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~------~~~~CP--~Cr~~~~~~~~~~   60 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR------GAGNCP--ECGTPLRKSNFRV   60 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHT------TSSSCT--TTCCCCSSCCCEE
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHc------CCCcCC--CCCCcccccccee
Confidence            577999999 554222 2244699999999999999852      246899  8999888766554

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

Probab=98.68  E-value=1.7e-08  Score=65.79  Aligned_cols=48  Identities=23%  Similarity=0.577  Sum_probs=39.4

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      +..++|+||++.+.  +++ +++|||.||..|+..|+..       ...||  .|...+.
T Consensus        13 ~~~~~C~IC~~~~~--~p~-~~~CgH~fC~~Ci~~~~~~-------~~~CP--~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQ--NPV-VTKCRHYFCESCALEHFRA-------TPRCY--ICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCC--SEE-ECTTSCEEEHHHHHHHHHH-------CSBCS--SSCCBCC
T ss_pred             CCCCCCcCCCchhc--Cee-EccCCCHhHHHHHHHHHHC-------CCcCC--CcCcccc
Confidence            45788999999885  445 4699999999999999963       45899  8988876

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

Probab=98.67  E-value=1e-08  Score=62.27  Aligned_cols=45  Identities=24%  Similarity=0.721  Sum_probs=34.3

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCC
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCP   95 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP   95 (234)
                      ++..++|+||++.+.  +++. ++|||.||..|+.+|+..    ......||
T Consensus        12 ~~~~~~C~IC~~~~~--~p~~-~~CgH~fC~~Ci~~~~~~----~~~~~~CP   56 (58)
T 2ecj_A           12 LQVEASCSVCLEYLK--EPVI-IECGHNFCKACITRWWED----LERDFPCP   56 (58)
T ss_dssp             SCCCCBCSSSCCBCS--SCCC-CSSCCCCCHHHHHHHTTS----SCCSCCCS
T ss_pred             cccCCCCccCCcccC--ccEe-CCCCCccCHHHHHHHHHh----cCCCCCCC
Confidence            355788999999986  4444 599999999999999752    12356788

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

Probab=98.66  E-value=1.1e-08  Score=64.49  Aligned_cols=51  Identities=22%  Similarity=0.709  Sum_probs=39.5

Q ss_pred             CCcccccccccCCCC----CCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           45 ETSFICDICVEPKST----DESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~----~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      +...+|+||++.+..    .+.+.+++|||.||..|+..|+..       ...||  .|+..+.
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-------~~~CP--~Cr~~~~   67 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-------ANTCP--TCRKKIN   67 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHH-------CSSCT--TTCCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHc-------CCCCC--CCCCccC
Confidence            457889999998742    233356799999999999999964       34799  8887765

>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=98.65  E-value=1.9e-08  Score=67.44  Aligned_cols=60  Identities=20%  Similarity=0.475  Sum_probs=45.9

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCC-CCHHH
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGV-LEPEY  107 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~-l~~~~  107 (234)
                      ...+.|+||++.+.  +++.+..|||+||+.|+..|+...-. +.....||..+|... +...+
T Consensus         5 ~~~~~CPI~~~~~~--dPV~~~~cGh~f~r~cI~~~l~~~~~-~~~~~~CP~tgc~~~~l~~~~   65 (94)
T 2yu4_A            5 SSGFTCPITKEEMK--KPVKNKVCGHTYEEDAIVRMIESRQK-RKKKAYCPQIGCSHTDIRKSD   65 (94)
T ss_dssp             SSCCBCTTTCSBCS--SEEEESSSCCEEEHHHHHHHHHHHHT-TTCCBCCCSTTCCCCCBCGGG
T ss_pred             CcEeECcCcCchhc--CCEEcCCCCCeecHHHHHHHHHHccC-cCCCCCCCcCcCcccccCHhh
Confidence            44788999999886  77776459999999999999976421 124678997779877 76544

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

Probab=98.65  E-value=1.1e-08  Score=65.62  Aligned_cols=52  Identities=19%  Similarity=0.633  Sum_probs=41.4

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      +...+|+||++++...+.+..++|+|.||..|+..|+...       ..||  .|...+..
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            3467899999999766666667999999999999998632       3799  88877653

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

Probab=98.64  E-value=1.9e-08  Score=67.13  Aligned_cols=52  Identities=21%  Similarity=0.590  Sum_probs=41.4

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      +...+|+||++.+...+.+..++|+|.||..|+..|+..       .-.||  .|...+..
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            457789999999976666666699999999999999852       23799  88877653

>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=98.63  E-value=1.5e-09  Score=76.02  Aligned_cols=52  Identities=25%  Similarity=0.707  Sum_probs=41.2

Q ss_pred             hhcCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHH
Q 048114           42 ERIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPE  106 (234)
Q Consensus        42 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  106 (234)
                      ..+...++|+||++.+.  +++.+.+|||+||..|+..|+.         ..||  .|...+...
T Consensus        17 ~~l~~~~~C~IC~~~~~--~pv~~~~CgH~fC~~Ci~~~~~---------~~CP--~Cr~~~~~~   68 (117)
T 1jm7_B           17 DRLEKLLRCSRCTNILR--EPVCLGGCEHIFCSNCVSDCIG---------TGCP--VCYTPAWIQ   68 (117)
T ss_dssp             HHHHHTTSCSSSCSCCS--SCBCCCSSSCCBCTTTGGGGTT---------TBCS--SSCCBCSCS
T ss_pred             HhchhCCCCCCCChHhh--CccEeCCCCCHHHHHHHHHHhc---------CCCc--CCCCcCccc
Confidence            34566889999999885  5555449999999999998874         6799  898887543

>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=98.63  E-value=1.2e-08  Score=70.30  Aligned_cols=51  Identities=25%  Similarity=0.704  Sum_probs=41.6

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      ++..++|+||++.+.  +++.+.+|||.||..|+..|+..       ...||  .|...+..
T Consensus        12 ~~~~~~C~IC~~~~~--~p~~~~~CgH~fC~~Ci~~~~~~-------~~~CP--~Cr~~~~~   62 (108)
T 2ckl_A           12 LNPHLMCVLCGGYFI--DATTIIECLHSFCKTCIVRYLET-------SKYCP--ICDVQVHK   62 (108)
T ss_dssp             HGGGTBCTTTSSBCS--SEEEETTTCCEEEHHHHHHHHTS-------CSBCT--TTCCBSCS
T ss_pred             cCCcCCCccCChHHh--CcCEeCCCCChhhHHHHHHHHHh-------CCcCc--CCCccccc
Confidence            456888999999886  66666699999999999999853       26899  89887764

>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=98.58  E-value=2e-08  Score=70.96  Aligned_cols=52  Identities=25%  Similarity=0.676  Sum_probs=41.6

Q ss_pred             hcCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           43 RIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        43 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      .++..++|+||++.+.  +++.+ +|||.||..|+..|+..      ....||  .|+..+..
T Consensus        48 ~~~~~~~C~IC~~~~~--~p~~~-~CgH~fC~~Ci~~~~~~------~~~~CP--~Cr~~~~~   99 (124)
T 3fl2_A           48 KVEETFQCICCQELVF--RPITT-VCQHNVCKDCLDRSFRA------QVFSCP--ACRYDLGR   99 (124)
T ss_dssp             HHHHHTBCTTTSSBCS--SEEEC-TTSCEEEHHHHHHHHHT------TCCBCT--TTCCBCCT
T ss_pred             hCccCCCCCcCChHHc--CcEEe-eCCCcccHHHHHHHHhH------CcCCCC--CCCccCCC
Confidence            3455789999999886  55554 99999999999999961      246899  89888765

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

Probab=98.55  E-value=1.7e-07  Score=61.56  Aligned_cols=52  Identities=8%  Similarity=0.023  Sum_probs=42.4

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY  107 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  107 (234)
                      +...+.|+||++.+.  +++.+ +|||+||+.|+..|+..       ...||  .|+..+....
T Consensus        11 ~p~~~~CpI~~~~m~--dPV~~-~cGhtf~r~~I~~~l~~-------~~~cP--~~~~~l~~~~   62 (85)
T 2kr4_A           11 APDEFRDPLMDTLMT--DPVRL-PSGTVMDRSIILRHLLN-------SPTDP--FNRQMLTESM   62 (85)
T ss_dssp             CCTTTBCTTTCSBCS--SEEEC-TTSCEEEHHHHHHHHHH-------CSBCT--TTCCBCCGGG
T ss_pred             CchheECcccCchhc--CCeEC-CCCCEECHHHHHHHHhc-------CCCCC--CCcCCCChHh
Confidence            355899999999886  66665 89999999999999973       25799  8888888653

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

Probab=98.54  E-value=5e-08  Score=61.21  Aligned_cols=48  Identities=31%  Similarity=0.708  Sum_probs=38.1

Q ss_pred             CcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           46 TSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        46 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ...+|+||++.+.  +....++|||.||..|+.+|+..       ...||  .|+..+.
T Consensus         4 ~~~~C~IC~~~~~--~~~~~~~C~H~fc~~Ci~~~~~~-------~~~CP--~Cr~~~~   51 (68)
T 1chc_A            4 VAERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQ-------NPTCP--LCKVPVE   51 (68)
T ss_dssp             CCCCCSSCCSCCC--SCEEETTTTEEESTTHHHHHHHH-------SCSTT--TTCCCCC
T ss_pred             CCCCCeeCCcccc--CCcEecCCCCeeHHHHHHHHHhC-------cCcCc--CCChhhH
Confidence            4667999999875  44456799999999999999853       24799  8887765

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

Probab=98.53  E-value=2.4e-08  Score=71.96  Aligned_cols=49  Identities=31%  Similarity=0.855  Sum_probs=38.6

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ++..++|+||++.+.  +++.+ +|||.||..|+..|+..       ...||  .|...+.
T Consensus        50 ~~~~~~C~iC~~~~~--~~~~~-~CgH~fc~~Ci~~~~~~-------~~~CP--~Cr~~~~   98 (138)
T 4ayc_A           50 LENELQCIICSEYFI--EAVTL-NCAHSFCSYCINEWMKR-------KIECP--ICRKDIK   98 (138)
T ss_dssp             HHHHSBCTTTCSBCS--SEEEE-TTSCEEEHHHHHHHTTT-------CSBCT--TTCCBCC
T ss_pred             ccccCCCcccCcccC--CceEC-CCCCCccHHHHHHHHHc-------CCcCC--CCCCcCC
Confidence            345678999999885  55554 99999999999999742       34799  8887765

>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=98.51  E-value=9.9e-08  Score=64.36  Aligned_cols=51  Identities=12%  Similarity=0.069  Sum_probs=41.7

Q ss_pred             cCCcccccccccCCCCCCceeeCCCC-ChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCS-HSYCTECMTKYVASKLQENITSINCPVADCKGVLEPE  106 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~-H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  106 (234)
                      +...+.|+||++.+.  +++.+ +|| |+||+.|+..|+..       ...||  .|+..+...
T Consensus        19 ~p~~~~CpI~~~~m~--dPV~~-~cG~htf~r~cI~~~l~~-------~~~cP--~~~~~l~~~   70 (98)
T 1wgm_A           19 ACDEFLDPIMSTLMC--DPVVL-PSSRVTVDRSTIARHLLS-------DQTDP--FNRSPLTMD   70 (98)
T ss_dssp             CCTTTBCTTTCSBCS--SEEEC-TTTCCEEEHHHHHHHTTT-------SCBCT--TTCSBCCTT
T ss_pred             CcHhcCCcCcccccc--CCeEC-CCCCeEECHHHHHHHHHh-------CCCCC--CCCCCCChh
Confidence            456899999999885  66665 999 99999999999963       24799  888888764

>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=98.48  E-value=7e-08  Score=70.39  Aligned_cols=52  Identities=27%  Similarity=0.734  Sum_probs=41.9

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPE  106 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  106 (234)
                      +...+.|+||++.+.  +++. ++|||.||..|+..|+..      ....||  .|...+...
T Consensus        75 l~~~~~C~IC~~~~~--~pv~-~~CgH~fC~~Ci~~~~~~------~~~~CP--~Cr~~~~~~  126 (150)
T 1z6u_A           75 LEQSFMCVCCQELVY--QPVT-TECFHNVCKDCLQRSFKA------QVFSCP--ACRHDLGQN  126 (150)
T ss_dssp             HHHHTBCTTTSSBCS--SEEE-CTTSCEEEHHHHHHHHHT------TCCBCT--TTCCBCCTT
T ss_pred             CccCCEeecCChhhc--CCEE-cCCCCchhHHHHHHHHHh------CCCcCC--CCCccCCCC
Confidence            345689999999885  5555 599999999999999963      246899  898888765

>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=98.47  E-value=1.4e-07  Score=65.51  Aligned_cols=54  Identities=24%  Similarity=0.524  Sum_probs=39.7

Q ss_pred             cccccccccCCCCCC---------------ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           47 SFICDICVEPKSTDE---------------SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~---------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ..+|+||++++....               .+.+++|+|.||..||..|+...  .......||  .|...+.
T Consensus        25 ~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~--~~~~~~~CP--~CR~~~~   93 (114)
T 1v87_A           25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNG--NKDGSLQCP--SCKTIYG   93 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHT--CCSSCCBCT--TTCCBSS
T ss_pred             CCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcc--cCCCCCcCC--CCCCccC
Confidence            468999999985322               23367999999999999999532  113457899  8887765

>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=98.44  E-value=5.1e-08  Score=76.40  Aligned_cols=59  Identities=20%  Similarity=0.468  Sum_probs=47.3

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHh
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR  109 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~  109 (234)
                      ....+.||||++.+.  +++....|||+||+.|+.+|+..    + ....||..+|...+...++.
T Consensus       178 ~~~el~CPIcl~~f~--DPVts~~CGHsFcR~cI~~~~~~----~-~~~~CPvtGCr~~l~~~dL~  236 (267)
T 3htk_C          178 GKIELTCPITCKPYE--APLISRKCNHVFDRDGIQNYLQG----Y-TTRDCPQAACSQVVSMRDFV  236 (267)
T ss_dssp             SBCCSBCTTTSSBCS--SEEEESSSCCEEEHHHHHHHSTT----C-SCEECSGGGCSCEECGGGEE
T ss_pred             CceeeECcCccCccc--CCeeeCCCCCcccHHHHHHHHHh----C-CCCCCCcccccCcCchhhCC
Confidence            356889999999986  77776699999999999999962    2 35789976799988876543

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

Probab=98.40  E-value=4.3e-08  Score=59.09  Aligned_cols=46  Identities=20%  Similarity=0.561  Sum_probs=35.6

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      .+.++|+||++.+.  +++ .++|||+||..|+..          ....||  .|+..+..
T Consensus         4 ~~~~~C~IC~~~~~--~p~-~l~CgH~fC~~Ci~~----------~~~~CP--~Cr~~~~~   49 (56)
T 1bor_A            4 FQFLRCQQCQAEAK--CPK-LLPCLHTLCSGCLEA----------SGMQCP--ICQAPWPL   49 (56)
T ss_dssp             CCCSSCSSSCSSCB--CCS-CSTTSCCSBTTTCSS----------SSSSCS--SCCSSSSC
T ss_pred             ccCCCceEeCCccC--CeE-EcCCCCcccHHHHcc----------CCCCCC--cCCcEeec
Confidence            34778999999886  444 459999999999866          356899  88876653

>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=98.38  E-value=1.3e-07  Score=70.24  Aligned_cols=50  Identities=26%  Similarity=0.808  Sum_probs=40.8

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ...+.|+||++.+.  +++.+.+|||.||..|+..|+..      ....||  .|...+.
T Consensus        52 ~~~~~C~IC~~~~~--~p~~~~~CgH~fC~~Ci~~~~~~------~~~~CP--~Cr~~~~  101 (165)
T 2ckl_B           52 HSELMCPICLDMLK--NTMTTKECLHRFCADCIITALRS------GNKECP--TCRKKLV  101 (165)
T ss_dssp             HHHHBCTTTSSBCS--SEEEETTTCCEEEHHHHHHHHHT------TCCBCT--TTCCBCC
T ss_pred             CCCCCCcccChHhh--CcCEeCCCCChhHHHHHHHHHHh------CcCCCC--CCCCcCC
Confidence            44678999999986  56666699999999999999962      146799  8998875

>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=98.36  E-value=2.3e-07  Score=62.82  Aligned_cols=51  Identities=8%  Similarity=0.010  Sum_probs=41.9

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPE  106 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  106 (234)
                      +...+.|+||++.+.  +++.+ +|||+||+.|+..|+..       ...||  .|+..+...
T Consensus        26 ~p~~~~CpI~~~~m~--dPV~~-~cGhtf~r~~I~~~l~~-------~~~cP--~~~~~l~~~   76 (100)
T 2kre_A           26 APDEFRDPLMDTLMT--DPVRL-PSGTIMDRSIILRHLLN-------SPTDP--FNRQTLTES   76 (100)
T ss_dssp             CSTTTBCTTTCSBCS--SEEEE-TTTEEEEHHHHHHHTTS-------CSBCS--SSCCBCCTT
T ss_pred             CcHhhCCcCccCccc--CCeEC-CCCCEEchHHHHHHHHc-------CCCCC--CCCCCCChh
Confidence            355899999999886  77766 79999999999999952       35799  888888764

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

Probab=98.36  E-value=2.2e-08  Score=63.25  Aligned_cols=47  Identities=30%  Similarity=0.794  Sum_probs=36.6

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ....+|+||++.+..   + +++|+|.||..|+..|+.       ....||  .|+..+.
T Consensus        13 ~~~~~C~IC~~~~~~---~-~~~CgH~fc~~Ci~~~~~-------~~~~CP--~Cr~~~~   59 (70)
T 2ecn_A           13 TDEEECCICMDGRAD---L-ILPCAHSFCQKCIDKWSD-------RHRNCP--ICRLQMT   59 (70)
T ss_dssp             CCCCCCSSSCCSCCS---E-EETTTEEECHHHHHHSSC-------CCSSCH--HHHHCTT
T ss_pred             CCCCCCeeCCcCccC---c-ccCCCCcccHHHHHHHHH-------CcCcCC--CcCCccc
Confidence            457789999999863   4 459999999999999875       245788  7766554

>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=98.33  E-value=1.8e-07  Score=65.08  Aligned_cols=48  Identities=29%  Similarity=0.755  Sum_probs=39.0

Q ss_pred             cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      .++|+||++.+.  +++.+ +|||.||..|+..|+..      ....||  .|...+..
T Consensus        15 ~~~C~iC~~~~~--~p~~~-~CgH~fC~~Ci~~~~~~------~~~~CP--~Cr~~~~~   62 (115)
T 3l11_A           15 ECQCGICMEILV--EPVTL-PCNHTLCKPCFQSTVEK------ASLCCP--FCRRRVSS   62 (115)
T ss_dssp             HHBCTTTCSBCS--SCEEC-TTSCEECHHHHCCCCCT------TTSBCT--TTCCBCHH
T ss_pred             CCCCccCCcccC--ceeEc-CCCCHHhHHHHHHHHhH------CcCCCC--CCCcccCc
Confidence            678999999885  55555 99999999999988742      247899  89998875

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

Probab=98.30  E-value=2.3e-07  Score=59.40  Aligned_cols=47  Identities=26%  Similarity=0.666  Sum_probs=35.2

Q ss_pred             hcCCcccccccccCCCCCCceeeCCCCCh-hhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           43 RIETSFICDICVEPKSTDESFSIKGCSHS-YCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        43 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      .++...+|+||++.+.  ++ .+++|||. ||..|+..           ...||  .|+..+..
T Consensus        21 ~~~~~~~C~IC~~~~~--~~-~~~pCgH~~~C~~C~~~-----------~~~CP--~Cr~~i~~   68 (75)
T 2ecg_A           21 RLQEEKLCKICMDRNI--AI-VFVPCGHLVTCKQCAEA-----------VDKCP--MCYTVITF   68 (75)
T ss_dssp             HHHHHHSCSSSCSSCC--CB-CCSSSCCCCBCHHHHHH-----------CSBCT--TTCCBCCC
T ss_pred             cCCCCCCCCcCCCCCC--CE-EEecCCCHHHHHHHhhC-----------CCCCc--cCCceecC
Confidence            3455778999999874  44 44699999 99999942           25799  88877653

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

Probab=98.24  E-value=2.2e-07  Score=59.35  Aligned_cols=46  Identities=26%  Similarity=0.687  Sum_probs=35.7

Q ss_pred             hcCCcccccccccCCCCCCceeeCCCCCh-hhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           43 RIETSFICDICVEPKSTDESFSIKGCSHS-YCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        43 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      .+++...|+||++.+.  +.+. ++|||. ||..|+..+           ..||  .|...+.
T Consensus        20 ~~~~~~~C~iC~~~~~--~~~~-~pCgH~~~C~~C~~~~-----------~~CP--~Cr~~i~   66 (74)
T 4ic3_A           20 RLQEEKLCKICMDRNI--AIVF-VPCGHLVTCKQCAEAV-----------DKCP--MCYTVIT   66 (74)
T ss_dssp             HHHHHTBCTTTSSSBC--CEEE-ETTCCBCCCHHHHTTC-----------SBCT--TTCCBCS
T ss_pred             cCccCCCCCCCCCCCC--CEEE-cCCCChhHHHHhhhcC-----------ccCC--CcCcCcc
Confidence            3455778999999874  5444 499999 999998765           5899  8887765

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

Probab=98.20  E-value=9.3e-07  Score=57.40  Aligned_cols=50  Identities=24%  Similarity=0.513  Sum_probs=35.7

Q ss_pred             cccccccccCCCC-----------CC-ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           47 SFICDICVEPKST-----------DE-SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        47 ~~~C~iC~~~~~~-----------~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      ..+|+||++++..           ++ .+.+++|+|.|+.+|+.+|+...       -.||  .|+..+..
T Consensus        15 ~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~-------~~CP--~CR~~~~~   76 (81)
T 2ecl_A           15 CDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQN-------NRCP--LCQQDWVV   76 (81)
T ss_dssp             CSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTC-------CBCT--TTCCBCCE
T ss_pred             CCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhC-------CCCC--CcCCCcch
Confidence            3457777777742           22 44555799999999999998532       3899  88887654

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

Probab=98.01  E-value=5.2e-06  Score=53.59  Aligned_cols=51  Identities=24%  Similarity=0.492  Sum_probs=40.4

Q ss_pred             cccccccccCCCCCCceeeCCCC-----ChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           47 SFICDICVEPKSTDESFSIKGCS-----HSYCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      ...|.||++++..++.. +++|.     |.|+.+||.+|+...     ....||  .|+..+..
T Consensus        15 ~~~C~IC~~~~~~~~~l-~~pC~C~Gs~h~fH~~Cl~~Wl~~~-----~~~~Cp--lCr~~~~~   70 (80)
T 2d8s_A           15 QDICRICHCEGDDESPL-ITPCHCTGSLHFVHQACLQQWIKSS-----DTRCCE--LCKYEFIM   70 (80)
T ss_dssp             SCCCSSSCCCCCSSSCE-ECSSSCCSSSCCEETTHHHHHHHHH-----CCSBCS--SSCCBCCC
T ss_pred             CCCCeEcCccccCCCee-EeccccCCcCCeeCHHHHHHHHhhC-----CCCCCC--CCCCeeec
Confidence            56799999998765655 46896     999999999999754     246899  88877654

>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=97.98  E-value=2.5e-06  Score=68.43  Aligned_cols=52  Identities=13%  Similarity=0.049  Sum_probs=41.5

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHH
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY  107 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  107 (234)
                      ...+.|+||++.+.  +++.+ +|||+||+.|+..|+..    +  ...||  .|+..++...
T Consensus       206 ~~~~~c~i~~~~~~--dPv~~-~~gh~f~~~~i~~~~~~----~--~~~cP--~~~~~~~~~~  257 (281)
T 2c2l_A          206 PDYLCGKISFELMR--EPCIT-PSGITYDRKDIEEHLQR----V--GHFNP--VTRSPLTQEQ  257 (281)
T ss_dssp             CSTTBCTTTCSBCS--SEEEC-SSCCEEETTHHHHHHHH----T--CSSCT--TTCCCCCGGG
T ss_pred             CcccCCcCcCCHhc--CCeEC-CCCCEECHHHHHHHHHH----C--CCCCc--CCCCCCchhc
Confidence            45889999999886  66665 89999999999999963    2  12399  8999887653

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

Probab=97.97  E-value=3.9e-06  Score=62.51  Aligned_cols=53  Identities=13%  Similarity=0.075  Sum_probs=42.8

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY  107 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  107 (234)
                      +...+.|+||++.+.  +++.+ +|||+||+.|+..|+...   +  . .||  .|+..+....
T Consensus       103 ip~~f~CPI~~elm~--DPV~~-~~Ghtfer~~I~~~l~~~---~--~-tcP--~t~~~l~~~~  155 (179)
T 2f42_A          103 IPDYLCGKISFELMR--EPCIT-PSGITYDRKDIEEHLQRV---G--H-FDP--VTRSPLTQDQ  155 (179)
T ss_dssp             CCGGGBCTTTCSBCS--SEEEC-TTSCEEEHHHHHHHHHHT---C--S-BCT--TTCCBCCGGG
T ss_pred             CcHhhcccCccccCC--CCeEC-CCCCEECHHHHHHHHHhC---C--C-CCC--CCcCCCChhh
Confidence            466899999999886  66665 999999999999999742   2  2 699  8888887653

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

Probab=97.95  E-value=1.8e-06  Score=61.32  Aligned_cols=57  Identities=19%  Similarity=0.621  Sum_probs=43.4

Q ss_pred             CCcccccccccCCCC----CCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114           45 ETSFICDICVEPKST----DESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD  110 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~----~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  110 (234)
                      +....|+||++.+..    ......++|||.||..|+..|+..       ...||  .|...+..+++..
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~-------~~~CP--~Cr~~~~~~~~~~  130 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN-------ANTCP--TCRKKINHKRYHP  130 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHH-------CSBCT--TTCCBCCGGGEEE
T ss_pred             CCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHc-------CCCCC--CCCCcCChhccee
Confidence            457789999998742    122345699999999999999963       24899  8999988776554

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

Probab=97.92  E-value=4.8e-06  Score=52.02  Aligned_cols=44  Identities=25%  Similarity=0.693  Sum_probs=33.8

Q ss_pred             CCcccccccccCCCCCCceeeCCCCCh-hhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHS-YCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      +....|.||++...  + +.+++|+|. ||..|+..           .-.||  .|...+.
T Consensus        13 ~~~~~C~IC~~~~~--~-~v~~pCgH~~~C~~C~~~-----------~~~CP--~CR~~i~   57 (68)
T 2ea5_A           13 ENSKDCVVCQNGTV--N-WVLLPCRHTCLCDGCVKY-----------FQQCP--MCRQFVQ   57 (68)
T ss_dssp             CCSSCCSSSSSSCC--C-CEETTTTBCCSCTTHHHH-----------CSSCT--TTCCCCC
T ss_pred             CCCCCCCCcCcCCC--C-EEEECCCChhhhHHHHhc-----------CCCCC--CCCcchh
Confidence            34678999999763  3 556699999 99999973           24799  8887665

>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=97.91  E-value=1.6e-06  Score=55.92  Aligned_cols=46  Identities=26%  Similarity=0.809  Sum_probs=35.2

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCCh-hhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHS-YCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      +.....|.||++...  +. .+++|||. ||..|+..+           ..||  .|...+..
T Consensus        15 l~~~~~C~IC~~~~~--~~-v~~pCgH~~~C~~C~~~~-----------~~CP--~Cr~~i~~   61 (79)
T 2yho_A           15 LKEAMLCMVCCEEEI--NS-TFCPCGHTVCCESCAAQL-----------QSCP--VCRSRVEH   61 (79)
T ss_dssp             HHHHTBCTTTSSSBC--CE-EEETTCBCCBCHHHHTTC-----------SBCT--TTCCBCCE
T ss_pred             CCCCCEeEEeCcccC--cE-EEECCCCHHHHHHHHHhc-----------CcCC--CCCchhhC
Confidence            445678999999764  44 44599999 999999754           2899  89887664

>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=97.91  E-value=1.2e-05  Score=66.80  Aligned_cols=51  Identities=31%  Similarity=0.694  Sum_probs=39.4

Q ss_pred             cCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           44 IETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      .+...+|+||++.+.  +++ +++|||.||..|+..|+..      ....||  .|...+..
T Consensus       329 ~~~~~~C~ICle~~~--~pv-~lpCGH~FC~~Ci~~wl~~------~~~~CP--~CR~~i~~  379 (389)
T 2y1n_A          329 GSTFQLCKICAENDK--DVK-IEPCGHLMCTSCLTSWQES------EGQGCP--FCRCEIKG  379 (389)
T ss_dssp             TTSSSBCTTTSSSBC--CEE-EETTCCEECHHHHHHHHHH------TCSBCT--TTCCBCCE
T ss_pred             cCCCCCCCccCcCCC--CeE-EeCCCChhhHHHHHHHHhc------CCCCCC--CCCCccCC
Confidence            344579999999874  444 4599999999999999863      245899  88887664

>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=97.84  E-value=7.9e-06  Score=50.38  Aligned_cols=47  Identities=21%  Similarity=0.420  Sum_probs=34.9

Q ss_pred             cccccccccCCCCCCcee-eCCCCCh-hhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           47 SFICDICVEPKSTDESFS-IKGCSHS-YCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~~~-~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ..+|.||++...  +.+. .++|||. ||.+|+..+...       .-.||  .|...+.
T Consensus         8 ~~~C~IC~~~~~--~~~~~~~pCgH~~~C~~C~~~~~~~-------~~~CP--iCR~~i~   56 (64)
T 2vje_A            8 IEPCVICQGRPK--NGCIVHGKTGHLMACFTCAKKLKKR-------NKPCP--VCRQPIQ   56 (64)
T ss_dssp             GSCCTTTSSSCS--CEEEEETTEEEEEECHHHHHHHHHT-------TCCCT--TTCCCCC
T ss_pred             cCCCCcCCCCCC--CEEEECCCCCChhhHHHHHHHHHHc-------CCcCC--CcCcchh
Confidence            557999999764  3332 2399999 899999988751       24799  8887764

>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=97.83  E-value=7.9e-06  Score=50.21  Aligned_cols=47  Identities=19%  Similarity=0.496  Sum_probs=34.8

Q ss_pred             cccccccccCCCCCCc-eeeCCCCCh-hhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           47 SFICDICVEPKSTDES-FSIKGCSHS-YCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~-~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ..+|.||++...  +. +.+.+|||. ||.+|..++...       .-.||  .|...+.
T Consensus         7 ~~~C~IC~~~~~--~~~~~~~pCgH~~~C~~C~~~~~~~-------~~~CP--iCR~~i~   55 (63)
T 2vje_B            7 LKPCSLCEKRPR--DGNIIHGRTGHLVTCFHCARRLKKA-------GASCP--ICKKEIQ   55 (63)
T ss_dssp             GSBCTTTSSSBS--CEEEEETTEEEEEECHHHHHHHHHT-------TCBCT--TTCCBCC
T ss_pred             CCCCcccCCcCC--CeEEEecCCCCHhHHHHHHHHHHHh-------CCcCC--CcCchhh
Confidence            567999999764  32 233499999 999999987742       24799  8887764

>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=97.82  E-value=1.5e-05  Score=54.28  Aligned_cols=49  Identities=18%  Similarity=0.391  Sum_probs=37.5

Q ss_pred             cccccccccCCCCCC---------------ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           47 SFICDICVEPKSTDE---------------SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~---------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ..+|.||++.+...-               .+.+++|+|.|+..|+..|+..       ...||  .|...+.
T Consensus        37 ~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~-------~~~CP--~Cr~~~~  100 (106)
T 3dpl_R           37 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-------RQVCP--LDNREWE  100 (106)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTT-------CSBCS--SSCSBCC
T ss_pred             CCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHc-------CCcCc--CCCCcce
Confidence            467999999986331               2455699999999999999852       35799  8887754

>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=97.50  E-value=1.5e-05  Score=55.23  Aligned_cols=50  Identities=18%  Similarity=0.358  Sum_probs=0.4

Q ss_pred             cccccccccCCCCCC---------------ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           47 SFICDICVEPKSTDE---------------SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~---------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      ..+|.||++++....               .+..++|+|.|+..|+..|+..       .-.||  .|...+..
T Consensus        48 ~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~-------~~~CP--~Cr~~~~~  112 (117)
T 4a0k_B           48 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-------RQVCP--LDNREWEF  112 (117)
T ss_dssp             C-------------------------------------------------------------------------
T ss_pred             CCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHc-------CCcCC--CCCCeeee
Confidence            357999999985311               2233589999999999999964       23699  78776543

>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=97.25  E-value=5.2e-05  Score=62.50  Aligned_cols=46  Identities=26%  Similarity=0.806  Sum_probs=36.3

Q ss_pred             hcCCcccccccccCCCCCCceeeCCCCCh-hhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           43 RIETSFICDICVEPKSTDESFSIKGCSHS-YCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        43 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      .++....|+||++.+.  +++. ++|||. ||..|+..+           ..||  .|...+.
T Consensus       291 ~l~~~~~C~IC~~~~~--~~v~-lpCgH~~fC~~C~~~~-----------~~CP--~CR~~i~  337 (345)
T 3t6p_A          291 RLQEERTCKVCMDKEV--SVVF-IPCGHLVVCQECAPSL-----------RKCP--ICRGIIK  337 (345)
T ss_dssp             HHHTTCBCTTTSSSBC--CEEE-ETTCCEEECTTTGGGC-----------SBCT--TTCCBCC
T ss_pred             hCcCCCCCCccCCcCC--ceEE-cCCCChhHhHHHHhcC-----------CcCC--CCCCCcc
Confidence            3466789999999875  5554 499999 999999754           5799  8887765

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

Probab=97.18  E-value=0.00044  Score=43.62  Aligned_cols=51  Identities=25%  Similarity=0.555  Sum_probs=38.1

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      +...+|.||++.+...  .....|+|.|...|+.+|++..     ..-.||  .|...+.
T Consensus        13 ~~i~~C~IC~~~i~~g--~~C~~C~h~fH~~Ci~kWl~~~-----~~~~CP--~Cr~~w~   63 (74)
T 2ct0_A           13 DAVKICNICHSLLIQG--QSCETCGIRMHLPCVAKYFQSN-----AEPRCP--HCNDYWP   63 (74)
T ss_dssp             SSSCBCSSSCCBCSSS--EECSSSCCEECHHHHHHHSTTC-----SSCCCT--TTCSCCC
T ss_pred             CCCCcCcchhhHcccC--CccCCCCchhhHHHHHHHHHhc-----CCCCCC--CCcCcCC
Confidence            3356799999998643  3344999999999999999532     235799  7877665

>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=96.83  E-value=0.00061  Score=41.28  Aligned_cols=52  Identities=15%  Similarity=0.171  Sum_probs=39.5

Q ss_pred             cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHh
Q 048114           47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR  109 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~  109 (234)
                      .+.|+|+++.+.  +++...++||.|++.++.+|+...   +    +||  ..+..|..+++.
T Consensus         3 ~~~CpIs~~~m~--dPV~~~~sG~~yer~~I~~~l~~~---~----~cP--~t~~~L~~~~Li   54 (61)
T 2bay_A            3 HMLCAISGKVPR--RPVLSPKSRTIFEKSLLEQYVKDT---G----NDP--ITNEPLSIEEIV   54 (61)
T ss_dssp             -CCCTTTCSCCS--SEEEETTTTEEEEHHHHHHHHHHH---S----BCT--TTCCBCCGGGCE
T ss_pred             eEEecCCCCCCC--CCEEeCCCCcEEcHHHHHHHHHhC---C----CCc--CCcCCCChhhcE
Confidence            467999999886  666554899999999999999742   2    388  677777766544

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

Probab=96.40  E-value=0.0015  Score=53.23  Aligned_cols=59  Identities=19%  Similarity=0.458  Sum_probs=42.3

Q ss_pred             CCcccccccccCCCC-CCce----eeCCCCChhhHHHHHHHHHHHHhc----CCccccCCCCCCCCCCCH
Q 048114           45 ETSFICDICVEPKST-DESF----SIKGCSHSYCTECMTKYVASKLQE----NITSINCPVADCKGVLEP  105 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~-~~~~----~~~~C~H~fC~~Cl~~~~~~~i~~----~~~~i~CP~~~C~~~l~~  105 (234)
                      +...+|+|||+.+.. ...+    ....|+|.|...|+.+|+.+.-..    +...=.||  .|+..++-
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CP--yCr~pIs~  373 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCP--FCKAKLST  373 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECT--TTCCEEEG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCC--CCCCcCCc
Confidence            457789999999865 2222    124899999999999999876432    22233799  89987763

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

Probab=96.20  E-value=0.0044  Score=37.26  Aligned_cols=38  Identities=37%  Similarity=0.950  Sum_probs=31.7

Q ss_pred             CeecCCCCCCCCceecCCCCccCcccCcc--ccccccccCCCCC
Q 048114          133 QKFYCPFKDCSALLIDDGGEAIRESVCPD--CNRMFCAQCKVPW  174 (234)
Q Consensus       133 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~  174 (234)
                      +...||  .|...+...++  -+.+.|..  |+..||+.|+.+|
T Consensus         5 ~~k~CP--~C~~~Iek~~G--CnhmtC~~~~C~~~FCw~C~~~~   44 (60)
T 1wd2_A            5 NTKECP--KCHVTIEKDGG--CNHMVCRNQNCKAEFCWVCLGPW   44 (60)
T ss_dssp             CCCCCT--TTCCCCSSCCS--CCSSSCCSSGGGSCCSSSSCSCS
T ss_pred             cceECc--CCCCeeEeCCC--CCcEEECCCCcCCEEeeCcCCCc
Confidence            446799  99999887653  56799988  9999999999987

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

Probab=95.97  E-value=0.011  Score=35.56  Aligned_cols=49  Identities=18%  Similarity=0.476  Sum_probs=35.3

Q ss_pred             CcccccccccCCCCCCceeeCCCC--C---hhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           46 TSFICDICVEPKSTDESFSIKGCS--H---SYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        46 ~~~~C~iC~~~~~~~~~~~~~~C~--H---~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ....|-||+++..  +.. +.+|.  +   .|..+||.+|+...     ....||  .|+..+.
T Consensus         5 ~~~~CrIC~~~~~--~~l-~~PC~C~gs~~~~H~~Cl~~W~~~~-----~~~~C~--~C~~~~~   58 (60)
T 1vyx_A            5 DVPVCWICNEELG--NER-FRACGCTGELENVHRSCLSTWLTIS-----RNTACQ--ICGVVYN   58 (60)
T ss_dssp             SCCEETTTTEECS--CCC-CCSCCCSSGGGSCCHHHHHHHHHHH-----TCSBCT--TTCCBCC
T ss_pred             CCCEeEEeecCCC--Cce-ecCcCCCCchhhhHHHHHHHHHHhC-----CCCccC--CCCCeee
Confidence            3567999998743  323 35765  4   79999999999754     246899  8887664

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

Probab=95.75  E-value=0.0062  Score=40.18  Aligned_cols=46  Identities=24%  Similarity=0.588  Sum_probs=31.2

Q ss_pred             cccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           49 ICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        49 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      -|++|--++.  .-..+.+|.|.||.+|...|.+..      .=.||  .|...+.
T Consensus         3 fC~~C~~Pi~--iygRmIPCkHvFCydCa~~~~~~~------~k~Cp--~C~~~V~   48 (101)
T 3vk6_A            3 FCDKCGLPIK--VYGRMIPCKHVFCYDCAILHEKKG------DKMCP--GCSDPVQ   48 (101)
T ss_dssp             BCTTTCSBCS--EEEEEETTCCEEEHHHHHHHHHTT------CCBCT--TTCCBCS
T ss_pred             ecCccCCCeE--EEeeeccccccHHHHHHHHHHhcc------CCCCc--CcCCeee
Confidence            4888855543  334566999999999999887532      22566  6665544

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

Probab=95.70  E-value=0.006  Score=40.76  Aligned_cols=34  Identities=26%  Similarity=0.700  Sum_probs=24.8

Q ss_pred             cccccccccCCCCCCceeeCCCCChhhHHHHHHH
Q 048114           47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKY   80 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~   80 (234)
                      ...|+||.+.+.......-+.|+|+||..|++.+
T Consensus         3 e~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            3 KVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CCBCTTCCSSSCCBCCEEETTTTEEECHHHHHHH
T ss_pred             CCCCcCCCCCCCCCceEECCcCChHHhHHHCHHH
Confidence            5679999976432222333699999999999983

>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=95.62  E-value=0.019  Score=35.90  Aligned_cols=50  Identities=20%  Similarity=0.489  Sum_probs=38.8

Q ss_pred             CCcccccccccCCCCCCceeeCCC-CChhhHHHHHHHHHHHHhcCCccccCCC
Q 048114           45 ETSFICDICVEPKSTDESFSIKGC-SHSYCTECMTKYVASKLQENITSINCPV   96 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C-~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   96 (234)
                      ...+.|.+|.+.++....++.++= .|.||..|-+.+|+.+-.  ...+.||.
T Consensus        13 ~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~q~~--~~EvyCPS   63 (93)
T 2cs3_A           13 SGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKAQGA--TGEVYCPS   63 (93)
T ss_dssp             CCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHHHHS--SSCCCCTT
T ss_pred             CCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHhcCC--CCcEECCC
Confidence            447789999999987776654322 799999999999998743  35778885

>2k4x_A 30S ribosomal protein S27AE; metal-binding, ribonucleoprotein, zinc, zinc-finger, structural genomics, PSI-2; NMR {Thermoplasma acidophilum} SCOP: g.41.8.8

Probab=93.26  E-value=0.04  Score=32.34  Aligned_cols=29  Identities=24%  Similarity=0.344  Sum_probs=21.0

Q ss_pred             CCcccCCCCCceeeeccCCCceEe-cCCCC
Q 048114          205 ENWRRCPNCKIFVEKKEGCRYMRC-SSNPQ  233 (234)
Q Consensus       205 ~~~k~CP~C~~~i~k~~GCnhm~C-~C~~~  233 (234)
                      ...+.||+|+..+.-...-+.++| +||+.
T Consensus        16 ~~~~fCPkCG~~~~ma~~~dr~~C~kCgyt   45 (55)
T 2k4x_A           16 RKHRFCPRCGPGVFLAEHADRYSCGRCGYT   45 (55)
T ss_dssp             CSSCCCTTTTTTCCCEECSSEEECTTTCCC
T ss_pred             EccccCcCCCCceeEeccCCEEECCCCCCE
Confidence            346899999985543344479999 59986

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

Probab=92.78  E-value=0.11  Score=40.47  Aligned_cols=52  Identities=27%  Similarity=0.522  Sum_probs=39.5

Q ss_pred             CcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHH
Q 048114           46 TSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPE  106 (234)
Q Consensus        46 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~  106 (234)
                      ....|.||.+-+..  ......|+|.|...|+..|+..     .....||  .|+..++.+
T Consensus       179 ~i~~C~iC~~iv~~--g~~C~~C~~~~H~~C~~~~~~~-----~~~~~CP--~C~~~W~~~  230 (238)
T 3nw0_A          179 AVKICNICHSLLIQ--GQSCETCGIRMHLPCVAKYFQS-----NAEPRCP--HCNDYWPHE  230 (238)
T ss_dssp             TCCBCTTTCSBCSS--CEECSSSCCEECHHHHHHHTTT-----CSSCBCT--TTCCBCCSC
T ss_pred             CCCcCcchhhHHhC--CcccCccChHHHHHHHHHHHHh-----CCCCCCC--CCCCCCCCC
Confidence            46789999998863  3444469999999999999853     2356899  898876643

>3j20_Y 30S ribosomal protein S27AE; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=92.13  E-value=0.068  Score=30.63  Aligned_cols=29  Identities=17%  Similarity=0.248  Sum_probs=20.0

Q ss_pred             CCcccCCCCCceeeeccCCCceEe-cCCCC
Q 048114          205 ENWRRCPNCKIFVEKKEGCRYMRC-SSNPQ  233 (234)
Q Consensus       205 ~~~k~CP~C~~~i~k~~GCnhm~C-~C~~~  233 (234)
                      ...+.||+|+..+.-...=+.++| +||+.
T Consensus        17 ~~~k~CP~CG~~~fm~~~~~R~~C~kCG~t   46 (50)
T 3j20_Y           17 RKNKFCPRCGPGVFMADHGDRWACGKCGYT   46 (50)
T ss_dssp             CSSEECSSSCSSCEEEECSSEEECSSSCCE
T ss_pred             EecccCCCCCCceEEecCCCeEECCCCCCE
Confidence            456899999984332222278999 59975

>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=91.70  E-value=0.087  Score=33.97  Aligned_cols=30  Identities=10%  Similarity=0.256  Sum_probs=23.3

Q ss_pred             CCcccCCCCCceeeeccCCCceEec-CCCCC
Q 048114          205 ENWRRCPNCKIFVEKKEGCRYMRCS-SNPQL  234 (234)
Q Consensus       205 ~~~k~CP~C~~~i~k~~GCnhm~C~-C~~~F  234 (234)
                      .+.+-||+|...+...++-..++|. |++.|
T Consensus        23 ~~~~wCP~C~~~~~~~~~~~~v~C~~C~~~F   53 (86)
T 2ct7_A           23 PKFLWCAQCSFGFIYEREQLEATCPQCHQTF   53 (86)
T ss_dssp             CCEECCSSSCCCEECCCSCSCEECTTTCCEE
T ss_pred             CCEeECcCCCchheecCCCCceEeCCCCCcc
Confidence            4566799999988877777778884 88765

>1vq8_Z 50S ribosomal protein L37AE; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: g.41.8.1 PDB: 1vq4_Z* 1vq6_Z* 1vq5_Z* 1vq7_Z* 1vq9_Z* 1vqk_Z* 1vql_Z* 1vqm_Z* 1vqn_Z* 1vqo_Z* 1vqp_Z* 1yhq_Z* 1yi2_Z* 1yij_Z* 1yit_Z* 1yj9_Z* 1yjn_Z* 1yjw_Z* 2qa4_Z* 1s72_Z* ...

Probab=91.67  E-value=0.065  Score=34.28  Aligned_cols=30  Identities=23%  Similarity=0.501  Sum_probs=25.7

Q ss_pred             CCcccCCCCCceeeeccCCCceEec-CCCCC
Q 048114          205 ENWRRCPNCKIFVEKKEGCRYMRCS-SNPQL  234 (234)
Q Consensus       205 ~~~k~CP~C~~~i~k~~GCnhm~C~-C~~~F  234 (234)
                      ....+||.|+....+..+=..+.|. ||+.|
T Consensus        25 ~~~y~Cp~CG~~~v~r~atGiW~C~~Cg~~~   55 (83)
T 1vq8_Z           25 NEDHACPNCGEDRVDRQGTGIWQCSYCDYKF   55 (83)
T ss_dssp             HSCEECSSSCCEEEEEEETTEEEETTTCCEE
T ss_pred             cccCcCCCCCCcceeccCCCeEECCCCCCEe
Confidence            3457999999999998888899995 99876

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

Probab=91.08  E-value=0.095  Score=33.31  Aligned_cols=30  Identities=17%  Similarity=0.282  Sum_probs=25.5

Q ss_pred             CCcccCCC--CCceeeeccCCCceEe------cCCCCC
Q 048114          205 ENWRRCPN--CKIFVEKKEGCRYMRC------SSNPQL  234 (234)
Q Consensus       205 ~~~k~CP~--C~~~i~k~~GCnhm~C------~C~~~F  234 (234)
                      ...+-||.  |+..|...++...++|      .||+.|
T Consensus        23 ~~~~~CP~p~C~~~v~~~~~~~~v~C~~~~~~~C~~~F   60 (80)
T 2jmo_A           23 MGGVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGCGFAF   60 (80)
T ss_dssp             CSSCCCCSSSCCCCCCCCSCTTSBCTTSSSTTCCSCCE
T ss_pred             CCcEECCCCCCCcccEECCCCCcCCCCCCCCCCCCCee
Confidence            45789997  9999988888888999      688877

>1pft_A TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus} SCOP: g.41.3.1

Probab=90.58  E-value=0.24  Score=28.19  Aligned_cols=29  Identities=14%  Similarity=0.308  Sum_probs=22.4

Q ss_pred             CcccCCCCCc-eeeeccCCCceEec-CCCCC
Q 048114          206 NWRRCPNCKI-FVEKKEGCRYMRCS-SNPQL  234 (234)
Q Consensus       206 ~~k~CP~C~~-~i~k~~GCnhm~C~-C~~~F  234 (234)
                      ....||.|+. .+.-+..=..+.|. ||.-|
T Consensus         4 ~~~~CP~C~~~~l~~d~~~gelvC~~CG~v~   34 (50)
T 1pft_A            4 KQKVCPACESAELIYDPERGEIVCAKCGYVI   34 (50)
T ss_dssp             SCCSCTTTSCCCEEEETTTTEEEESSSCCBC
T ss_pred             ccEeCcCCCCcceEEcCCCCeEECcccCCcc
Confidence            3468999998 77777666789996 99743

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1

Probab=90.20  E-value=0.41  Score=30.64  Aligned_cols=59  Identities=22%  Similarity=0.521  Sum_probs=38.5

Q ss_pred             cCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHHHhcCCcccCCCCCc
Q 048114          136 YCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKI  215 (234)
Q Consensus       136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~  215 (234)
                      .|.  -|+.-+-..... ...+.|..|++.+|..|          .+|.+                  +...+.||+|+.
T Consensus        18 iCq--iCGD~VG~~~~G-e~FVAC~eC~FPvCrpC----------yEYEr------------------keG~q~CpqCkt   66 (93)
T 1weo_A           18 FCE--ICGDQIGLTVEG-DLFVACNECGFPACRPC----------YEYER------------------REGTQNCPQCKT   66 (93)
T ss_dssp             BCS--SSCCBCCBCSSS-SBCCSCSSSCCCCCHHH----------HHHHH------------------HTSCSSCTTTCC
T ss_pred             ccc--cccCccccCCCC-CEEEeeeccCChhhHHH----------HHHHH------------------hccCccccccCC
Confidence            455  555443333222 24589999999999844          44433                  467799999999


Q ss_pred             eeeeccCCCc
Q 048114          216 FVEKKEGCRY  225 (234)
Q Consensus       216 ~i~k~~GCnh  225 (234)
                      ...+..|...
T Consensus        67 rYkr~kgsp~   76 (93)
T 1weo_A           67 RYKRLRGSPR   76 (93)
T ss_dssp             CCCCCTTCCC
T ss_pred             ccccccCCCC
Confidence            9877666543

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

Probab=89.72  E-value=0.17  Score=35.47  Aligned_cols=31  Identities=13%  Similarity=0.395  Sum_probs=23.5

Q ss_pred             cCCcccCCCCCceee-ecc---CCCceEec-CCCCC
Q 048114          204 KENWRRCPNCKIFVE-KKE---GCRYMRCS-SNPQL  234 (234)
Q Consensus       204 ~~~~k~CP~C~~~i~-k~~---GCnhm~C~-C~~~F  234 (234)
                      ...++.||.|+.++. +.+   |.+.+.|+ |||++
T Consensus        21 ~~~~~FCPeCgNmL~pked~~~~~l~~~CrtCgY~~   56 (133)
T 3qt1_I           21 MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVE   56 (133)
T ss_dssp             -CCCCBCTTTCCBCBCCBCTTTCCBCCBCSSSCCBC
T ss_pred             ccCCeeCCCCCCEeeECccCCCceeEEECCCCCCcE
Confidence            467899999999664 332   68899996 99964

>2jr6_A UPF0434 protein NMA0874; solution, structural genomics, PSI, structure initiative, northeast structural genomics consort NESG; NMR {Neisseria meningitidis}

Probab=83.60  E-value=0.4  Score=29.30  Aligned_cols=29  Identities=14%  Similarity=0.121  Sum_probs=24.3

Q ss_pred             CcccCCCCCceeeeccCCCceEec-CCCCC
Q 048114          206 NWRRCPNCKIFVEKKEGCRYMRCS-SNPQL  234 (234)
Q Consensus       206 ~~k~CP~C~~~i~k~~GCnhm~C~-C~~~F  234 (234)
                      .+-.||.|+...+-..+...++|. ||..|
T Consensus         7 ~iL~CP~ck~~L~~~~~~~~LiC~~cg~~Y   36 (68)
T 2jr6_A            7 DILVCPVTKGRLEYHQDKQELWSRQAKLAY   36 (68)
T ss_dssp             CCCBCSSSCCBCEEETTTTEEEETTTTEEE
T ss_pred             hheECCCCCCcCeEeCCCCEEEcCCCCcEe
Confidence            456899999999888888999995 98654

>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=82.16  E-value=0.3  Score=28.96  Aligned_cols=36  Identities=33%  Similarity=0.762  Sum_probs=24.9

Q ss_pred             ecCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCC
Q 048114          135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAG  177 (234)
Q Consensus       135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~  177 (234)
                      ..|-  +|...+..     .....|+.|+..||..|..-.|..
T Consensus        16 ~~C~--~C~~~~~~-----~~~y~C~~C~~~FC~dCD~fiHe~   51 (59)
T 1z60_A           16 RFCY--GCQGELKD-----QHVYVCAVCQNVFCVDCDVFVHDS   51 (59)
T ss_dssp             CEET--TTTEECTT-----SEEECCTTTTCCBCHHHHHTTTTT
T ss_pred             Cccc--ccCcccCC-----CccEECCccCcCcccchhHHHHhh
Confidence            3576  77766531     112689999999999887766643

>2jne_A Hypothetical protein YFGJ; zinc fingers, two zinc, structural genomics, PSI-2, protein structure initiative; NMR {Escherichia coli} SCOP: g.41.18.1

Probab=81.99  E-value=0.66  Score=30.22  Aligned_cols=27  Identities=22%  Similarity=0.617  Sum_probs=22.1

Q ss_pred             CcccCCCCCceeeeccCCCceEec-CCCCC
Q 048114          206 NWRRCPNCKIFVEKKEGCRYMRCS-SNPQL  234 (234)
Q Consensus       206 ~~k~CP~C~~~i~k~~GCnhm~C~-C~~~F  234 (234)
                      +...||.|+..++..+|  +.+|. |+.+|
T Consensus        31 M~~~CP~Cq~eL~~~g~--~~hC~~C~~~f   58 (101)
T 2jne_A           31 MELHCPQCQHVLDQDNG--HARCRSCGEFI   58 (101)
T ss_dssp             CCCBCSSSCSBEEEETT--EEEETTTCCEE
T ss_pred             ccccCccCCCcceecCC--EEECccccchh
Confidence            34799999999998887  77895 88765

>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=81.52  E-value=0.6  Score=28.05  Aligned_cols=32  Identities=28%  Similarity=0.649  Sum_probs=25.2

Q ss_pred             CcccccccccCCCCCCceeeCCC-CChhhHHHHHHHH
Q 048114           46 TSFICDICVEPKSTDESFSIKGC-SHSYCTECMTKYV   81 (234)
Q Consensus        46 ~~~~C~iC~~~~~~~~~~~~~~C-~H~fC~~Cl~~~~   81 (234)
                      +..-|.||.++-    .+....| +-.||..||++.-
T Consensus         7 e~pWC~ICneDA----tlrC~gCdgDLYC~rC~rE~H   39 (67)
T 2d8v_A            7 GLPWCCICNEDA----TLRCAGCDGDLYCARCFREGH   39 (67)
T ss_dssp             CCSSCTTTCSCC----CEEETTTTSEEECSSHHHHHT
T ss_pred             CCCeeEEeCCCC----eEEecCCCCceehHHHHHHHc
Confidence            355699998872    3566799 8889999999876

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}

Probab=81.44  E-value=0.7  Score=29.20  Aligned_cols=24  Identities=21%  Similarity=0.555  Sum_probs=14.4

Q ss_pred             ccCCCCCceeeeccCCCceEec-CCCC
Q 048114          208 RRCPNCKIFVEKKEGCRYMRCS-SNPQ  233 (234)
Q Consensus       208 k~CP~C~~~i~k~~GCnhm~C~-C~~~  233 (234)
                      ..||.|+..|+.++|  +..|. |+..
T Consensus         3 ~~CP~C~~~l~~~~~--~~~C~~C~~~   27 (81)
T 2jrp_A            3 ITCPVCHHALERNGD--TAHCETCAKD   27 (81)
T ss_dssp             CCCSSSCSCCEECSS--EEECTTTCCE
T ss_pred             CCCCCCCCccccCCC--ceECcccccc
Confidence            457777776666665  44563 6554

---

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	234
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	2e-08
d1wd2a_	60	g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Ho	1e-04
d2ct7a1	73	g.44.1.4 (A:8-80) Ring finger protein 31 {Human (H	0.001

>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 = 48.2 bits (114), Expect = 2e-08
 Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 3/79 (3%)

Query: 45  ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQE-NITSINCPVADCK--G 101
             S  C +C+     ++  +I  C   +CT C+ +YV   ++E   T+I+CP A C   G
Sbjct: 3   SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQG 62

Query: 102 VLEPEYCRDILPEDVFNRW 120
            L+      ++  ++  R+
Sbjct: 63  HLQENEIECMVAAEIMQRY 81

>d1wd2a_ g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Homo sapiens) [TaxId: 9606]} Length = 60

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]

 Score = 36.8 bits (85), Expect = 1e-04
 Identities = 10/25 (40%), Positives = 14/25 (56%)

Query: 204 KENWRRCPNCKIFVEKKEGCRYMRC 228
             N + CP C + +EK  GC +M C
Sbjct: 3   AANTKECPKCHVTIEKDGGCNHMVC 27

>d2ct7a1 g.44.1.4 (A:8-80) Ring finger protein 31 {Human (Homo sapiens) [TaxId: 9606]} Length = 73

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]

 Score = 34.6 bits (79), Expect = 0.001
 Identities = 4/31 (12%), Positives = 7/31 (22%)

Query: 200 TLAQKENWRRCPNCKIFVEKKEGCRYMRCSS 230
            L +   +  C  C      +       C  
Sbjct: 11  VLMRDPKFLWCAQCSFGFIYEREQLEATCPQ 41

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	234
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	99.73
d1wd2a_	60	Ariadne-1 protein homolog {Human (Homo sapiens) [T	99.4
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	99.2
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	98.99
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	98.86
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	98.85
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	98.81
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	98.73
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.72
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	98.67
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.67
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	98.65
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	98.63
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	98.61
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	98.59
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	98.5
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	98.37
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.08
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.07
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	97.87
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	96.3
d1wd2a_	60	Ariadne-1 protein homolog {Human (Homo sapiens) [T	96.21
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	94.31
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	92.8
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	89.05
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	84.79
d2jnea1	71	Hypothetical protein YfgJ {Escherichia coli [TaxId	81.28
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	80.53

>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=99.73  E-value=1.8e-18  Score=115.61  Aligned_cols=83  Identities=24%  Similarity=0.531  Sum_probs=73.0

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcC-CccccCCCCCCCC--CCCHHHHhccCCHHHHHHHH
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQEN-ITSINCPVADCKG--VLEPEYCRDILPEDVFNRWG  121 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~-~~~i~CP~~~C~~--~l~~~~i~~~l~~~~~~~~~  121 (234)
                      ....+|+||+++++.++++.++.|+|.||.+||+.|++.+|.++ ..+|+||...|..  .+...+|+.+++++++++|+
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~~~i~~ll~~~~~~ky~   82 (94)
T d1wima_           3 SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQENEIECMVAAEIMQRYK   82 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECHHHHHHHSCHHHHHHHH
T ss_pred             CCCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCCCCCcccCHHHHHHhCCHHHHHHHH
Confidence            34678999999998878888889999999999999999999885 5689999888865  58889999999999999999


Q ss_pred             HHHHHH
Q 048114          122 NALCEA  127 (234)
Q Consensus       122 ~~~~~~  127 (234)
                      ++..+.
T Consensus        83 ~~~l~~   88 (94)
T d1wima_          83 KLQFER   88 (94)
T ss_dssp             HHHHHS
T ss_pred             HHHHHh
Confidence            987664

>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=99.40  E-value=2.5e-14  Score=85.71  Aligned_cols=31  Identities=32%  Similarity=0.862  Sum_probs=28.9

Q ss_pred             cCCcccCCCCCceeeeccCCCceEec---CCCCC
Q 048114          204 KENWRRCPNCKIFVEKKEGCRYMRCS---SNPQL  234 (234)
Q Consensus       204 ~~~~k~CP~C~~~i~k~~GCnhm~C~---C~~~F  234 (234)
                      ..++|+||+|+++|||++|||||+|+   ||++|
T Consensus         3 ~~ntK~CP~C~~~ieK~~GCnhM~C~~~~C~~~f   36 (60)
T d1wd2a_           3 AANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEF   36 (60)
T ss_dssp             CCCCCCCTTTCCCCSSCCSCCSSSCCSSGGGSCC
T ss_pred             hhcCcCCCCCCCeEEECCCCCCeEeCCCCCCCeE
Confidence            46789999999999999999999996   99998

>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=99.20  E-value=4.9e-13  Score=83.97  Aligned_cols=54  Identities=33%  Similarity=0.902  Sum_probs=47.2

Q ss_pred             CCCeecCCCCCCCCceecCCCCccCcccCccccccccccCCCCC---CCCCChhhHHHhhh
Q 048114          131 GAQKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPW---HAGIRCAEFQKLHK  188 (234)
Q Consensus       131 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~---H~~~~C~~~~~~~~  188 (234)
                      +++.+|||  +|++.++.+++  .+.+.|+.|+..||+.|+.+|   |.|.+|+++++|.+
T Consensus        15 ~~~~k~CP--~C~~~~~~~~~--~~~~~C~~C~~~fC~~C~~~w~~~H~~~tC~~~~~wk~   71 (73)
T d2ct7a1          15 DPKFLWCA--QCSFGFIYERE--QLEATCPQCHQTFCVRCKRQWEEQHRGRSCEDFQNWKR   71 (73)
T ss_dssp             CCCEECCS--SSCCCEECCCS--CSCEECTTTCCEECSSSCSBCCTTTTTSCHHHHHHHHH
T ss_pred             CCCCCCCC--CCCCEeEECCC--CCEEEcCCCCCeECcccCcchhcCCCCCCHHHHHHHHH
Confidence            46778998  89999988764  466999999999999999999   99999999998853

>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=98.99  E-value=1e-10  Score=78.45  Aligned_cols=74  Identities=23%  Similarity=0.526  Sum_probs=53.3

Q ss_pred             hcCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc-cCCHHHHHHHH
Q 048114           43 RIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD-ILPEDVFNRWG  121 (234)
Q Consensus        43 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~-~l~~~~~~~~~  121 (234)
                      .+++.++|+||++.+.  +++. ++|||+||..|+.+|+..    ......||  .|+..+....++. ..-.++++++.
T Consensus        17 ~l~~~l~CpIC~~~~~--~pv~-~~CgH~fC~~Ci~~~~~~----~~~~~~CP--~Cr~~~~~~~l~~n~~l~~~ve~l~   87 (103)
T d1jm7a_          17 AMQKILECPICLELIK--EPVS-TKCDHIFCKFCMLKLLNQ----KKGPSQCP--LCKNDITKRSLQESTRFSQLVEELL   87 (103)
T ss_dssp             HHHHHTSCSSSCCCCS--SCCB-CTTSCCCCSHHHHHHHHS----SSSSCCCT--TTSCCCCTTTCBCCCSSSHHHHHHH
T ss_pred             hcccCcCCCccCchhC--CeEE-cCCCCchhhHHHHHHHHH----CCCCCcCc--CCCCcCChhhCCcCHHHHHHHHHHH
Confidence            3456788999999885  5555 489999999999999863    23346899  8999988776543 33345666665


Q ss_pred             HHHH
Q 048114          122 NALC  125 (234)
Q Consensus       122 ~~~~  125 (234)
                      +...
T Consensus        88 ~~~~   91 (103)
T d1jm7a_          88 KIIC   91 (103)
T ss_dssp             HHHH
T ss_pred             HHHc
Confidence            4443

>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=98.86  E-value=1.4e-10  Score=67.55  Aligned_cols=50  Identities=24%  Similarity=0.585  Sum_probs=37.9

Q ss_pred             ccccccccCCCCCCc-eeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           48 FICDICVEPKSTDES-FSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        48 ~~C~iC~~~~~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      .+|+||++++..++. +.+++|||.||.+|+.+|++.+      ..+||  .|+..++.
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            369999999864433 3456899999999999998521      34799  89887753

>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=98.85  E-value=2.6e-10  Score=73.22  Aligned_cols=54  Identities=22%  Similarity=0.588  Sum_probs=42.3

Q ss_pred             CcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhc
Q 048114           46 TSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRD  110 (234)
Q Consensus        46 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~  110 (234)
                      +.++|+||++.+.  +++. ++|||.||..|+.+|++..      .-+||  .|+..+...++..
T Consensus        22 ~~l~C~IC~~~~~--~pv~-~~CgH~FC~~Ci~~~~~~~------~~~CP--~Cr~p~~~~~l~~   75 (86)
T d1rmda2          22 KSISCQICEHILA--DPVE-TSCKHLFCRICILRCLKVM------GSYCP--SCRYPCFPTDLES   75 (86)
T ss_dssp             HHTBCTTTCSBCS--SEEE-CTTSCEEEHHHHHHHHHHT------CSBCT--TTCCBCCGGGCBC
T ss_pred             cCcCCccCCcchh--ccee-cCCCChhhHHHHHHHHhhC------CCcCc--ccCCCCChhhccC
Confidence            4678999999875  5554 5999999999999999632      23699  8999888776543

>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=98.81  E-value=7.3e-10  Score=65.05  Aligned_cols=51  Identities=22%  Similarity=0.671  Sum_probs=39.4

Q ss_pred             cCCcccccccccCCCCCCcee-eCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCC
Q 048114           44 IETSFICDICVEPKSTDESFS-IKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVL  103 (234)
Q Consensus        44 ~~~~~~C~iC~~~~~~~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l  103 (234)
                      +++..+|+||++++..++.+. ++.|+|.||.+|+.+|++.       .-.||  .|+..+
T Consensus         2 ~ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~-------~~~CP--~CR~~i   53 (55)
T d1iyma_           2 MDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGS-------HSTCP--LCRLTV   53 (55)
T ss_dssp             CCCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTT-------CCSCS--SSCCCS
T ss_pred             CCCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHh-------CCcCC--CCCCEe
Confidence            355678999999997655554 4579999999999999852       23699  787655

>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=98.73  E-value=1.2e-09  Score=66.51  Aligned_cols=55  Identities=24%  Similarity=0.558  Sum_probs=40.0

Q ss_pred             cccccccccCC--CCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHh
Q 048114           47 SFICDICVEPK--STDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR  109 (234)
Q Consensus        47 ~~~C~iC~~~~--~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~  109 (234)
                      ..+|+||++++  ..+..+.+.+|||.||.+|+.+|++..      .-.||  .|+..+....++
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            46799999875  222334556999999999999999622      23699  899888655443

>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=98.72  E-value=3e-09  Score=67.32  Aligned_cols=65  Identities=15%  Similarity=0.374  Sum_probs=47.6

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHh-ccCCHHHHHHH
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCR-DILPEDVFNRW  120 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~-~~l~~~~~~~~  120 (234)
                      .+.+.|+||++.+.  +++.+ +|||+||+.|+.+|+...      .-.||  .|+..++..++. ++.-.++++.|
T Consensus         6 P~~l~CpIc~~~m~--dPV~~-~cgh~fc~~ci~~~~~~~------~~~cP--~~~~~l~~~~l~pN~~L~~~I~~~   71 (78)
T d1t1ha_           6 PEYFRCPISLELMK--DPVIV-STGQTYERSSIQKWLDAG------HKTCP--KSQETLLHAGLTPNYVLKSLIALW   71 (78)
T ss_dssp             SSSSSCTTTSCCCS--SEEEE-TTTEEEEHHHHHHHHTTT------CCBCT--TTCCBCSSCCCEECTTTHHHHHHH
T ss_pred             CccCCCcCcCchhh--CceEc-cCCCcchHHHHHHHHHHC------CCCCC--cccccCCcccccchHHHHHHHHHH
Confidence            45889999999886  67765 899999999999998521      33688  788887765544 34445555555

>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=98.67  E-value=6.2e-09  Score=63.93  Aligned_cols=47  Identities=32%  Similarity=0.723  Sum_probs=37.4

Q ss_pred             cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      ..+|+||++.+.  +...+++|||.||.+|+.+|++.       .-.||  .|+..+.
T Consensus         5 ~d~C~IC~~~~~--~~~~~~~C~H~Fc~~Ci~~w~~~-------~~~CP--~CR~~i~   51 (68)
T d1chca_           5 AERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQ-------NPTCP--LCKVPVE   51 (68)
T ss_dssp             CCCCSSCCSCCC--SCEEETTTTEEESTTHHHHHHHH-------SCSTT--TTCCCCC
T ss_pred             CCCCccCCcCcc--CCcEEeCCCCcCcHHHHHHHHHh-------CCcCC--CCCcchH
Confidence            456999999985  45566799999999999999963       23699  8887654

>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=98.67  E-value=5.2e-10  Score=74.01  Aligned_cols=52  Identities=25%  Similarity=0.671  Sum_probs=40.5

Q ss_pred             hcCCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHH
Q 048114           43 RIETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEY  107 (234)
Q Consensus        43 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~  107 (234)
                      .+++.++|+||++.+.  +++.+.+|||+||.+|+.+|+.         -.||  .|+..+....
T Consensus        18 ~l~~~l~C~IC~~~~~--~pv~~~~CgH~fC~~Ci~~~~~---------~~CP--~Cr~~~~~~~   69 (97)
T d1jm7b_          18 RLEKLLRCSRCTNILR--EPVCLGGCEHIFCSNCVSDCIG---------TGCP--VCYTPAWIQD   69 (97)
T ss_dssp             HHHHTTSCSSSCSCCS--SCBCCCSSSCCBCTTTGGGGTT---------TBCS--SSCCBCSCSS
T ss_pred             hhhhcCCCccCCchhh--cCceeCCCCCchhHHHHHHHHh---------cccc--ccCCcCchhh
Confidence            3455789999999886  6666668999999999988873         1499  8988776543

>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=98.65  E-value=1.1e-08  Score=64.58  Aligned_cols=48  Identities=31%  Similarity=0.780  Sum_probs=36.8

Q ss_pred             cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      ...|+||++.+.  ++ .+++|||.||.+|+..|+..    +  .-.||  .|+..+..
T Consensus        23 ~~~C~IC~~~~~--~~-~~~~CgH~fC~~Ci~~wl~~----~--~~~CP--~Cr~~i~~   70 (79)
T d1fbva4          23 FQLCKICAENDK--DV-KIEPCGHLMCTSCLTSWQES----E--GQGCP--FCRCEIKG   70 (79)
T ss_dssp             TTBCTTTSSSBC--CE-ECSSSCCEECHHHHHHHHHT----T--CCSCT--TTCCCCCC
T ss_pred             CCCCccCCCcCC--Ce-EEeCCCCeeeHHHHHHHHHH----C--cCcCC--CCCcCccC
Confidence            356999999874  44 45699999999999999852    2  23699  88887753

>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=98.63  E-value=4.9e-09  Score=66.61  Aligned_cols=53  Identities=13%  Similarity=0.046  Sum_probs=41.6

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHH
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYC  108 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  108 (234)
                      .+.+.|+||++.+.  +++. ++|||+||+.|+.+|+...      .-.||  .|+..++..++
T Consensus         5 P~~l~CpIc~~l~~--dPv~-~~cGhtfc~~ci~~~l~~~------~~~cP--~c~~~l~~~~l   57 (80)
T d2c2la2           5 PDYLCGKISFELMR--EPCI-TPSGITYDRKDIEEHLQRV------GHFNP--VTRSPLTQEQL   57 (80)
T ss_dssp             CSTTBCTTTCSBCS--SEEE-CSSCCEEETTHHHHHHHHT------CSSCT--TTCCCCCGGGC
T ss_pred             CccccCcCcCchhh--hhcc-cCCcCeecHHHHHHHHhcC------CccCC--Ccccccccccc
Confidence            45789999999885  6665 5999999999999998532      23689  78888876543

>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=98.61  E-value=8.7e-09  Score=60.62  Aligned_cols=52  Identities=17%  Similarity=0.204  Sum_probs=42.1

Q ss_pred             cccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHHhcc
Q 048114           49 ICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYCRDI  111 (234)
Q Consensus        49 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i~~~  111 (234)
                      .|+||++.+.  +++.+..|||.||++|+.+|+...   +    +||  .|+..++.+++-.+
T Consensus         2 ~C~Ic~~~~~--~Pv~~~~cGh~fc~~cI~~~l~~~---~----~CP--~c~~~l~~~dLipi   53 (56)
T d2baya1           2 LCAISGKVPR--RPVLSPKSRTIFEKSLLEQYVKDT---G----NDP--ITNEPLSIEEIVEI   53 (56)
T ss_dssp             CCTTTCSCCS--SEEEETTTTEEEEHHHHHHHHHHH---S----BCT--TTCCBCCGGGCEEC
T ss_pred             CCccCCchHH--hcCccCCCCCcccHHHHHHHHhhc---c----CCC--ccCCcCCHHhceeC
Confidence            6999999875  777776899999999999999753   1    599  79999888765433

>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=98.59  E-value=2e-08  Score=68.20  Aligned_cols=57  Identities=23%  Similarity=0.466  Sum_probs=42.0

Q ss_pred             CCcccccccccCCCC---------------CCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           45 ETSFICDICVEPKST---------------DESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~---------------~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      .+...|+||++++..               ...+.+++|+|.||..||..|+...  .....++||  .|+.++..
T Consensus        23 ~~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~--~~~~~~~CP--~CR~~~~~   94 (114)
T d1v87a_          23 APEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNG--NKDGSLQCP--SCKTIYGE   94 (114)
T ss_dssp             CCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHT--CCSSCCBCT--TTCCBSSS
T ss_pred             cccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhc--CcCCCCccc--cccchhcc
Confidence            335679999998742               1234567999999999999999754  223467899  88877643

>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=98.50  E-value=5.4e-09  Score=61.36  Aligned_cols=44  Identities=20%  Similarity=0.616  Sum_probs=34.2

Q ss_pred             cccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           47 SFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        47 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      .++|+||++.+.  +.+ +++|||.||..|+.+          ...+||  .|+..++.
T Consensus         6 ~l~C~IC~~~~~--~p~-~lpCgH~fC~~Ci~~----------~~~~CP--~Cr~~~~~   49 (56)
T d1bora_           6 FLRCQQCQAEAK--CPK-LLPCLHTLCSGCLEA----------SGMQCP--ICQAPWPL   49 (56)
T ss_dssp             CSSCSSSCSSCB--CCS-CSTTSCCSBTTTCSS----------SSSSCS--SCCSSSSC
T ss_pred             CCCCcccCcccC--CCE-EecCCCHHhHHHHHc----------CCCcCc--CCCCcccC
Confidence            578999999885  444 459999999999842          255899  88887764

>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=98.37  E-value=3.2e-08  Score=61.44  Aligned_cols=32  Identities=9%  Similarity=0.259  Sum_probs=29.0

Q ss_pred             hcCCcccCCCCCceeeeccCCCceEe-cCCCCC
Q 048114          203 QKENWRRCPNCKIFVEKKEGCRYMRC-SSNPQL  234 (234)
Q Consensus       203 ~~~~~k~CP~C~~~i~k~~GCnhm~C-~C~~~F  234 (234)
                      ...+++.||+|+..|++++||++|+| .||+.|
T Consensus        14 ~~~~~k~CP~C~~~~~~~~~~~~~~C~~C~~~f   46 (73)
T d2ct7a1          14 RDPKFLWCAQCSFGFIYEREQLEATCPQCHQTF   46 (73)
T ss_dssp             SCCCEECCSSSCCCEECCCSCSCEECTTTCCEE
T ss_pred             HCCCCCCCCCCCCEeEECCCCCEEEcCCCCCeE
Confidence            34678999999999999999999999 699987

>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=98.08  E-value=1.4e-06  Score=51.60  Aligned_cols=53  Identities=19%  Similarity=0.377  Sum_probs=36.9

Q ss_pred             CCcccccccccCCCCCCce--eeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCC
Q 048114           45 ETSFICDICVEPKSTDESF--SIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLE  104 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~--~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~  104 (234)
                      +....|.||++++......  ....|+|.|+..||.+|+..+     ...+||  .|+..+.
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~-----~~~~CP--~Cr~~~~   58 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTIS-----RNTACQ--ICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHH-----TCSBCT--TTCCBCC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhC-----CCCCCc--ccCCeee
Confidence            3466799999987532211  122346999999999999754     235799  8887765

>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=98.07  E-value=8.7e-07  Score=58.03  Aligned_cols=53  Identities=9%  Similarity=0.058  Sum_probs=39.3

Q ss_pred             CCcccccccccCCCCCCceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCHHHH
Q 048114           45 ETSFICDICVEPKSTDESFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEPEYC  108 (234)
Q Consensus        45 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~~~i  108 (234)
                      ...+.|+||++-+.  +++.+..|+|+||+.|+.+|+..    +   -.||  .|+..+..+.+
T Consensus        20 P~~f~CPI~~~lm~--dPV~~~~~~~ty~r~~I~~~l~~----~---~~~P--~~~~~l~~~~L   72 (98)
T d1wgma_          20 CDEFLDPIMSTLMC--DPVVLPSSRVTVDRSTIARHLLS----D---QTDP--FNRSPLTMDQI   72 (98)
T ss_dssp             CTTTBCTTTCSBCS--SEEECTTTCCEEEHHHHHHHTTT----S---CBCT--TTCSBCCTTTS
T ss_pred             cHHhCCcCchhHHH--HHHhcccccchhhHHHHHHHHHh----c---CCcc--cccccccchhh
Confidence            45799999999886  77766444568999999999842    2   2588  67777776543

>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=97.87  E-value=5.7e-06  Score=52.91  Aligned_cols=49  Identities=18%  Similarity=0.372  Sum_probs=35.3

Q ss_pred             ccccccccCCCCCC---------------ceeeCCCCChhhHHHHHHHHHHHHhcCCccccCCCCCCCCCCCH
Q 048114           48 FICDICVEPKSTDE---------------SFSIKGCSHSYCTECMTKYVASKLQENITSINCPVADCKGVLEP  105 (234)
Q Consensus        48 ~~C~iC~~~~~~~~---------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~i~CP~~~C~~~l~~  105 (234)
                      ..|.||++++....               .+.+++|+|.|+..||.+|++.       .-.||  .|...+..
T Consensus        22 d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~-------~~~CP--~CR~~~~~   85 (88)
T d3dplr1          22 DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT-------RQVCP--LDNREWEF   85 (88)
T ss_dssp             CCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTT-------CSBCS--SSCSBCCE
T ss_pred             CcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHH-------CCcCC--CCCCcccc
Confidence            34888877664322               2455699999999999999953       23699  88877653

>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=96.30  E-value=0.0032  Score=36.86  Aligned_cols=49  Identities=20%  Similarity=0.501  Sum_probs=38.2

Q ss_pred             CcccccccccCCCCCCceeeCCC-CChhhHHHHHHHHHHHHhcCCccccCCC
Q 048114           46 TSFICDICVEPKSTDESFSIKGC-SHSYCTECMTKYVASKLQENITSINCPV   96 (234)
Q Consensus        46 ~~~~C~iC~~~~~~~~~~~~~~C-~H~fC~~Cl~~~~~~~i~~~~~~i~CP~   96 (234)
                      ..+.|.+|.+.++....++..+= +|.||..|-+.+++.+...  ..+.||.
T Consensus         7 ~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~q~~~--~evyCPS   56 (80)
T d2cs3a1           7 GPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKAQGAT--GEVYCPS   56 (80)
T ss_dssp             CSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHHHHSS--SCCCCTT
T ss_pred             CceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHhcCCC--CcEECCC
Confidence            35779999999987776654322 7999999999999988554  3678885

>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=96.21  E-value=0.002  Score=37.25  Aligned_cols=38  Identities=37%  Similarity=0.950  Sum_probs=30.7

Q ss_pred             CeecCCCCCCCCceecCCCCccCcccCc--cccccccccCCCCC
Q 048114          133 QKFYCPFKDCSALLIDDGGEAIRESVCP--DCNRMFCAQCKVPW  174 (234)
Q Consensus       133 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~--~C~~~~C~~C~~~~  174 (234)
                      +.+.||  .|...+...++  -+.+.|.  .|+..||+.|+++|
T Consensus         5 ntK~CP--~C~~~ieK~~G--CnhM~C~~~~C~~~fCw~C~~~~   44 (60)
T d1wd2a_           5 NTKECP--KCHVTIEKDGG--CNHMVCRNQNCKAEFCWVCLGPW   44 (60)
T ss_dssp             CCCCCT--TTCCCCSSCCS--CCSSSCCSSGGGSCCSSSSCSCS
T ss_pred             cCcCCC--CCCCeEEECCC--CCCeEeCCCCCCCeEECCCCCcc
Confidence            356798  99999887543  5669995  69999999999976

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=94.31  E-value=0.028  Score=34.10  Aligned_cols=60  Identities=22%  Similarity=0.521  Sum_probs=41.9

Q ss_pred             cCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCCCChhhHHHhhhccCChHHHHHHHHHhcCCcccCCCCCc
Q 048114          136 YCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAGIRCAEFQKLHKDEREPEDIMLMTLAQKENWRRCPNCKI  215 (234)
Q Consensus       136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~~~~~~~~l~~~~~~~~~k~CP~C~~  215 (234)
                      .|.  -|+.-+-..... ...+.|..|+..+|..          |-+|.+                  +...+.||.|+.
T Consensus        18 ~Cq--iCGd~VG~~~~G-e~FVAC~eC~FPvCrp----------CyEYEr------------------keG~q~CpqCkt   66 (93)
T d1weoa_          18 FCE--ICGDQIGLTVEG-DLFVACNECGFPACRP----------CYEYER------------------REGTQNCPQCKT   66 (93)
T ss_dssp             BCS--SSCCBCCBCSSS-SBCCSCSSSCCCCCHH----------HHHHHH------------------HTSCSSCTTTCC
T ss_pred             hhh--hcccccccCCCC-CEEEEecccCCccchH----------HHHHHH------------------hccCccCcccCC
Confidence            455  566544443322 3458999999999984          455433                  467799999999


Q ss_pred             eeeeccCCCce
Q 048114          216 FVEKKEGCRYM  226 (234)
Q Consensus       216 ~i~k~~GCnhm  226 (234)
                      +..+-.|+..|
T Consensus        67 ~Ykr~kgsprv   77 (93)
T d1weoa_          67 RYKRLRGSPRV   77 (93)
T ss_dssp             CCCCCTTCCCC
T ss_pred             hhhhhcCCCCC
Confidence            99988887765

>d2k4xa1 g.41.8.8 (A:1-55) Ribosomal protein S27ae {Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27a
domain: Ribosomal protein S27ae
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=92.80  E-value=0.023  Score=31.40  Aligned_cols=27  Identities=26%  Similarity=0.354  Sum_probs=21.5

Q ss_pred             cccCCCCCceeeeccCCCceEe-cCCCC
Q 048114          207 WRRCPNCKIFVEKKEGCRYMRC-SSNPQ  233 (234)
Q Consensus       207 ~k~CP~C~~~i~k~~GCnhm~C-~C~~~  233 (234)
                      -+.||+|+--|....-=|.++| +||+.
T Consensus        18 ~k~CP~CG~GvFmA~H~dR~~CGKCgyT   45 (55)
T d2k4xa1          18 HRFCPRCGPGVFLAEHADRYSCGRCGYT   45 (55)
T ss_dssp             SCCCTTTTTTCCCEECSSEEECTTTCCC
T ss_pred             cCcCcCCCCcEEeeecCCCccccCCccc
Confidence            4789999886666666689999 69974

>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=89.05  E-value=0.037  Score=31.17  Aligned_cols=38  Identities=29%  Similarity=0.680  Sum_probs=26.3

Q ss_pred             CeecCCCCCCCCceecCCCCccCcccCccccccccccCCCCCCCC
Q 048114          133 QKFYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPWHAG  177 (234)
Q Consensus       133 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~  177 (234)
                      ..++|-  +|+..+.     ......|+.|+..||..|..-.|..
T Consensus        14 ~~~~C~--gC~~~l~-----~~~~y~C~~C~~~FC~dCD~fiHe~   51 (59)
T d1z60a1          14 GERFCY--GCQGELK-----DQHVYVCAVCQNVFCVDCDVFVHDS   51 (59)
T ss_dssp             SCCEET--TTTEECT-----TSEEECCTTTTCCBCHHHHHTTTTT
T ss_pred             CCCCcc--CCCCcCC-----CCceEECcCCCCccccccchhhhhh
Confidence            345677  7875542     1233789999999999887655643

>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=84.79  E-value=0.33  Score=30.26  Aligned_cols=31  Identities=23%  Similarity=0.750  Sum_probs=21.7

Q ss_pred             ecCCCCCCCCceecCCCCccCcccCccccccccccCCCCC
Q 048114          135 FYCPFKDCSALLIDDGGEAIRESVCPDCNRMFCAQCKVPW  174 (234)
Q Consensus       135 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~  174 (234)
                      ..||  -|...+...       +....||+.||..|...|
T Consensus        23 l~C~--IC~~~~~~p-------v~~~~CgH~fC~~Ci~~~   53 (97)
T d1jm7b_          23 LRCS--RCTNILREP-------VCLGGCEHIFCSNCVSDC   53 (97)
T ss_dssp             TSCS--SSCSCCSSC-------BCCCSSSCCBCTTTGGGG
T ss_pred             CCCc--cCCchhhcC-------ceeCCCCCchhHHHHHHH
Confidence            3688  787765321       455579999999997644

>d2jnea1 g.41.18.1 (A:1-71) Hypothetical protein YfgJ {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: YfgJ-like
family: YfgJ-like
domain: Hypothetical protein YfgJ
species: Escherichia coli [TaxId: 562]

Probab=81.28  E-value=0.36  Score=27.97  Aligned_cols=25  Identities=24%  Similarity=0.752  Sum_probs=19.4

Q ss_pred             ccCCCCCceeeeccCCCceEec-CCCCC
Q 048114          208 RRCPNCKIFVEKKEGCRYMRCS-SNPQL  234 (234)
Q Consensus       208 k~CP~C~~~i~k~~GCnhm~C~-C~~~F  234 (234)
                      ..||.|...++-.+|  +.+|. |...|
T Consensus         3 ~~CP~C~~eL~~~~~--~~~C~~C~~~~   28 (71)
T d2jnea1           3 LHCPQCQHVLDQDNG--HARCRSCGEFI   28 (71)
T ss_dssp             CBCSSSCSBEEEETT--EEEETTTCCEE
T ss_pred             CcCCCccCcccccCC--CEehhhhhhhh
Confidence            479999998888776  88885 87654

>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=80.53  E-value=0.29  Score=24.71  Aligned_cols=26  Identities=31%  Similarity=0.855  Sum_probs=16.9

Q ss_pred             cCCCCCCCCceecCCCCccCcccCccccccc
Q 048114          136 YCPFKDCSALLIDDGGEAIRESVCPDCNRMF  166 (234)
Q Consensus       136 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~~  166 (234)
                      .||  .|+.-+....+   ..+.||.|++.+
T Consensus         5 ~CP--~C~seytYedg---~l~vCPeC~hEW   30 (38)
T d2akla2           5 PCP--QCNSEYTYEDG---ALLVCPECAHEW   30 (38)
T ss_dssp             CCT--TTCCCCCEECS---SSEEETTTTEEE
T ss_pred             cCC--CCCCcceEcCC---CEEECCcccCcC
Confidence            477  78866555333   348888888764