Citrus Sinensis ID: 045388

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210----
Protein Sequence
MAQEESSAAFATLAEELEIQEALMASTITSQMAKSASPSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLHMTCL
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccccccccccccccccHHHHHccccHHHHHHHHHHHHHHHHcccccEEccccccccEEEEcccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccEEEccccccEEEc
Secondary Structure Prediction (SSPRO)
cccccccccEEEcHHHHHHHHHHHHHHHHcccccccccccccccccccEEcccccccHcccHcccccHHHHHHHHHHEEEEEccccccEEEcccccccccccHHHHHHHccHHHHHHHHHHHHHHcccccccEEcccccccHEEEEEccccccccEEEccccccEEEEcccccccccccHHHHHHHHHHcccccccccccEEEEcccccEEEEc
Coil and Loop (DISEMBL)
MAQEESSAAFATLAEELEIQEALMASTITSqmaksaspssppsrssceiCRERRENDQMFKIESCIHSFCSDCINKHVATkiqggiitpvtcpgpdcksvlkfdacksVLSKNVLELWEKALSQELIdasqgiycpfkdcsaklvyendgedvlsesecpychrlfcahcyvpwhpgrEELMMRELVKKkqlrkcpnckyhiertggclhmtcl
Flexible Loop (DISEMBL)
MAQEESSAAFATLAEELEIQEALMASTITSQmaksaspssppsrssCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKkqlrkcpnckyhiertggclhmtcl
Low Complexity Region (SEG)
MAQEESSAAFATLAEELEIQEALMASTITSQMAKsaspssppsrssceicrerreNDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLHMTCL
Disordered region (IsUnstruct)
*********************************************************QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLHMT**
Disordered Region (DISOPRED)
***********************************************EICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLHMTCL
Disordered Region (DISEMBL)
*********FATLAEELEIQEALMASTI********************ICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLHMTCL
Disordered Region (DISPRO)
***EESSAAFATLAEELEIQEALMASTITSQ************RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLHMTCL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAQEESSAAFATLAEELEIQEALMASTITSQMAKSASPSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLHMTCL
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	214	2.2.26 [Sep-21-2011]
A4IIY1	292	Probable E3 ubiquitin-pro	yes	no	0.785	0.575	0.248	1e-11
P50876	292	Probable E3 ubiquitin-pro	yes	no	0.785	0.575	0.254	1e-11
Q925F3	292	Probable E3 ubiquitin-pro	yes	no	0.785	0.575	0.248	4e-11
Q54CX4	903	Uncharacterized protein D	no	no	0.757	0.179	0.291	1e-10
Q7Z419	303	E3 ubiquitin-protein liga	no	no	0.850	0.600	0.241	2e-10
Q8BKD6	301	E3 ubiquitin-protein liga	no	no	0.878	0.624	0.247	3e-10
A5PK27	304	E3 ubiquitin-protein liga	no	no	0.775	0.546	0.259	4e-10
D3YYI7	515	Probable E3 ubiquitin-pro	no	no	0.906	0.376	0.25	4e-10
O76924	509	Protein ariadne-2 OS=Dros	yes	no	0.855	0.359	0.242	7e-10
P0CE10	1787	Putative uncharacterized	no	no	0.761	0.091	0.265	7e-10

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

 Score = 69.7 bits (169), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 46/185 (24%), Positives = 82/185 (44%), Gaps = 17/185 (9%)

Query: 46  SCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDC--KSVLKF 103
           SC++C      +QM  I  C   FC+ C+ ++V   I+ G+ T ++CP   C  +  L+ 
Sbjct: 19  SCKLCLGEYTVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDASCPKRGHLQE 78

Query: 104 DACKSVLSKNVLELWEK-ALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYC 162
           +  + +++  +++ ++K    +E++      +CP   C A    +  G       +C  C
Sbjct: 79  NEIECMVAAEIMQKYKKLQFEKEILLDPCRTWCPSSSCQAVCKLQEKGIQNPQLVQCSAC 138

Query: 163 HRLFCAHCYVPWHPGR--------------EELMMRELVKKKQLRKCPNCKYHIERTGGC 208
              FC+ C   WHPG+                   + L     +++CP CK +IER  GC
Sbjct: 139 DIEFCSACKANWHPGQGCPENMAITFLPGDSSSFFKSLEDDVPIKRCPKCKVYIERDEGC 198

Query: 209 LHMTC 213
             M C
Sbjct: 199 AQMMC 203

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: 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 = 69.7 bits (169), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 85/185 (45%), Gaps = 17/185 (9%)

Query: 46  SCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDC--KSVLKF 103
           SC++C      +QM  I  C   FC+ C+ ++V   I+ G+ T ++CP   C  +  L+ 
Sbjct: 19  SCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQE 78

Query: 104 DACKSVLSKNVLELWEK-ALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYC 162
           +  + +++  +++ ++K    +E++      +CP   C A    ++ G       +C  C
Sbjct: 79  NEIECMVAAEIMQRYKKLQFEREVLFDPCRTWCPASTCQAVCQLQDVGLQTPQPVQCKAC 138

Query: 163 HRLFCAHCYVPWHPGR--EELMMRELVKKKQ------------LRKCPNCKYHIERTGGC 208
              FC+ C   WHPG+   E M    +  +             +++CP CK +IER  GC
Sbjct: 139 RMEFCSTCKASWHPGQGCPETMPITFLPGETSAAFKMEEDDAPIKRCPKCKVYIERDEGC 198

Query: 209 LHMTC 213
             M C
Sbjct: 199 AQMMC 203

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

 Score = 68.2 bits (165), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 46/185 (24%), Positives = 85/185 (45%), Gaps = 17/185 (9%)

Query: 46  SCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDC--KSVLKF 103
           SC++C      +QM  I  C   FC+ C+ ++V   I+ G+ T ++CP   C  +  L+ 
Sbjct: 19  SCKLCLGEYPAEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQE 78

Query: 104 DACKSVLSKNVLELWEK-ALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYC 162
           +  + +++  +++ ++K    +E++      +CP   C A    ++ G       +C  C
Sbjct: 79  NEIECMVAAEIMQRYKKLQFEREVLFDPCRTWCPASTCQAVCQLQDIGLQTPQLVQCKAC 138

Query: 163 HRLFCAHCYVPWHPGR--EELMMRELVKKKQ------------LRKCPNCKYHIERTGGC 208
              FC+ C   WHPG+   E M    +  +             +++CP C+ +IER  GC
Sbjct: 139 DMEFCSACKARWHPGQGCPETMPITFLPGETSSAFKMEEGDAPIKRCPKCRVYIERDEGC 198

Query: 209 LHMTC 213
             M C
Sbjct: 199 AQMMC 203

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|Q54CX4|Y5521_DICDI Uncharacterized protein DDB_G0292642 OS=Dictyostelium discoideum GN=DDB_G0292642 PE=4 SV=2

 Score = 66.2 bits (160), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 56/192 (29%), Positives = 90/192 (46%), Gaps = 30/192 (15%)

Query: 47  CEICR-ERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDA 105
           C+IC  E  +++++F +E C H +C DCI +H+   I  G +  ++CP P CK  +K   
Sbjct: 616 CKICYMEYDQSNEVFTLE-CDHVYCFDCITEHLRILITEGRVLDISCPHPQCKKEIKESE 674

Query: 106 CKSVLS-KNVLELWEKALSQELIDASQGI-YCPFKDCSAKLVYENDGEDVLSESECPYCH 163
              + + KN L+  + ++   L   ++ I +CP  DC   +   ++   +L+   CP C 
Sbjct: 675 IYMLTNEKNWLKYQKFSMIASL--KTEPIKWCPTPDCDTPVRGGSERNPILN---CPKCS 729

Query: 164 RLFCAHCYVPWHPGRE---ELMMRELVKKKQL------------------RKCPNCKYHI 202
             FC  C    H G +   E M  +  K K +                  + CP CK HI
Sbjct: 730 NDFCWICGEYSHEGAKCGTEAMELQGRKNKSIESAATAYIDFLESNKHFVKPCPTCKSHI 789

Query: 203 ERTGGCLHMTCL 214
           E+  GC HMTC+
Sbjct: 790 EKHDGCNHMTCI 801

Dictyostelium discoideum (taxid: 44689)

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

 Score = 65.5 bits (158), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 49/203 (24%), Positives = 91/203 (44%), Gaps = 21/203 (10%)

Query: 30  SQMAKSASPS--SPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGII 87
           +  A++ +P   +P    +C++C   +  D+M  ++ C   FC+ C+ +++   I+ G  
Sbjct: 11  AMTAENPTPGDLAPAPLITCKLCLCEQSLDKMTTLQECQCIFCTACLKQYMQLAIREGCG 70

Query: 88  TPVTCPGPDC--KSVLKFDACKSVLSKNVLELWEK-ALSQELIDASQGIYCPFKDCSA-- 142
           +P+TCP   C     L+      ++  +  +L+++    +E+       +CP  DC    
Sbjct: 71  SPITCPDMVCLNHGTLQEAEIACLVPVDQFQLYQRLKFEREVHLDPYRTWCPVADCQTVC 130

Query: 143 KLVYENDGEDVLSESECPYCHRLFCAHCYVPWHP------------GREELMMRELVKKK 190
            +   + G+ VL   ECP CH  FC+ C   WH               E   +     + 
Sbjct: 131 PVASSDPGQPVL--VECPSCHLKFCSCCKDAWHAEVSCRDSQPIVLPTEHRALFGTDAEA 188

Query: 191 QLRKCPNCKYHIERTGGCLHMTC 213
            +++CP C+ +IER  GC  M C
Sbjct: 189 PIKQCPVCRVYIERNEGCAQMMC 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|Q8BKD6|R144B_MOUSE E3 ubiquitin-protein ligase RNF144B OS=Mus musculus GN=Rnf144b PE=2 SV=2

 Score = 65.5 bits (158), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 52/210 (24%), Positives = 92/210 (43%), Gaps = 22/210 (10%)

Query: 21  EALMASTITSQMAKSASPSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVAT 80
           + L   T+T++   S     P    +C++C   +  D+M  ++ C   FC+ C+ +++  
Sbjct: 5   DGLQCLTMTAENPPSGD-LIPAPLVTCKLCLCEQSLDKMTMLQECQCIFCTPCLKQYMVL 63

Query: 81  KIQGGIITPVTCPGPDC--KSVLKFDACKSVLSKNVLELWEK-ALSQELIDASQGIYCPF 137
            I+ G  +P+TCP   C     L+      ++  +  +L+++    +E+       +CP 
Sbjct: 64  SIREGCGSPITCPDMVCLNHGTLQETEIACLVPLDEFQLYQRLKFEREVHMDPLRTWCPV 123

Query: 138 KDCSA--KLVYENDGEDVLSESECPYCHRLFCAHCYVPWH------------PGREELMM 183
            DC     +   + G+ VL   ECP CH  FC+ C   WH            P    L  
Sbjct: 124 ADCQTVCHISAGDPGQPVL--VECPSCHLKFCSCCKDAWHEESSCRDSQSAMPEHGALFG 181

Query: 184 RELVKKKQLRKCPNCKYHIERTGGCLHMTC 213
            +      +++CP C+ +IER  GC  M C
Sbjct: 182 TD--ADAPIKQCPVCRIYIERNEGCAQMMC 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|A5PK27|R144B_BOVIN E3 ubiquitin-protein ligase RNF144B OS=Bos taurus GN=RNF144B PE=2 SV=1

 Score = 65.1 bits (157), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 84/185 (45%), Gaps = 19/185 (10%)

Query: 46  SCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDC--KSVLKF 103
           +C++C   +  D+M  ++ C   FC+ C+ +++   I+ G  +P+TCP   C     L+ 
Sbjct: 30  TCKLCLCEQSLDKMTTLQECRCIFCTACLKQYMQLAIREGCGSPITCPDMVCLNHGTLQE 89

Query: 104 DACKSVLSKNVLELWEK-ALSQELIDASQGIYCPFKDCSA--KLVYENDGEDVLSESECP 160
                ++  +  +L+++    +E+       +CP  DC     +   + G+ VL   ECP
Sbjct: 90  AEIACLVPVDQFQLYQRLKFEREVHLDPCRTWCPVADCQTVCPVATSDPGQPVL--VECP 147

Query: 161 YCHRLFCAHCYVPWH---------PG---REELMMRELVKKKQLRKCPNCKYHIERTGGC 208
            CH  FC+ C   WH         PG    E   +        +++CP C+ +IER  GC
Sbjct: 148 SCHLKFCSCCKDAWHAEVSCRDSQPGILPTEHGTLFGTETDAPIKQCPVCRVYIERNEGC 207

Query: 209 LHMTC 213
             M C
Sbjct: 208 AQMMC 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|D3YYI7|RN217_MOUSE Probable E3 ubiquitin-protein ligase RNF217 OS=Mus musculus GN=Rnf217 PE=3 SV=2

 Score = 65.1 bits (157), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 55/220 (25%), Positives = 94/220 (42%), Gaps = 26/220 (11%)

Query: 13  LAEELEIQEALMASTITSQMAKSASPSSPPSRSSCEICRERRENDQMFKIESCIHSFCSD 72
           LA E      L+ +   S +     P +P     C +C E   +  +  +  C  + C +
Sbjct: 202 LAPEPFSVPGLLGAPPYSGLGGVGDPYAPLMVLMCRVCLE---DKPIKPLPCCKKAVCEE 258

Query: 73  CINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWEKALSQELIDASQG 132
           C+  ++++++Q G +  + CP  +C   L+       L+      ++  L    ID+S  
Sbjct: 259 CLKIYLSSQVQLGQVE-IKCPVTECFEFLEETTVVYNLTHEDSIKYKYFLELGRIDSSTK 317

Query: 133 IYCPFKDCSAKLVYENDGE---DVLSES----ECPYCHRLFCAHCYVPWHPG-------R 178
              P   C     ++  G       SES    +CP C  ++C  C+ PWH G       +
Sbjct: 318 ---PCPQCKHFTTFKKKGHIPTPSRSESRYKIQCPTCQLIWCFKCHSPWHEGVNCKEYKK 374

Query: 179 EELMMRELVK-----KKQLRKCPNCKYHIERTGGCLHMTC 213
            + ++R         ++  +KCP CK HI+RT GC HMTC
Sbjct: 375 GDKLLRHWASEIEHGQRNAQKCPKCKIHIQRTEGCDHMTC 414

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|O76924|ARI2_DROME Protein ariadne-2 OS=Drosophila melanogaster GN=ari-2 PE=2 SV=1

 Score = 63.9 bits (154), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 49/202 (24%), Positives = 91/202 (45%), Gaps = 19/202 (9%)

Query: 28  ITSQMAKSASPSSPPSRSS-CEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGI 86
           + S   K+ + ++P  RS  C +C   +  D+ + + +C HSFC DC   +  T+I  GI
Sbjct: 133 LGSSGYKTTASATPQYRSQMCPVCASSQLGDKFYSL-ACGHSFCKDCWTIYFETQIFQGI 191

Query: 87  ITPVTCPGPDCKSVLKFDACKSVLSKNVL-ELWEKALSQELIDASQGI-YCPFKDCSAKL 144
            T + C    C   +  D   +++++ V+ + +++   ++ + +   + +CP  +C    
Sbjct: 192 STQIGCMAQMCNVRVPEDLVLTLVTRPVMRDKYQQFAFKDYVKSHPELRFCPGPNCQ--- 248

Query: 145 VYENDGEDVLSESECPYCHRLFCAHCYVPWH-PGREELMMRELVK-----------KKQL 192
           +     E     + C  CH  FC  C + +H P   +++ + L K               
Sbjct: 249 IIVQSSEISAKRAICKACHTGFCFRCGMDYHAPTDCQVIKKWLTKCADDSETANYISAHT 308

Query: 193 RKCPNCKYHIERTGGCLHMTCL 214
           + CP C   IE+ GGC HM C 
Sbjct: 309 KDCPKCHICIEKNGGCNHMQCF 330

Might act as an E3 ubiquitin-protein ligase, or as part of E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates.

Drosophila melanogaster (taxid: 7227)

>sp|P0CE10|Y4102_ARATH Putative uncharacterized protein At4g01020, chloroplastic OS=Arabidopsis thaliana GN=At4g01020 PE=4 SV=1

 Score = 63.9 bits (154), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 48/181 (26%), Positives = 79/181 (43%), Gaps = 18/181 (9%)

Query: 47   CEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC 106
            C IC    E D  + +E C H FC  C+ +     ++     P+ C   DC + +     
Sbjct: 1561 CPICLS--EVDDGYSLEGCSHLFCKACLLEQFEASMRNFDAFPILCSHIDCGAPIVVADM 1618

Query: 107  KSVLSKNVLELWEKALSQELIDASQGI--YCPFKDCSAKLVYENDGEDVLSESE-CPYCH 163
            +++LS+  L+    A     + +S G   +C   DC +  +Y   G     E   C  CH
Sbjct: 1619 RALLSQEKLDELISASLSAFVTSSDGKLRFCSTPDCPS--IYRVAGPQESGEPFICGACH 1676

Query: 164  RLFCAHCYVPWHP-----------GREELMMRELVKKKQLRKCPNCKYHIERTGGCLHMT 212
               C  C++ +HP              +L +++  K K +++CP CK  IE+T GC H+ 
Sbjct: 1677 SETCTRCHLEYHPLITCERYKKFKENPDLSLKDWAKGKDVKECPICKSTIEKTDGCNHLQ 1736

Query: 213  C 213
            C
Sbjct: 1737 C 1737

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	214
224057194	305	predicted protein [Populus trichocarpa]	0.934	0.655	0.518	3e-61
224144459	305	predicted protein [Populus trichocarpa]	0.934	0.655	0.518	3e-61
224073092	286	predicted protein [Populus trichocarpa]	0.925	0.692	0.471	4e-56
255543433	308	zinc finger protein, putative [Ricinus c	0.939	0.652	0.475	3e-55
225443207	301	PREDICTED: probable E3 ubiquitin-protein	0.939	0.667	0.440	2e-49
147816926	793	hypothetical protein VITISV_024826 [Viti	0.789	0.213	0.505	6e-47
356522438	303	PREDICTED: probable E3 ubiquitin-protein	0.920	0.650	0.392	3e-42
356522436	292	PREDICTED: probable E3 ubiquitin-protein	0.766	0.561	0.450	6e-41
356560194	294	PREDICTED: probable E3 ubiquitin-protein	0.920	0.670	0.396	2e-40
225443209	378	PREDICTED: probable E3 ubiquitin-protein	0.836	0.473	0.434	6e-40

>gi|224057194|ref|XP_002299166.1| predicted protein [Populus trichocarpa] gi|222846424|gb|EEE83971.1| predicted protein [Populus trichocarpa]

 Score =  240 bits (613), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 127/245 (51%), Positives = 155/245 (63%), Gaps = 45/245 (18%)

Query: 11  ATLAEELEIQEALMASTITSQMAKSASPS---------------------------SPPS 43
           A  AEEL+ QE LM S I SQM KS  PS                              S
Sbjct: 40  AKYAEELQFQETLMGSVIVSQM-KSIGPSPMMIEGIPVVLPISDQPMRVEIIDLEAGESS 98

Query: 44  RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF 103
            S CEIC ER+ENDQMFK ESC+HSFC+DCI++HVATK+Q  I   VTCPG  C++VL+ 
Sbjct: 99  LSFCEICAERKENDQMFKTESCVHSFCNDCISRHVATKVQDNIRI-VTCPGLSCRAVLEM 157

Query: 104 DACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCH 163
           D C+ VL++ V++ WE AL +E+I+ASQ  YCPFKDCSA LV +N+GE  + ESECP+CH
Sbjct: 158 DTCRPVLTRGVIDRWENALCEEMINASQRFYCPFKDCSALLVDDNEGE-TIRESECPFCH 216

Query: 164 RLFCAHCYVPWHP---------------GREELMMRELVKKKQLRKCPNCKYHIERTGGC 208
           RLFCA C VPWHP               GRE+LM+REL K KQ  +CP CK+++ERT GC
Sbjct: 217 RLFCAQCSVPWHPGVDCDEYQRLNEDERGREDLMVRELAKNKQWGRCPKCKFYVERTEGC 276

Query: 209 LHMTC 213
            HM C
Sbjct: 277 PHMVC 281

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224144459|ref|XP_002336150.1| predicted protein [Populus trichocarpa] gi|222874330|gb|EEF11461.1| predicted protein [Populus trichocarpa]

 Score =  240 bits (612), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 127/245 (51%), Positives = 155/245 (63%), Gaps = 45/245 (18%)

Query: 11  ATLAEELEIQEALMASTITSQMAKSASPS---------------------------SPPS 43
           A  AEEL+ QE LM S I SQM KS  PS                              S
Sbjct: 40  AKYAEELQFQETLMGSVIVSQM-KSIGPSPMMIEGIPVVLPISDQPMRVEIIDLEAGESS 98

Query: 44  RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF 103
            S CEIC ER+ENDQMFK ESC+HSFC+DCI++HVATK+Q  I   VTCPG  C++VL+ 
Sbjct: 99  LSFCEICAERKENDQMFKTESCVHSFCNDCISRHVATKVQDNIRI-VTCPGLSCRAVLEM 157

Query: 104 DACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCH 163
           D C+ VL++ V++ WE AL +E+I+ASQ  YCPFKDCSA LV +N+GE  + ESECP+CH
Sbjct: 158 DTCRPVLTRGVIDRWENALCEEMINASQRFYCPFKDCSALLVDDNEGE-TIRESECPFCH 216

Query: 164 RLFCAHCYVPWHP---------------GREELMMRELVKKKQLRKCPNCKYHIERTGGC 208
           RLFCA C VPWHP               GRE+LM+REL K KQ  +CP CK+++ERT GC
Sbjct: 217 RLFCAQCSVPWHPGVDCDEYQRLNEDERGREDLMVRELAKDKQWGRCPKCKFYVERTEGC 276

Query: 209 LHMTC 213
            HM C
Sbjct: 277 PHMVC 281

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224073092|ref|XP_002303968.1| predicted protein [Populus trichocarpa] gi|222841400|gb|EEE78947.1| predicted protein [Populus trichocarpa]

 Score =  223 bits (568), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 114/242 (47%), Positives = 150/242 (61%), Gaps = 44/242 (18%)

Query: 14  AEELEIQEALMASTITSQMAKSASPSS---------------------------PPSRSS 46
           AEEL+ QEALM S I S+M  +   SS                             S   
Sbjct: 44  AEELQFQEALMGSVIVSRMKNNGPISSMMIEGTPVLLRISDQPMHMEINQSGAVESSLRF 103

Query: 47  CEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC 106
           C+IC ER++NDQMFK ESC+HSFC+DCI+++VA K+Q G    VTCPG +C++VL    C
Sbjct: 104 CDICAERKQNDQMFKTESCVHSFCNDCISRYVAAKVQDGT-RIVTCPGLNCRAVLDLVTC 162

Query: 107 KSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLF 166
           + +L+  V++LWE AL +E+I+ SQ  YCPFKDCSA L+ +N+GE ++ ESECP+CHRLF
Sbjct: 163 RPILTSVVIDLWEDALCEEVINVSQRFYCPFKDCSALLIDDNEGEAII-ESECPFCHRLF 221

Query: 167 CAHCYVPWHP---------------GREELMMRELVKKKQLRKCPNCKYHIERTGGCLHM 211
           CA C VPWH                GRE+LM+REL K K+  +CP CK+++ERT GC HM
Sbjct: 222 CALCSVPWHSGIECEEFQRLNEDERGREDLMLRELAKDKKWSRCPQCKFYVERTEGCPHM 281

Query: 212 TC 213
            C
Sbjct: 282 IC 283

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255543433|ref|XP_002512779.1| zinc finger protein, putative [Ricinus communis] gi|223547790|gb|EEF49282.1| zinc finger protein, putative [Ricinus communis]

 Score =  220 bits (560), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 118/248 (47%), Positives = 154/248 (62%), Gaps = 47/248 (18%)

Query: 11  ATLAEELEIQEALMASTITSQMAKS------------ASPSS------PP---------- 42
           A  AE L+ QEALM S + SQM  S            ++PSS      PP          
Sbjct: 39  AKYAEALQFQEALMGSVMISQMKNSITTATIINTCKISNPSSLLMIEPPPVVPNSPTETG 98

Query: 43  --SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSV 100
             S+  CEIC E++E DQMF  +SCIHSFC DC+ K+V TKIQ    T VTCPG +C++V
Sbjct: 99  QSSQIFCEICVEKKETDQMFATDSCIHSFCLDCVGKYVGTKIQESQ-TIVTCPGMNCRAV 157

Query: 101 LKFDACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECP 160
           L+ D C++ L+K V++ WE+AL +E+I   Q  YCPF+DCSA LV +N+GE V+ ESECP
Sbjct: 158 LELDICRTKLAKGVIDSWEEALCKEMISTLQSFYCPFRDCSALLVNDNEGE-VIRESECP 216

Query: 161 YCHRLFCAHCYVPWHP---------------GREELMMRELVKKKQLRKCPNCKYHIERT 205
           +CHRLFCA CYVPWH                GRE+LM+ EL K+K+  +CP C++++ERT
Sbjct: 217 FCHRLFCAQCYVPWHSGIECEAFQRLNEDERGREDLMVIELAKEKKWSRCPKCRFYVERT 276

Query: 206 GGCLHMTC 213
            GC HM C
Sbjct: 277 QGCPHMVC 284

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225443207|ref|XP_002270687.1| PREDICTED: probable E3 ubiquitin-protein ligase RNF144A [Vitis vinifera] gi|298204735|emb|CBI25233.3| unnamed protein product [Vitis vinifera]

 Score =  201 bits (510), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 108/245 (44%), Positives = 144/245 (58%), Gaps = 44/245 (17%)

Query: 11  ATLAEELEIQEALMAST--ITSQMAKSASPS-------------------------SPPS 43
           A  AEEL+ QEALMAS    ++   +  +PS                            S
Sbjct: 35  AKYAEELQFQEALMASVEAASNTAVQETAPSIKEIGSSSGSSSAADAAVDMAVVEEGQTS 94

Query: 44  RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF 103
            + CEIC ERR  D+MF+   C H+FCS CI+KHVA KIQ  +   VTCP   C+ VL+ 
Sbjct: 95  ENFCEICAERRGLDEMFRSGKCCHTFCSYCISKHVAVKIQESV-RMVTCPALSCEGVLEV 153

Query: 104 DACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCH 163
           D C+ ++++ V+E WE+   + +I ASQ  YCPF+DCSA LV +N GE V+ ESECP C 
Sbjct: 154 DDCRGIVAREVMEKWEEVSCESIIAASQRFYCPFRDCSAMLVDDNGGE-VIRESECPVCR 212

Query: 164 RLFCAHCYVPWHP---------------GREELMMRELVKKKQLRKCPNCKYHIERTGGC 208
           RLFCA CYVPWH                GRE+LM+REL ++K+ R+CP CK+++E+  GC
Sbjct: 213 RLFCAACYVPWHSGVGCEEYQMMNEDEKGREDLMLRELAQEKKWRRCPQCKFYVEKIEGC 272

Query: 209 LHMTC 213
           LH+TC
Sbjct: 273 LHITC 277

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147816926|emb|CAN64393.1| hypothetical protein VITISV_024826 [Vitis vinifera]

 Score =  192 bits (489), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 94/186 (50%), Positives = 125/186 (67%), Gaps = 17/186 (9%)

Query: 43  SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK 102
           S + CEIC E RE D+MF+   C H+FCS CI+KHVA KIQ  +   VTCP   C+ VL+
Sbjct: 58  SENFCEICAEMREVDEMFRSGKCCHTFCSYCISKHVAVKIQESVRM-VTCPALXCEGVLE 116

Query: 103 FDACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYC 162
            D C+ ++++ V+E WE+   + +I ASQ  YCPF+DCSA LV +N GE V+ ESECP C
Sbjct: 117 VDDCRGIVAREVMEKWEEVSCESIIAASQRFYCPFRDCSAMLVDDNGGE-VIRESECPVC 175

Query: 163 HRLFCAHCYVPWH---------------PGREELMMRELVKKKQLRKCPNCKYHIERTGG 207
            RLFCA CYVPWH                GRE+LM+REL ++K+ R+CP CK+++E+  G
Sbjct: 176 RRLFCAXCYVPWHSGVGCEEYQMMNEDEKGREDLMLRELAQEKKWRRCPQCKFYVEKIEG 235

Query: 208 CLHMTC 213
           CLH+TC
Sbjct: 236 CLHITC 241

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356522438|ref|XP_003529853.1| PREDICTED: probable E3 ubiquitin-protein ligase RNF144A-like [Glycine max]

 Score =  177 bits (448), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 93/237 (39%), Positives = 132/237 (55%), Gaps = 40/237 (16%)

Query: 14  AEELEIQEALMASTITSQ----------------------MAKSASPSSPPSRSSCEICR 51
           AEEL++QE L +ST++S                         K         +  C IC 
Sbjct: 45  AEELQLQEVLYSSTVSSTGVTKEVIQIDVDVDCDTPLRILKGKQKETGESSQQVYCGICM 104

Query: 52  ERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLS 111
           + +  ++MF+ ++C HSFC DCI ++VATK+Q  I + V CP P CK V++   C+S + 
Sbjct: 105 DAKYGEEMFRNQNCSHSFCDDCIGRYVATKVQENI-SMVKCPHPKCKGVIEPQYCRSFIP 163

Query: 112 KNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCY 171
           K V + WE AL + L+  SQ  YCPFKDCSA L+  ND E++++ SECP+C+RLFCA C 
Sbjct: 164 KEVFDRWENALCENLVLGSQKFYCPFKDCSAVLI--NDAEEIVTVSECPHCNRLFCAQCK 221

Query: 172 VPWHPG---------------REELMMRELVKKKQLRKCPNCKYHIERTGGCLHMTC 213
           V WH G               RE+LM+ EL K K  ++CP C +++ER  GC  +TC
Sbjct: 222 VSWHAGVDCKEFQNLKEYEREREDLMVMELAKNKSWKRCPKCIFYVERIDGCTRITC 278

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356522436|ref|XP_003529852.1| PREDICTED: probable E3 ubiquitin-protein ligase ARI3-like [Glycine max]

 Score =  172 bits (437), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 82/182 (45%), Positives = 116/182 (63%), Gaps = 18/182 (9%)

Query: 47  CEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC 106
           C IC + +  ++MF+ ++C HSFC DCI ++VATK+Q  I + V CP P CK V++   C
Sbjct: 90  CGICMDAKYGEEMFRNQNCSHSFCDDCIGRYVATKVQENI-SMVKCPHPKCKGVIEPQYC 148

Query: 107 KSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLF 166
           +S + K V + WE AL + L+  SQ  YCPFKDCSA L+  ND E++++ SECP+C+RLF
Sbjct: 149 RSFIPKEVFDRWEDALCENLVPGSQKFYCPFKDCSAMLI--NDAEEIVTVSECPHCNRLF 206

Query: 167 CAHCYVPWHPG---------------REELMMRELVKKKQLRKCPNCKYHIERTGGCLHM 211
           CA C V WH G               RE+LM+ EL K K  ++CP C +++ER  GC H+
Sbjct: 207 CAQCKVSWHAGVECKEFQNLKEYEREREDLMVMELAKNKNWKRCPKCSFYVERIDGCTHI 266

Query: 212 TC 213
           +C
Sbjct: 267 SC 268

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356560194|ref|XP_003548379.1| PREDICTED: probable E3 ubiquitin-protein ligase RNF144A-like [Glycine max]

 Score =  171 bits (432), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 94/237 (39%), Positives = 132/237 (55%), Gaps = 40/237 (16%)

Query: 14  AEELEIQEALMASTITS---------QMAKSASPSSP-------------PSRSSCEICR 51
           AEEL++QEAL +S I+S         Q+       +P              S+  C IC 
Sbjct: 37  AEELQLQEALYSSIISSTTKVKNEVIQVNVDVDGDTPLRTLKKKHKEIGESSQVYCGICM 96

Query: 52  ERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLS 111
           + +  +++F+  +C HSFCSDCI K+V  KIQ  I T V CP   CK V++   C+S++ 
Sbjct: 97  DAKSGEEIFRNRNCSHSFCSDCIGKYVTAKIQENIST-VKCPDTKCKEVVEPQYCRSIIP 155

Query: 112 KNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCY 171
           K V + WE A+ +  +  SQ  YCPFKDCSA  +Y  D  +V++ SECPYC+RLFCA C 
Sbjct: 156 KEVFDRWENAIFENSVLRSQKFYCPFKDCSA--MYIRDAGEVVTVSECPYCNRLFCAQCK 213

Query: 172 VPWHP---------------GREELMMRELVKKKQLRKCPNCKYHIERTGGCLHMTC 213
           VPWH                 RE+LM+ EL K K  ++CP C +++ER  GC H++C
Sbjct: 214 VPWHSEIGCNEFQNLKKYEREREDLMVMELAKNKSWKRCPKCDFYVERIDGCAHISC 270

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225443209|ref|XP_002270721.1| PREDICTED: probable E3 ubiquitin-protein ligase RNF144A-B [Vitis vinifera]

 Score =  169 bits (428), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 86/198 (43%), Positives = 123/198 (62%), Gaps = 19/198 (9%)

Query: 34  KSASPSSPPSR--SSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVT 91
           K   PS    R    CEIC ER+E+  MF+ E C HS C+DCI+KHV  KI+      + 
Sbjct: 157 KVGEPSQGRFRFYGMCEICCERKESTGMFRNEGCRHSVCTDCISKHVEVKIESNSGM-IL 215

Query: 92  CPGPDCKSVLKFDACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYEN-DG 150
           CPG DC+ VL  + C+  L K V+E WEKA+ + LI  S+  YCPFKDCSA L+ +N + 
Sbjct: 216 CPGMDCRGVLDPERCRGFLPKTVVERWEKAIIETLILDSEKFYCPFKDCSAMLLNDNAEA 275

Query: 151 EDVLSESECPYCHRLFCAHCYVPWHP---------------GREELMMRELVKKKQLRKC 195
             ++ ESECP+C RLFC  C VPWH                GRE++++++L ++K+ ++C
Sbjct: 276 VMMMRESECPHCRRLFCVQCRVPWHSGMECREVQRLNADERGREDMLLKKLAEEKKWKRC 335

Query: 196 PNCKYHIERTGGCLHMTC 213
           P CK+++E+  GC+H+TC
Sbjct: 336 PQCKFYVEKIEGCVHLTC 353

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	214
TAIR|locus:2084116	320	AT3G53690 [Arabidopsis thalian	0.719	0.481	0.368	1.1e-34
TAIR|locus:2091030	303	AT3G14250 [Arabidopsis thalian	0.528	0.372	0.403	1.1e-33
TAIR|locus:1006230127	384	AT2G26135 [Arabidopsis thalian	0.714	0.398	0.335	1.1e-23
TAIR|locus:2151689	444	AT5G37560 [Arabidopsis thalian	0.719	0.346	0.310	1.1e-23
TAIR|locus:2050100	468	AT2G21420 [Arabidopsis thalian	0.719	0.329	0.341	1.5e-23
TAIR|locus:2085622	222	AT3G45470 [Arabidopsis thalian	0.724	0.698	0.325	7.8e-23
TAIR|locus:2040065	373	AT2G25360 [Arabidopsis thalian	0.710	0.407	0.329	1e-22
TAIR|locus:2040025	603	AT2G25370 [Arabidopsis thalian	0.724	0.257	0.329	4.5e-22
TAIR|locus:504955785	213	AT3G45555 [Arabidopsis thalian	0.733	0.737	0.268	1.7e-20
TAIR|locus:2057401	398	AT2G26130 [Arabidopsis thalian	0.719	0.386	0.300	2.1e-20

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

 Score = 376 (137.4 bits), Expect = 1.1e-34, P = 1.1e-34
 Identities = 63/171 (36%), Positives = 106/171 (61%)

Query:    58 QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLEL 117
             + F+I  C H +C+DC++K++A K+Q  I++ + CP   C   L+ D C+ +L K V + 
Sbjct:   126 ESFRIGGCSHFYCNDCVSKYIAAKLQDNILS-IECPVSGCSGRLEPDQCRQILPKEVFDR 184

Query:   118 WEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHP- 176
             W  AL + ++  S+  YCP+KDCSA LV+  + E  + +SECP+CHR+ C  C   WHP 
Sbjct:   185 WGDALCEAVVMRSKKFYCPYKDCSA-LVFLEESEVKMKDSECPHCHRMVCVECGTQWHPE 243

Query:   177 --------------GREELMMRELVKKKQLRKCPNCKYHIERTGGCLHMTC 213
                           GR+++++  + K+K+ ++CP+CK++IE++ GCL+M C
Sbjct:   244 MTCEEFQKLAANERGRDDILLATMAKQKKWKRCPSCKFYIEKSQGCLYMKC 294

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 283 (104.7 bits), Expect = 1.1e-33, Sum P(2) = 1.1e-33
 Identities = 46/114 (40%), Positives = 73/114 (64%)

Query:    64 SCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWEKALS 123
             +C H++C+DC  ++VATKI+    + + CP  +C  +++   C+ ++ K+V + WEK L 
Sbjct:   113 NCTHAYCTDCTVRYVATKIKENA-SRIKCPDVECTRLIEPYTCRDLIPKDVFDRWEKILC 171

Query:   124 QELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPG 177
             + LI +    YCPFKDCSA +V   +G+  ++++EC  CHRLFC  C V WH G
Sbjct:   172 ESLISSWDKFYCPFKDCSAMMVNNENGDANVTQTECRSCHRLFCVQCKVTWHAG 225

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 272 (100.8 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 58/173 (33%), Positives = 88/173 (50%)

Query:    57 DQMFKIESCIHSFCSDCINKHVATKI-QGGIITPVTCPGPDCKSVLKFDACKSVLSKNVL 115
             D MF I+ C H FCS+C+ +H+   + QG +IT   CP   CKS L + +C ++L+  V 
Sbjct:   164 DMMFYIDQCGHMFCSECVKRHIEVSLLQGSLIT---CPSYRCKSKLTYGSCVNILTPKVK 220

Query:   116 ELWEKALSQELIDASQGIYCPFKDCSAKL-VYENDGEDVLSESECPYCHRLFCAHCYVPW 174
             E+W + + ++ I  +  +YCP   CSA + V E D +   S+  C  C   FC  C VPW
Sbjct:   221 EMWIQRMGEDSIPVTDRVYCPNPTCSALMSVTELD-QLTGSKRCCVKCGESFCIKCKVPW 279

Query:   175 HPG--------------REELMMRELVKKKQLRKCPNCKYHIERTGGCLHMTC 213
             H                  +  + EL  ++  R+C  CK+ IE T GC+ + C
Sbjct:   280 HDNLSCKRYKKLHSNRTTNDKQLNELANQESWRQCSKCKHMIELTQGCVRVIC 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:2151689 AT5G37560 [Arabidopsis thaliana (taxid:3702)]

 Score = 275 (101.9 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 54/174 (31%), Positives = 88/174 (50%)

Query:    57 DQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLE 116
             + M   + C+H  C  C+ + V  K++ GI+ P  C    CKS L  ++C  VL+  ++E
Sbjct:   191 EHMLLNDKCLHRHCFSCVKQQVKVKLRSGIVPP--CLEDGCKSELTLESCSMVLTPKLIE 248

Query:   117 LWEKALSQELIDASQGIYCPFKDCS---AKLVYENDGEDVLSESECPYCHRLFCAHCYVP 173
             +W++ + ++LI  ++ IYCP++ CS   +K     + E   +   C  C  LFC  C VP
Sbjct:   249 MWKRKMEEDLIPDAEKIYCPYRSCSMLMSKTELSREAEQS-NVRACIKCSELFCIDCKVP 307

Query:   174 WHPGRE--------------ELMMRELVKKKQLRKCPNCKYHIERTGGCLHMTC 213
             WH                  ++M++ L   +  R+C  CK+ IE T GC H+TC
Sbjct:   308 WHSDLSCADYKRIHSERLVNDMMLKVLANDQMWRQCSECKHMIELTEGCNHITC 361

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 275 (101.9 bits), Expect = 1.5e-23, P = 1.5e-23
 Identities = 59/173 (34%), Positives = 90/173 (52%)

Query:    57 DQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLE 116
             D+MF  E+C H  C  C+N+HV   +  GI +P TC    C S L F++C  VL+ N++E
Sbjct:   197 DRMFFTENCFHRQCFSCVNRHVQRMLLCGI-SP-TCLHFPCNSELTFESCSKVLTPNLIE 254

Query:   117 LWEKALSQELIDASQGIYCPFKDCS---AKLVYENDGEDVLSESECPYCHRLFCAHCYVP 173
              W++ + ++L+ A+  IYCP++ CS   +K     +  D  +   C  C RLFC  C VP
Sbjct:   255 FWKRKIEEDLVPAADKIYCPYRRCSMLMSKTALSRE-TDQSNVRACIKCCRLFCIDCKVP 313

Query:   174 WHPGRE-------------ELMMRELVKKKQLRKCPNCKYHIERTGGCLHMTC 213
              H G               ++ ++ L  KK+ R+C  C   +E   GC H+TC
Sbjct:   314 SHAGLSCVDYKKLNPDPLYDVKLKSLANKKKWRQCVQCSNLVELFEGCNHITC 366

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 56/172 (32%), Positives = 88/172 (51%)

Query:    57 DQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLE 116
             D+MF ++ C+H  C  C+N+ V  K++ G + P TC   +CK  L  + C  VL   V+E
Sbjct:    16 DRMFVMDKCLHRHCYPCVNQLVEVKLRNGTV-P-TCLDYECKLKLSLENCFKVLKPKVIE 73

Query:   117 LWEKALSQELIDASQGIYCPFKDCSAKLVY-ENDGEDVLSESECPYCHRLFCAHCYVPWH 175
             LW+  + +E I  ++ IYCP+ +CS  +   E    +  ++  C  C  L C  C VPWH
Sbjct:    74 LWKHMMKEESIPLAKRIYCPYINCSTLMSKTEISRSNKSNDRACIKCSGLVCIDCKVPWH 133

Query:   176 --------------PGREELMMRELVKKKQLRKCPNCKYHIERTGGCLHMTC 213
                           P  ++L ++ L   ++ R+C  C++ IE   GC HMTC
Sbjct:   134 SDLSCAEYKKLHPDPVLDDLTLKLLANDQKWRQCVKCRHLIELNQGCNHMTC 185

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 263 (97.6 bits), Expect = 1.0e-22, P = 1.0e-22
 Identities = 56/170 (32%), Positives = 89/170 (52%)

Query:    60 FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWE 119
             F  E C+H  C  C+ ++V  K+  G + P TC    CK  L  ++C  VL+  ++E+W+
Sbjct:   104 FTTEKCVHRHCFPCVKQYVEVKLLSGTV-P-TCLDDGCKFKLTLESCSKVLTLELIEMWK 161

Query:   120 KALSQELIDASQGIYCPFKDCSAKLVY-ENDGE-DVLSESECPYCHRLFCAHCYVPWH-- 175
             + + ++ I A++ IYCP+ +CS  +   E   E D+ ++  C  C  LFC  C VP H  
Sbjct:   162 QKMKEDSIPAAERIYCPYPNCSMLMSKTELSSESDLSNDRSCVKCCGLFCIDCKVPSHSD 221

Query:   176 ------------PGREELMMRELVKKKQLRKCPNCKYHIERTGGCLHMTC 213
                         P  +EL ++ L K K+ R+C  C++ IE +  C HMTC
Sbjct:   222 LSCAEYKKLHHDPLVDELKLKSLAKDKKWRQCKMCRHMIELSHACNHMTC 271

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2040025 AT2G25370 [Arabidopsis thaliana (taxid:3702)]

 Score = 265 (98.3 bits), Expect = 4.5e-22, P = 4.5e-22
 Identities = 57/173 (32%), Positives = 88/173 (50%)

Query:    57 DQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLE 116
             + MF  E C+H  C  C+ +HV  K++ G  T  TC    CK  L  + C  VL+  ++E
Sbjct:   314 EHMFVTEKCLHRHCFPCVKQHVKVKLRSG--TEPTCLEYGCKFKLTLERCSKVLTLKLIE 371

Query:   117 LWEKALSQELIDASQGIYCPFKDCSAKLVY-ENDGE-DVLSESECPYCHRLFCAHCYVPW 174
             +W++ + ++ I A++ IYCP+ +CS  +   E   E D+ +   C  C  LFC  C VP 
Sbjct:   372 MWKQKMKEDSIPAAERIYCPYPNCSMLMSKTELSSEADLSNVRTCVKCCGLFCIDCKVPS 431

Query:   175 H--------------PGREELMMRELVKKKQLRKCPNCKYHIERTGGCLHMTC 213
             H              P  ++L ++ L   K  R+C  C++ IE + GC HMTC
Sbjct:   432 HTDLSYDDYKKLHPDPLVDDLKLKSLANDKMWRQCVKCRHMIELSHGCNHMTC 484

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 242 (90.2 bits), Expect = 1.7e-20, P = 1.7e-20
 Identities = 47/175 (26%), Positives = 89/175 (50%)

Query:    56 NDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVL 115
             ++QM+ +  C H FC +C+ +++  ++  G  T + CP   C+S L   +C  +L+  + 
Sbjct:    27 SEQMYYVALCNHKFCLECMKRYIEVRLLEG--TVLICPYYQCESKLTLKSCFHILTSKLK 84

Query:   116 ELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSES--ECPYCHRLFCAHCYVP 173
              +WE+ + +E I  ++  YCP   CSA +      +  L +    C  C   FC +C V 
Sbjct:    85 AMWEQKIEEESIPVTERFYCPNPRCSALMSKIELSKSTLEDGFVRCFQCGERFCINCKVS 144

Query:   174 W--------------HPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLHMTCL 214
             W              +P  ++ M++ L  +K+ R+C  C++ I+ + GC+H+TC+
Sbjct:   145 WQSNLSCDNCKKLGNNPTSDDKMLKVLANEKKWRQCEKCQHMIKLSEGCIHVTCM 199

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2057401 AT2G26130 [Arabidopsis thaliana (taxid:3702)]

 Score = 244 (91.0 bits), Expect = 2.1e-20, P = 2.1e-20
 Identities = 52/173 (30%), Positives = 84/173 (48%)

Query:    57 DQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLE 116
             DQMF ++   H  CS+C+ +H+  ++  G +  +TCP   C S+L    C ++L+  + +
Sbjct:   170 DQMFSVDKSGHMCCSECVKRHIEVRLLEGSL--ITCPHYRCNSLLTSVRCGNLLTPKLNK 227

Query:   117 LWEKALSQELIDASQGIYCPFKDCSAKLVYEND--GEDVLSESECPYCHRLFCAHCYVPW 174
             +WE+    ELI     +YCP   CS  L+ E +  G ++     C  C   FC  C V W
Sbjct:   228 MWEQKTKDELIPVMDRVYCPNPRCST-LMSETELSGLNIGVRRCCVKCGEPFCVKCKVSW 286

Query:   175 H--------------PGREELMMRELVKKKQLRKCPNCKYHIERTGGCLHMTC 213
             H              P   +  +R+L  +K  R+C  CK+ IE + GC+ + C
Sbjct:   287 HNNLSCDEYKTLHPNPTENDGRLRDLANEKSWRQCSKCKHMIELSSGCISVVC 339

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	214
smart00647	64	smart00647, IBR, In Between Ring fingers	4e-06
pfam01485	63	pfam01485, IBR, IBR domain	1e-04

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

 Score = 42.8 bits (101), Expect = 4e-06
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 3/63 (4%)

Query: 116 ELWEKALSQELIDASQG-IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPW 174
           E +E+ L +  ++++    +CP  DCSA        E+  +   CP C   FC  C VPW
Sbjct: 1   EKYERLLLESYVESNPDLKWCPAPDCSA--AIIVTEEEGCNRVTCPKCGFSFCFRCKVPW 58

Query: 175 HPG 177
           H  
Sbjct: 59  HSP 61

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

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

 Score = 38.7 bits (90), Expect = 1e-04
 Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 4/63 (6%)

Query: 116 ELWEKALSQELIDASQGI-YCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPW 174
           E + K   ++ +++ + + +CP  DC   +   + G   +    C  C   FC  C  PW
Sbjct: 1   EKYLKLSLKKYVESPKNLKWCPTPDCGNIIEKTDGGSQNV---TCSKCGTEFCFSCKEPW 57

Query: 175 HPG 177
           H G
Sbjct: 58  HEG 60

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	214
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	100.0
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	99.97
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	99.93
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	99.92
smart00647	64	IBR In Between Ring fingers. the domains occurs be	99.23
PF01485	64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	99.16
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.77
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	98.74
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.66
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.59
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	98.56
PF14634	44	zf-RING_5: zinc-RING finger domain	98.53
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.48
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.43
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.37
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.25
PHA02926	242	zinc finger-like protein; Provisional	98.21
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.21
PHA02929	238	N1R/p28-like protein; Provisional	98.16
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	98.09
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.03
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.0
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	97.98
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	97.91
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	97.9
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	97.83
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	97.73
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	97.72
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	97.63
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	97.35
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.33
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.28
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.24
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.04
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	96.96
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	96.8
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	96.78
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	96.69
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	96.51
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	96.32
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.28
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	95.87
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	95.85
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	95.77
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	95.3
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	95.26
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	95.21
KOG2660	331	consensus Locus-specific chromosome binding protei	95.06
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	94.97
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	94.94
KOG4367	699	consensus Predicted Zn-finger protein [Function un	94.79
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	94.65
COG5152	259	Uncharacterized conserved protein, contains RING a	94.6
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	94.57
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	94.47
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	94.36
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	94.34
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	94.03
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	93.96
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	93.72
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	93.6
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	93.56
PF14569	80	zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.	93.48
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	93.35
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	93.35
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	93.34
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	93.23
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	93.22
TIGR00622	112	ssl1 transcription factor ssl1. This family is bas	93.15
PHA03096	284	p28-like protein; Provisional	93.12
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	93.03
KOG4739	233	consensus Uncharacterized protein involved in syna	93.01
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	93.01
smart00647	64	IBR In Between Ring fingers. the domains occurs be	92.82
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	92.45
KOG3039	303	consensus Uncharacterized conserved protein [Funct	92.4
PF09788	256	Tmemb_55A: Transmembrane protein 55A; InterPro: IP	91.64
KOG1941	518	consensus Acetylcholine receptor-associated protei	91.28
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	91.23
KOG0297	391	consensus TNF receptor-associated factor [Signal t	90.57
PF01485	64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	90.32
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	90.02
PF04641	260	Rtf2: Rtf2 RING-finger	89.91
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	89.86
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	89.74
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	89.21
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	88.9
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	88.25
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	88.22
KOG0825	1134	consensus PHD Zn-finger protein [General function	87.95
PRK14714	1337	DNA polymerase II large subunit; Provisional	87.94
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	87.72
KOG4445	368	consensus Uncharacterized conserved protein, conta	87.65
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	87.56
COG5219	1525	Uncharacterized conserved protein, contains RING Z	87.54
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	87.35
KOG3579	352	consensus Predicted E3 ubiquitin ligase [Posttrans	87.27
KOG2807	378	consensus RNA polymerase II transcription initiati	87.24
PF14803	34	Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.	86.76
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	86.63
COG5175	480	MOT2 Transcriptional repressor [Transcription]	86.18
KOG1940	276	consensus Zn-finger protein [General function pred	85.8
PLN02189	1040	cellulose synthase	85.26
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	85.16
PF13248	26	zf-ribbon_3: zinc-ribbon domain	84.79
PRK04023	1121	DNA polymerase II large subunit; Validated	84.72
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	84.71
smart00661	52	RPOL9 RNA polymerase subunit 9.	84.61
PLN02638	1079	cellulose synthase A (UDP-forming), catalytic subu	84.59
PRK14559	645	putative protein serine/threonine phosphatase; Pro	84.41
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	84.09
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	83.91
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	83.87
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	82.86
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	82.66
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	82.55
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	82.17
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	82.02
KOG3053	293	consensus Uncharacterized conserved protein [Funct	81.97
KOG3002	299	consensus Zn finger protein [General function pred	81.87
PF05605	54	zf-Di19: Drought induced 19 protein (Di19), zinc-b	81.1
PLN02436	1094	cellulose synthase A	80.95
PF06844	68	DUF1244: Protein of unknown function (DUF1244); In	80.89
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	80.68
COG5222	427	Uncharacterized conserved protein, contains RING Z	80.22

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

Probab=100.00  E-value=1.6e-33  Score=227.71  Aligned_cols=169  Identities=29%  Similarity=0.645  Sum_probs=145.5

Q ss_pred             cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCHHHHHHHHHH
Q 045388           42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWEKA  121 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~~~~~~~~~~  121 (214)
                      .+.+.|.|||++.....-+..++|+|.||+.|++.|++..|++|.+..++||+.+|+..-....|+.+++.+++++|++.
T Consensus       182 ~slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~l  261 (445)
T KOG1814|consen  182 NSLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCGSVAPPGQVKELVGDELFARYEKL  261 (445)
T ss_pred             hhcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCcccCCchHHHHHHHHHHHHHHHHH
Confidence            35789999999998877777899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcC-CCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCC------hH------------HHH
Q 045388          122 LSQELIDA-SQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPG------RE------------ELM  182 (214)
Q Consensus       122 ~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~------~~------------~~~  182 (214)
                      +.++.+.. .+.++||++.|....-.+++.    ..+.|..|+..||..|+..||..      .+            |.+
T Consensus       262 ~lqk~l~~msdv~yCPr~~Cq~p~~~d~~~----~l~~CskCnFaFCtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a  337 (445)
T KOG1814|consen  262 MLQKTLELMSDVVYCPRACCQLPVKQDPGR----ALAICSKCNFAFCTLCKLTWHGVSPCKVKAEKLIELYLEYLEADEA  337 (445)
T ss_pred             HHHHHHHhhcccccCChhhccCccccCchh----hhhhhccCccHHHHHHHHhhcCCCcccCchHHHHHHHHHHhhcCHH
Confidence            99988876 678999999999998555443    67889999999999999999997      00            000


Q ss_pred             H-----HH----------------HHHhCCCccCCCCCccceecCCCCCeecC
Q 045388          183 M-----RE----------------LVKKKQLRKCPNCKYHIERTGGCLHMTCL  214 (214)
Q Consensus       183 ~-----~~----------------~~~~~~~k~CP~C~~~iek~~GCnhm~C~  214 (214)
                      -     ++                -+-..+.|+||+|+++|+|.+|||||+|.
T Consensus       338 ~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~IEr~eGCnKM~C~  390 (445)
T KOG1814|consen  338 RKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVVIERSEGCNKMHCT  390 (445)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccceeecCCCccceeec
Confidence            0     00                01135779999999999999999999995

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

Probab=99.97  E-value=6.7e-32  Score=225.30  Aligned_cols=173  Identities=34%  Similarity=0.829  Sum_probs=143.6

Q ss_pred             CCCcccccccccccccc-cccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCHHHHHH
Q 045388           39 SSPPSRSSCEICRERRE-NDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLEL  117 (214)
Q Consensus        39 ~~~~~~~~C~iC~~~~~-~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~~~~~~  117 (214)
                      +......+|.||+.+.+ .+.++....|+|.||.+|++.|++.+...+  ..++||..+|...+..+....+|++++.++
T Consensus       141 ~~~~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~~~--~~~~C~~~~C~~~l~~~~c~~llt~kl~e~  218 (384)
T KOG1812|consen  141 PSKLPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLLSG--TVIRCPHDGCESRLTLESCRKLLTPKLREM  218 (384)
T ss_pred             ccccccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhccC--CCccCCCCCCCccCCHHHHhhhcCHHHHHH
Confidence            34445789999995544 447777889999999999999999995444  489999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCCCCcccCccCCCceeeecCCCC-CCcCcccCCCCChhhccccCCCCCCChHHHHHH------------
Q 045388          118 WEKALSQELIDASQGIYCPFKDCSAKLVYENDGE-DVLSESECPYCHRLFCAHCYVPWHPGREELMMR------------  184 (214)
Q Consensus       118 ~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~-~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~------------  184 (214)
                      |+.++.+.++...+.+|||+|+|...+....... .......|+.|+..||..|+.+||++.....++            
T Consensus       219 ~e~~~~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~~sC~eykk~~~~~~~d~~~  298 (384)
T KOG1812|consen  219 WEQRLKEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHANLSCEEYKKLNPEEYVDDIT  298 (384)
T ss_pred             HHHHHHHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCCCCHHHHHHhCCcccccHHH
Confidence            9999999999987777999999999988776421 233556799999999999999999982222222            


Q ss_pred             -HHHHhCCCccCCCCCccceecCCCCCeecC
Q 045388          185 -ELVKKKQLRKCPNCKYHIERTGGCLHMTCL  214 (214)
Q Consensus       185 -~~~~~~~~k~CP~C~~~iek~~GCnhm~C~  214 (214)
                       .++. .+||+||+|+..|++++|||||+|+
T Consensus       299 ~~~la-~~wr~CpkC~~~ie~~~GCnhm~Cr  328 (384)
T KOG1812|consen  299 LKYLA-KRWRQCPKCKFMIELSEGCNHMTCR  328 (384)
T ss_pred             HHHHH-HhcCcCcccceeeeecCCcceEEee
Confidence             2222 7899999999999999999999996

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

Probab=99.93  E-value=5e-26  Score=178.75  Aligned_cols=168  Identities=26%  Similarity=0.571  Sum_probs=134.9

Q ss_pred             CCCcccccccccccccccccccccCCCC--ccccHHHHHHHHHHHhhCCCc-------ccccCCCCCCCCcC-cHHHHhh
Q 045388           39 SSPPSRSSCEICRERRENDQMFKIESCI--HSFCSDCINKHVATKIQGGII-------TPVTCPGPDCKSVL-KFDACKS  108 (214)
Q Consensus        39 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~--H~fC~~Cl~~~~~~~i~~~~~-------~~i~CP~~~C~~~l-~~~~~~~  108 (214)
                      ..+....+|..|.+.-..  ++ ..+|.  |..|.+|++.|....+.+.++       +.+.||+ +|...| ..-+...
T Consensus       216 ~~N~~ni~C~~Ctdv~~~--vl-vf~Cns~HvtC~dCFr~yc~~Rl~~rqf~~~p~~gyslpc~a-gc~~s~i~e~HHF~  291 (446)
T KOG0006|consen  216 ATNSRNITCITCTDVRSP--VL-VFQCNSRHVTCLDCFRLYCVTRLNDRQFVHDPQLGYSLPCVA-GCPNSLIKELHHFR  291 (446)
T ss_pred             hcccccceeEEecCCccc--eE-EEecCCceeehHHhhhhHhhhcccccccccCccccccccccC-CCchHHHHhhhhhe
Confidence            345668899999885332  22 46787  999999999999999987764       6789987 677655 3334467


Q ss_pred             cCCHHHHHHHHHHHHHHHhcCCCCcccCccCCCceeeecCCCCCCcCcccCCC-CChhhccccCCCCCCCh---------
Q 045388          109 VLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPY-CHRLFCAHCYVPWHPGR---------  178 (214)
Q Consensus       109 ~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~-C~~~~C~~C~~~~h~~~---------  178 (214)
                      +|..+.|.+|+++..++.+...+.+.||.|+|+..+..+++.    ..++|+. |+..||..|+..+|.+.         
T Consensus       292 ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EPD~----rkvtC~~gCgf~FCR~C~e~yh~geC~~~~~as~  367 (446)
T KOG0006|consen  292 ILGEEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEPDQ----RKVTCEGGCGFAFCRECKEAYHEGECSAVFEASG  367 (446)
T ss_pred             ecchhHHHHHHHhhhhhheeecCCEecCCCCCCcccccCCCC----CcccCCCCchhHhHHHHHhhhccccceeeecccc
Confidence            899999999999999999999999999999999999988765    7889986 99999999999999980         


Q ss_pred             -------HHHHHH---HH------HHhCCCccCCCCCccceecCCCCCeecC
Q 045388          179 -------EELMMR---EL------VKKKQLRKCPNCKYHIERTGGCLHMTCL  214 (214)
Q Consensus       179 -------~~~~~~---~~------~~~~~~k~CP~C~~~iek~~GCnhm~C~  214 (214)
                             .|....   .|      .....+|+||+|.++.||+|||.||.|+
T Consensus       368 t~tc~y~vde~~a~~arwd~as~~TIk~tTkpCPkChvptErnGGCmHm~Ct  419 (446)
T KOG0006|consen  368 TTTCAYRVDERAAEQARWDAASKETIKKTTKPCPKCHVPTERNGGCMHMKCT  419 (446)
T ss_pred             ccceeeecChhhhhhhhhhhhhhhhhhhccCCCCCccCccccCCceEEeecC
Confidence                   011111   11      1235679999999999999999999996

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

Probab=99.92  E-value=5.7e-25  Score=188.19  Aligned_cols=168  Identities=25%  Similarity=0.533  Sum_probs=138.3

Q ss_pred             CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCH-HHHHHHH
Q 045388           41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSK-NVLELWE  119 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~-~~~~~~~  119 (214)
                      .....+|+||++.++. . ...+.|+|.||..||..|+..+|.++....|+||..+|...+..+.|..++++ +..++|.
T Consensus        67 ~~~~~~c~ic~~~~~~-~-~~~~~c~H~~c~~cw~~yl~~kI~~~~~~~i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~  144 (444)
T KOG1815|consen   67 KKGDVQCGICVESYDG-E-IIGLGCGHPFCPPCWTGYLGTKIHEGEEAKIKCPAHGCPALVGEDTVEKLVSDKEDKEKYQ  144 (444)
T ss_pred             CCccccCCcccCCCcc-h-hhhcCCCcHHHHHHHHHHhhheeeccccccccCCCCCccccCCCceeeeecCCHHHHHHHH
Confidence            3456899999999876 3 33689999999999999999999988744499999999999999999999888 5999999


Q ss_pred             HHHHHHHhcCC-CCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHH------------
Q 045388          120 KALSQELIDAS-QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMREL------------  186 (214)
Q Consensus       120 ~~~~~~~~~~~-~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~------------  186 (214)
                      +.+.++++..+ ...|||+|+|+..+....   .....+.| .|++.||+.|..+||.+........|            
T Consensus       145 ~~i~~syve~~~~lkwCP~~~C~~av~~~~---~~~~~v~C-~~g~~FC~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~  220 (444)
T KOG1815|consen  145 RYILRSYVEDNVPLKWCPAPGCGLAVKFGS---LESVEVDC-GCGHEFCFACGEESHSPVSCPGAKKWLKKCRDDSETIN  220 (444)
T ss_pred             HHHHHHHHhcCCccccCCCCCCCceeeccC---CCccceeC-CCCchhHhhccccccCCCcccchHHHHHhhhhhhhhhh
Confidence            99999999874 568999999999887631   22477889 57779999999999999322211111            


Q ss_pred             HHhCCCccCCCCCccceecCCCCCeecC
Q 045388          187 VKKKQLRKCPNCKYHIERTGGCLHMTCL  214 (214)
Q Consensus       187 ~~~~~~k~CP~C~~~iek~~GCnhm~C~  214 (214)
                      +...++++||+|.++|+|++|||||+|.
T Consensus       221 wi~~ntk~CP~c~~~iek~~gc~~~~~~  248 (444)
T KOG1815|consen  221 WILANTKECPKCKVPIEKDGGCNHMTCK  248 (444)
T ss_pred             hhhccCccCCCcccchhccCCccccccc
Confidence            2356789999999999999999999884

>smart00647 IBR In Between Ring fingers

Probab=99.23  E-value=1.5e-11  Score=77.37  Aligned_cols=60  Identities=32%  Similarity=0.785  Sum_probs=50.8

Q ss_pred             HHHHHHHHHHHhcC-CCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCC
Q 045388          116 ELWEKALSQELIDA-SQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPG  177 (214)
Q Consensus       116 ~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~  177 (214)
                      ++|++++.++++.. .+.+|||+|+|+.++...+.  .....+.|+.|+..||+.|+.+||.+
T Consensus         1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~--~~~~~v~C~~C~~~fC~~C~~~~H~~   61 (64)
T smart00647        1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEE--EGCNRVTCPKCGFSFCFRCKVPWHSP   61 (64)
T ss_pred             ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCC--CCCCeeECCCCCCeECCCCCCcCCCC
Confidence            47888888888887 57889999999999988741  12378899999999999999999987

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=99.16  E-value=6.7e-12  Score=79.01  Aligned_cols=60  Identities=28%  Similarity=0.679  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHHhcC-CCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCC
Q 045388          116 ELWEKALSQELIDA-SQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPG  177 (214)
Q Consensus       116 ~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~  177 (214)
                      ++|++++.+.++.. .+.+|||+|+|+.++..++...  ...+.|+.|+..||+.|+.+||.+
T Consensus         1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~--~~~~~C~~C~~~fC~~C~~~~H~~   61 (64)
T PF01485_consen    1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCN--SPIVTCPSCGTEFCFKCGEPWHEG   61 (64)
T ss_dssp             HCHHHCCCHS---S---CC--TTSST---ECS-SSTT--S--CCTTSCCSEECSSSTSESCTT
T ss_pred             ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCC--CCeeECCCCCCcCccccCcccCCC
Confidence            45777777777765 4668999999999999988741  124899999999999999999987

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=98.77  E-value=2.2e-09  Score=61.36  Aligned_cols=41  Identities=27%  Similarity=0.666  Sum_probs=28.5

Q ss_pred             ccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388           47 CEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPG   94 (214)
Q Consensus        47 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~   94 (214)
                      |+||++.+..+.   .+.|||+||..||..++...-.    ..+.||.
T Consensus         1 CpiC~~~~~~Pv---~l~CGH~FC~~Cl~~~~~~~~~----~~~~CP~   41 (42)
T PF15227_consen    1 CPICLDLFKDPV---SLPCGHSFCRSCLERLWKEPSG----SGFSCPE   41 (42)
T ss_dssp             ETTTTSB-SSEE---E-SSSSEEEHHHHHHHHCCSSS----ST---SS
T ss_pred             CCccchhhCCcc---ccCCcCHHHHHHHHHHHHccCC----cCCCCcC
Confidence            899999988765   5899999999999999854321    2378987

>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=5.2e-09  Score=60.64  Aligned_cols=41  Identities=29%  Similarity=0.628  Sum_probs=33.0

Q ss_pred             cccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388           46 SCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPG   94 (214)
Q Consensus        46 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~   94 (214)
                      +|+||++++...+.+..+.|+|.||.+||..|++..        .+||.
T Consensus         2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~--------~~CP~   42 (44)
T PF13639_consen    2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN--------NSCPV   42 (44)
T ss_dssp             CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS--------SB-TT
T ss_pred             CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC--------CcCCc
Confidence            699999999765555567899999999999999652        27887

...

>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=98.66  E-value=2e-08  Score=57.19  Aligned_cols=40  Identities=40%  Similarity=0.842  Sum_probs=33.2

Q ss_pred             ccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388           47 CEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPG   94 (214)
Q Consensus        47 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~   94 (214)
                      |+||++.+..+.  ..++|+|.||..||.+|+..   .   ..++||.
T Consensus         1 C~iC~~~~~~~~--~~~~C~H~fC~~C~~~~~~~---~---~~~~CP~   40 (41)
T PF00097_consen    1 CPICLEPFEDPV--ILLPCGHSFCRDCLRKWLEN---S---GSVKCPL   40 (41)
T ss_dssp             ETTTSSBCSSEE--EETTTSEEEEHHHHHHHHHH---T---SSSBTTT
T ss_pred             CCcCCccccCCC--EEecCCCcchHHHHHHHHHh---c---CCccCCc
Confidence            899999887665  25899999999999999987   2   3567987

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=98.59  E-value=2.6e-08  Score=56.13  Aligned_cols=38  Identities=34%  Similarity=0.859  Sum_probs=29.1

Q ss_pred             ccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388           47 CEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPG   94 (214)
Q Consensus        47 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~   94 (214)
                      |+||++.+..+.  ..+.|||.||.+||..|++..        .+||.
T Consensus         1 C~iC~~~~~~~~--~~~~CGH~fC~~C~~~~~~~~--------~~CP~   38 (39)
T PF13923_consen    1 CPICLDELRDPV--VVTPCGHSFCKECIEKYLEKN--------PKCPV   38 (39)
T ss_dssp             ETTTTSB-SSEE--EECTTSEEEEHHHHHHHHHCT--------SB-TT
T ss_pred             CCCCCCcccCcC--EECCCCCchhHHHHHHHHHCc--------CCCcC
Confidence            899999887642  268999999999999998742        47876

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=98.56  E-value=4.7e-08  Score=73.60  Aligned_cols=63  Identities=25%  Similarity=0.517  Sum_probs=47.2

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhh---------CCCcccccCCCCCCCCcCcHHHHhhcCC
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQ---------GGIITPVTCPGPDCKSVLKFDACKSVLS  111 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~---------~~~~~~i~CP~~~C~~~l~~~~~~~~l~  111 (214)
                      +.++|+||++.+..+.   .+.|+|.||..||..|+...-.         ... ...+||.  |...+....+..+..
T Consensus        17 ~~~~CpICld~~~dPV---vT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k-~~~~CPv--CR~~Is~~~LvPiyg   88 (193)
T PLN03208         17 GDFDCNICLDQVRDPV---VTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKR-EPPKCPV--CKSDVSEATLVPIYG   88 (193)
T ss_pred             CccCCccCCCcCCCcE---EcCCCchhHHHHHHHHHHhccccccccccccccC-CCCcCCC--CCCcCChhcEEEeec
Confidence            4689999999876553   4689999999999999764321         112 4679999  999998777666543

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.53  E-value=6.1e-08  Score=56.09  Aligned_cols=43  Identities=35%  Similarity=0.851  Sum_probs=35.3

Q ss_pred             cccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCC
Q 045388           46 SCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCK   98 (214)
Q Consensus        46 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~   98 (214)
                      .|++|++.+.....+.+++|||.||..|+....       . ..+.||.  |+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-------~-~~~~CP~--C~   43 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-------G-KSVKCPI--CR   43 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-------C-CCCCCcC--CC
Confidence            489999999555556689999999999999987       2 4689998  64

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

Probab=98.48  E-value=1.2e-07  Score=69.85  Aligned_cols=59  Identities=24%  Similarity=0.602  Sum_probs=43.8

Q ss_pred             CCCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh
Q 045388           38 PSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK  107 (214)
Q Consensus        38 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~  107 (214)
                      +..+...+.|+||++.+.....+ ...|||.||..|++.-+.        ..-+||.  |...+...++.
T Consensus       125 ~~~~~~~~~CPiCl~~~sek~~v-sTkCGHvFC~~Cik~alk--------~~~~CP~--C~kkIt~k~~~  183 (187)
T KOG0320|consen  125 PLRKEGTYKCPICLDSVSEKVPV-STKCGHVFCSQCIKDALK--------NTNKCPT--CRKKITHKQFH  183 (187)
T ss_pred             ccccccccCCCceecchhhcccc-ccccchhHHHHHHHHHHH--------hCCCCCC--cccccchhhhe
Confidence            33445678999999999876544 479999999999988765        2458999  66566555443

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

Probab=98.43  E-value=1.6e-07  Score=53.67  Aligned_cols=42  Identities=31%  Similarity=0.714  Sum_probs=22.5

Q ss_pred             cccccccccc-ccccccCCCCccccHHHHHHHHHHHhhCCCcccccCC
Q 045388           47 CEICRERREN-DQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCP   93 (214)
Q Consensus        47 C~iC~~~~~~-~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP   93 (214)
                      |+||.+ +.. ......+.|||.||++|+.++.....   . ..++||
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~---~-~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSD---R-NRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-----S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCC---C-CeeeCc
Confidence            899999 644 33334688999999999999987543   1 367887

>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=98.37  E-value=3.9e-07  Score=52.42  Aligned_cols=44  Identities=34%  Similarity=0.788  Sum_probs=33.2

Q ss_pred             cccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCc
Q 045388           46 SCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSV  100 (214)
Q Consensus        46 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~  100 (214)
                      +|+||++.+..  .+....|+|.||..|+..|+..       ...+||.  |+..
T Consensus         1 ~C~iC~~~~~~--~~~~~~C~H~~c~~C~~~~~~~-------~~~~Cp~--C~~~   44 (45)
T cd00162           1 ECPICLEEFRE--PVVLLPCGHVFCRSCIDKWLKS-------GKNTCPL--CRTP   44 (45)
T ss_pred             CCCcCchhhhC--ceEecCCCChhcHHHHHHHHHh-------CcCCCCC--CCCc
Confidence            58999998733  2335669999999999999875       2457998  7654

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

Probab=98.25  E-value=3.7e-07  Score=70.12  Aligned_cols=60  Identities=23%  Similarity=0.563  Sum_probs=46.4

Q ss_pred             CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcC
Q 045388           41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVL  110 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l  110 (214)
                      +...++|.||+|....+.   +.-|||-||+.||.+|+..+...     -.||.  |+..+..+.|-.|.
T Consensus        44 ~~~~FdCNICLd~akdPV---vTlCGHLFCWpClyqWl~~~~~~-----~~cPV--CK~~Vs~~~vvPlY  103 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKDPV---VTLCGHLFCWPCLYQWLQTRPNS-----KECPV--CKAEVSIDTVVPLY  103 (230)
T ss_pred             CCCceeeeeeccccCCCE---EeecccceehHHHHHHHhhcCCC-----eeCCc--cccccccceEEeee
Confidence            567899999999866553   46799999999999999776542     35899  88877776665443

>PHA02926 zinc finger-like protein; Provisional

Probab=98.21  E-value=1.3e-06  Score=66.87  Aligned_cols=55  Identities=33%  Similarity=0.680  Sum_probs=39.7

Q ss_pred             cccccccccccccc-----cc-ccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388           43 SRSSCEICRERREN-----DQ-MFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL  101 (214)
Q Consensus        43 ~~~~C~iC~~~~~~-----~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l  101 (214)
                      +..+|+||++....     +. +..+.+|+|.||..|++.|.......|.  .-.||.  |...+
T Consensus       169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~--~rsCPi--CR~~f  229 (242)
T PHA02926        169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGA--SDNCPI--CRTRF  229 (242)
T ss_pred             CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCc--CCcCCC--Cccee
Confidence            45899999998632     11 2226799999999999999986543332  458999  87654

>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=98.21  E-value=1.1e-06  Score=52.28  Aligned_cols=46  Identities=26%  Similarity=0.722  Sum_probs=34.9

Q ss_pred             cccccccccccccccccccCCCCcc-ccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           44 RSSCEICRERRENDQMFKIESCIHS-FCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ...|.||++.....   ...+|+|. ||..|+..++.        ...+||.  |...+.
T Consensus         2 ~~~C~iC~~~~~~~---~~~pCgH~~~C~~C~~~~~~--------~~~~CP~--Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRDV---VLLPCGHLCFCEECAERLLK--------RKKKCPI--CRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSSE---EEETTCEEEEEHHHHHHHHH--------TTSBBTT--TTBB-S
T ss_pred             cCCCccCCccCCce---EEeCCCChHHHHHHhHHhcc--------cCCCCCc--CChhhc
Confidence            46899999985442   25799999 99999999987        2468999  887653

...

>PHA02929 N1R/p28-like protein; Provisional

Probab=98.16  E-value=3.6e-06  Score=66.12  Aligned_cols=50  Identities=28%  Similarity=0.720  Sum_probs=37.5

Q ss_pred             cccccccccccccccccc-----cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388           42 PSRSSCEICRERRENDQM-----FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL  101 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~-----~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l  101 (214)
                      ....+|+||++.+..+..     ....+|+|.||.+|+..|+..        ...||.  |...+
T Consensus       172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~--------~~tCPl--CR~~~  226 (238)
T PHA02929        172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE--------KNTCPV--CRTPF  226 (238)
T ss_pred             CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc--------CCCCCC--CCCEe
Confidence            346899999998765431     235689999999999999752        247999  87655

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

Probab=98.09  E-value=1.8e-06  Score=68.37  Aligned_cols=53  Identities=30%  Similarity=0.714  Sum_probs=41.7

Q ss_pred             CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHH
Q 045388           41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC  106 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~  106 (214)
                      ......|.+|++....+.   .++|||.||..|+.+|..++-        .||.  |...+.+..+
T Consensus       236 ~~a~~kC~LCLe~~~~pS---aTpCGHiFCWsCI~~w~~ek~--------eCPl--CR~~~~pskv  288 (293)
T KOG0317|consen  236 PEATRKCSLCLENRSNPS---ATPCGHIFCWSCILEWCSEKA--------ECPL--CREKFQPSKV  288 (293)
T ss_pred             CCCCCceEEEecCCCCCC---cCcCcchHHHHHHHHHHcccc--------CCCc--ccccCCCcce
Confidence            344688999999876655   689999999999999986433        3999  8877766544

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

Probab=98.03  E-value=2.6e-06  Score=69.68  Aligned_cols=46  Identities=28%  Similarity=0.772  Sum_probs=39.0

Q ss_pred             CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388           41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS   99 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~   99 (214)
                      ..+..+|+||++.+..+   ..++|+|.||..|+..++.        ..+.||.  |..
T Consensus        10 ~~~~~~C~iC~~~~~~p---~~l~C~H~~c~~C~~~~~~--------~~~~Cp~--cr~   55 (386)
T KOG2177|consen   10 LQEELTCPICLEYFREP---VLLPCGHNFCRACLTRSWE--------GPLSCPV--CRP   55 (386)
T ss_pred             ccccccChhhHHHhhcC---ccccccchHhHHHHHHhcC--------CCcCCcc--cCC
Confidence            44678999999999887   3689999999999999987        3589999  763

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

Probab=98.00  E-value=2.4e-06  Score=72.64  Aligned_cols=60  Identities=27%  Similarity=0.534  Sum_probs=47.5

Q ss_pred             cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCC
Q 045388           44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLS  111 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~  111 (214)
                      ...|+||++..+.+.   .+.|||.||..||-.|+......   ...+||.  |...+.+.+++.+.-
T Consensus       186 ~~~CPICL~~~~~p~---~t~CGHiFC~~CiLqy~~~s~~~---~~~~CPi--C~s~I~~kdl~pv~~  245 (513)
T KOG2164|consen  186 DMQCPICLEPPSVPV---RTNCGHIFCGPCILQYWNYSAIK---GPCSCPI--CRSTITLKDLLPVFI  245 (513)
T ss_pred             CCcCCcccCCCCccc---ccccCceeeHHHHHHHHhhhccc---CCccCCc--hhhhccccceeeeee
Confidence            678999999876655   45699999999999999876221   4579999  988888877766543

>smart00184 RING Ring finger

Probab=97.98  E-value=5.8e-06  Score=45.72  Aligned_cols=38  Identities=37%  Similarity=0.797  Sum_probs=28.5

Q ss_pred             ccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388           47 CEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPG   94 (214)
Q Consensus        47 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~   94 (214)
                      |+||++....   ...+.|+|.||..|+..|+.    .   ...+||.
T Consensus         1 C~iC~~~~~~---~~~~~C~H~~c~~C~~~~~~----~---~~~~CP~   38 (39)
T smart00184        1 CPICLEELKD---PVVLPCGHTFCRSCIRKWLK----S---GNNTCPI   38 (39)
T ss_pred             CCcCccCCCC---cEEecCCChHHHHHHHHHHH----h---CcCCCCC
Confidence            7899987332   23578999999999999987    1   2356876

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

>smart00504 Ubox Modified RING finger domain

Probab=97.91  E-value=1.3e-05  Score=49.92  Aligned_cols=51  Identities=18%  Similarity=0.131  Sum_probs=40.0

Q ss_pred             ccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhh
Q 045388           45 SSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKS  108 (214)
Q Consensus        45 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~  108 (214)
                      +.|+||++.+..+.   ...|||.||+.|+..|+..        ...||.  |+..+..+++..
T Consensus         2 ~~Cpi~~~~~~~Pv---~~~~G~v~~~~~i~~~~~~--------~~~cP~--~~~~~~~~~l~~   52 (63)
T smart00504        2 FLCPISLEVMKDPV---ILPSGQTYERRAIEKWLLS--------HGTDPV--TGQPLTHEDLIP   52 (63)
T ss_pred             cCCcCCCCcCCCCE---ECCCCCEEeHHHHHHHHHH--------CCCCCC--CcCCCChhhcee
Confidence            57999999887653   4689999999999999975        136999  777776655443

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

>TIGR00599 rad18 DNA repair protein rad18

Probab=97.90  E-value=1.1e-05  Score=67.85  Aligned_cols=66  Identities=24%  Similarity=0.582  Sum_probs=47.5

Q ss_pred             cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHH-hhcCCHHHHHHHHH
Q 045388           42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC-KSVLSKNVLELWEK  120 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~-~~~l~~~~~~~~~~  120 (214)
                      ...+.|+||++.+..+.   .+.|+|.||..|+..|+..        ...||.  |...+....+ .+.+..++++.|..
T Consensus        24 e~~l~C~IC~d~~~~Pv---itpCgH~FCs~CI~~~l~~--------~~~CP~--Cr~~~~~~~Lr~N~~L~~iVe~~~~   90 (397)
T TIGR00599        24 DTSLRCHICKDFFDVPV---LTSCSHTFCSLCIRRCLSN--------QPKCPL--CRAEDQESKLRSNWLVSEIVESFKN   90 (397)
T ss_pred             ccccCCCcCchhhhCcc---CCCCCCchhHHHHHHHHhC--------CCCCCC--CCCccccccCccchHHHHHHHHHHH
Confidence            35689999999887653   5799999999999999853        137998  8877765433 33444556666643

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

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

Probab=97.83  E-value=1.8e-05  Score=65.11  Aligned_cols=46  Identities=33%  Similarity=0.772  Sum_probs=39.6

Q ss_pred             ccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388           45 SSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS   99 (214)
Q Consensus        45 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~   99 (214)
                      .+|.||+|+|...+-...++|.|.|...|+..|+...   +.    .||.  |+.
T Consensus       230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~---r~----~CPv--CK~  275 (348)
T KOG4628|consen  230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT---RT----FCPV--CKR  275 (348)
T ss_pred             ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc---Cc----cCCC--CCC
Confidence            6999999999988888889999999999999999754   22    5999  554

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

Probab=97.73  E-value=2e-05  Score=63.82  Aligned_cols=65  Identities=25%  Similarity=0.497  Sum_probs=51.2

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh-hcCCHHHHHHHHH
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK-SVLSKNVLELWEK  120 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~-~~l~~~~~~~~~~  120 (214)
                      ....|.||++-|..+-   ..+|+|.||.-||+.|+.        +...||.  |...+...+++ +.+..++++.|.-
T Consensus        22 ~lLRC~IC~eyf~ip~---itpCsHtfCSlCIR~~L~--------~~p~CP~--C~~~~~Es~Lr~n~il~Eiv~S~~~   87 (442)
T KOG0287|consen   22 DLLRCGICFEYFNIPM---ITPCSHTFCSLCIRKFLS--------YKPQCPT--CCVTVTESDLRNNRILDEIVKSLNF   87 (442)
T ss_pred             HHHHHhHHHHHhcCce---eccccchHHHHHHHHHhc--------cCCCCCc--eecccchhhhhhhhHHHHHHHHHHH
Confidence            4678999999987764   467999999999999986        4567998  98888777775 4556777777754

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=97.72  E-value=6.8e-05  Score=60.81  Aligned_cols=53  Identities=23%  Similarity=0.682  Sum_probs=38.0

Q ss_pred             ccccccccccc-cccc--cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh
Q 045388           45 SSCEICRERRE-NDQM--FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK  107 (214)
Q Consensus        45 ~~C~iC~~~~~-~~~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~  107 (214)
                      ..||+|..+.. .+++  +.. .|||.||..|+...+.    .+   +..||.  |+..+....++
T Consensus         4 ~~CP~Ck~~~y~np~~kl~i~-~CGH~~C~sCv~~l~~----~~---~~~CP~--C~~~lrk~~fr   59 (309)
T TIGR00570         4 QGCPRCKTTKYRNPSLKLMVN-VCGHTLCESCVDLLFV----RG---SGSCPE--CDTPLRKNNFR   59 (309)
T ss_pred             CCCCcCCCCCccCcccccccC-CCCCcccHHHHHHHhc----CC---CCCCCC--CCCccchhhcc
Confidence            57999999733 3332  222 8999999999999863    22   358997  98877766544

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=97.63  E-value=2.8e-05  Score=62.07  Aligned_cols=52  Identities=21%  Similarity=0.572  Sum_probs=43.1

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcH
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF  103 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~  103 (214)
                      ...+|.||++++...+-+..++|.|.|...|+.+|+..       +...||.  |...+++
T Consensus       322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~-------y~~~CPv--Crt~iPP  373 (374)
T COG5540         322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLG-------YSNKCPV--CRTAIPP  373 (374)
T ss_pred             CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhh-------hcccCCc--cCCCCCC
Confidence            34899999999976666668999999999999999852       4678999  8877753

>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=97.35  E-value=0.00013  Score=46.94  Aligned_cols=42  Identities=33%  Similarity=0.620  Sum_probs=29.4

Q ss_pred             ccccccccccccc----------cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388           45 SSCEICRERREND----------QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPG   94 (214)
Q Consensus        45 ~~C~iC~~~~~~~----------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~   94 (214)
                      ..|.||++.+...          -.+....|+|.|...||..|+..        .-.||.
T Consensus        20 d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~--------~~~CP~   71 (73)
T PF12678_consen   20 DNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ--------NNTCPL   71 (73)
T ss_dssp             SBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT--------SSB-TT
T ss_pred             CcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc--------CCcCCC
Confidence            3499999998321          11224589999999999999842        227888

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 ....

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

Probab=97.33  E-value=0.00015  Score=62.12  Aligned_cols=62  Identities=31%  Similarity=0.675  Sum_probs=46.2

Q ss_pred             CCCCCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHH
Q 045388           36 ASPSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDA  105 (214)
Q Consensus        36 ~~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~  105 (214)
                      .....+.....|++|-+.-..  .+ ...|-|.||+-|+..|+.....+.   .+.||.  |...|..++
T Consensus       528 n~~~enk~~~~C~lc~d~aed--~i-~s~ChH~FCrlCi~eyv~~f~~~~---nvtCP~--C~i~LsiDl  589 (791)
T KOG1002|consen  528 NLPDENKGEVECGLCHDPAED--YI-ESSCHHKFCRLCIKEYVESFMENN---NVTCPV--CHIGLSIDL  589 (791)
T ss_pred             CCCccccCceeecccCChhhh--hH-hhhhhHHHHHHHHHHHHHhhhccc---CCCCcc--ccccccccc
Confidence            345556678999999886433  22 479999999999999998766543   389999  877666553

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

Probab=97.28  E-value=0.00014  Score=46.37  Aligned_cols=58  Identities=22%  Similarity=0.445  Sum_probs=27.5

Q ss_pred             cccccccccccc-cccc---cc-cCCCCccccHHHHHHHHHHHhhCCCcc-c--ccCCCCCCCCcCcH
Q 045388           44 RSSCEICRERRE-NDQM---FK-IESCIHSFCSDCINKHVATKIQGGIIT-P--VTCPGPDCKSVLKF  103 (214)
Q Consensus        44 ~~~C~iC~~~~~-~~~~---~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~-~--i~CP~~~C~~~l~~  103 (214)
                      ..+|+||++.+. ....   +. ...|+..|...||..|+...-.....+ +  =.||.  |...|..
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~--C~~~i~~   67 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPY--CSSPISW   67 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TT--T-SEEEG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcC--CCCeeeE
Confidence            468999999865 2222   11 358899999999999998766554322 2  26999  8877653

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

Probab=97.24  E-value=0.0001  Score=65.72  Aligned_cols=55  Identities=24%  Similarity=0.705  Sum_probs=42.8

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhc
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSV  109 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~  109 (214)
                      ...+|++|.+...  +++ ...|+|.||.+|++..+...-       =+||.  |+..|+..+|..+
T Consensus       642 ~~LkCs~Cn~R~K--d~v-I~kC~H~FC~~Cvq~r~etRq-------RKCP~--Cn~aFganDv~~I  696 (698)
T KOG0978|consen  642 ELLKCSVCNTRWK--DAV-ITKCGHVFCEECVQTRYETRQ-------RKCPK--CNAAFGANDVHRI  696 (698)
T ss_pred             hceeCCCccCchh--hHH-HHhcchHHHHHHHHHHHHHhc-------CCCCC--CCCCCCccccccc
Confidence            4678999985432  222 579999999999999987543       37998  9999998888754

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

Probab=97.04  E-value=0.00052  Score=41.73  Aligned_cols=49  Identities=24%  Similarity=0.425  Sum_probs=31.7

Q ss_pred             cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCC
Q 045388           42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCK   98 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~   98 (214)
                      ...+.|+|-+..+..+-  ....|+|.|-++-+..|+    + +. ..+.||..||.
T Consensus         9 ~~~~~CPiT~~~~~~PV--~s~~C~H~fek~aI~~~i----~-~~-~~~~CPv~GC~   57 (57)
T PF11789_consen    9 TISLKCPITLQPFEDPV--KSKKCGHTFEKEAILQYI----Q-RN-GSKRCPVAGCN   57 (57)
T ss_dssp             B--SB-TTTSSB-SSEE--EESSS--EEEHHHHHHHC----T-TT-S-EE-SCCC-S
T ss_pred             EeccCCCCcCChhhCCc--CcCCCCCeecHHHHHHHH----H-hc-CCCCCCCCCCC
Confidence            34689999999887653  356999999999999999    2 22 47899998884

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

Probab=96.96  E-value=0.00066  Score=53.42  Aligned_cols=52  Identities=23%  Similarity=0.481  Sum_probs=38.2

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHH-HHHHHhhCCCcccccCCCCCCCCcCcHHHH
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINK-HVATKIQGGIITPVTCPGPDCKSVLKFDAC  106 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~-~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~  106 (214)
                      ..+.|.||++....+   ..+.|||.||..||-. |-..       ..-.||.  |.....+..+
T Consensus       214 ~d~kC~lC~e~~~~p---s~t~CgHlFC~~Cl~~~~t~~-------k~~~Cpl--CRak~~pk~v  266 (271)
T COG5574         214 ADYKCFLCLEEPEVP---SCTPCGHLFCLSCLLISWTKK-------KYEFCPL--CRAKVYPKKV  266 (271)
T ss_pred             cccceeeeecccCCc---ccccccchhhHHHHHHHHHhh-------ccccCch--hhhhccchhh
Confidence            456799999975544   3689999999999998 4332       2346999  8876666655

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

Probab=96.80  E-value=0.0033  Score=51.87  Aligned_cols=54  Identities=26%  Similarity=0.534  Sum_probs=39.3

Q ss_pred             Cccccccccccccccccc----------ccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHH
Q 045388           41 PPSRSSCEICRERRENDQ----------MFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFD  104 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~----------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~  104 (214)
                      ......|.||+|+.-.++          -+..++|||.+...|++.|++.        .=.||.  |..++-.+
T Consensus       284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ER--------qQTCPI--Cr~p~ifd  347 (491)
T COG5243         284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLER--------QQTCPI--CRRPVIFD  347 (491)
T ss_pred             cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHh--------ccCCCc--ccCccccc
Confidence            455689999999942211          2237899999999999999873        237999  87765433

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

Probab=96.78  E-value=0.0012  Score=54.81  Aligned_cols=56  Identities=30%  Similarity=0.612  Sum_probs=40.5

Q ss_pred             Cccccccccccccccccc-----ccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388           41 PPSRSSCEICRERRENDQ-----MFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS   99 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~-----~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~   99 (214)
                      ..+..+|+||++......     +-.+..|.|.||..|++.|-...-.+.. ..-.||+  |..
T Consensus       158 ~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~-~sksCP~--CRv  218 (344)
T KOG1039|consen  158 KSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESK-TSKSCPF--CRV  218 (344)
T ss_pred             ccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccc-cccCCCc--ccC
Confidence            356789999999986654     3235789999999999999744332222 3568999  654

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

Probab=96.69  E-value=0.00023  Score=43.77  Aligned_cols=49  Identities=27%  Similarity=0.622  Sum_probs=23.0

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHH
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDA  105 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~  105 (214)
                      +...|.+|.+.+..+.  .+..|.|.||..|+...+          .-.||.  |..+--..+
T Consensus         6 ~lLrCs~C~~~l~~pv--~l~~CeH~fCs~Ci~~~~----------~~~CPv--C~~Paw~qD   54 (65)
T PF14835_consen    6 ELLRCSICFDILKEPV--CLGGCEHIFCSSCIRDCI----------GSECPV--CHTPAWIQD   54 (65)
T ss_dssp             HTTS-SSS-S--SS-B-----SSS--B-TTTGGGGT----------TTB-SS--S--B-S-SS
T ss_pred             HhcCCcHHHHHhcCCc--eeccCccHHHHHHhHHhc----------CCCCCC--cCChHHHHH
Confidence            3567999999876653  357999999999986643          124999  775443333

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

Probab=96.51  E-value=0.0019  Score=51.57  Aligned_cols=65  Identities=31%  Similarity=0.493  Sum_probs=45.7

Q ss_pred             cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh-hcCCHHHHHHHH
Q 045388           42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK-SVLSKNVLELWE  119 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~-~~l~~~~~~~~~  119 (214)
                      .....|-||-+-+..+-   ...|||.||.-||+.|+.+        ...||.  |........++ ..+..++.+.|.
T Consensus        23 Ds~lrC~IC~~~i~ip~---~TtCgHtFCslCIR~hL~~--------qp~CP~--Cr~~~~esrlr~~s~~~ei~es~~   88 (391)
T COG5432          23 DSMLRCRICDCRISIPC---ETTCGHTFCSLCIRRHLGT--------QPFCPV--CREDPCESRLRGSSGSREINESHA   88 (391)
T ss_pred             hhHHHhhhhhheeecce---ecccccchhHHHHHHHhcC--------CCCCcc--ccccHHhhhcccchhHHHHHHhhh
Confidence            34678999999876653   5799999999999999853        456888  76555443332 344556666654

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

Probab=96.32  E-value=0.0023  Score=41.01  Aligned_cols=51  Identities=18%  Similarity=0.160  Sum_probs=35.8

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHH
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDA  105 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~  105 (214)
                      +.+.|+|+.+-+..+.   .+++||.|.+.++..|+..       ....||.  ++..+...+
T Consensus         3 ~~f~CpIt~~lM~dPV---i~~~G~tyer~~I~~~l~~-------~~~~~P~--t~~~l~~~~   53 (73)
T PF04564_consen    3 DEFLCPITGELMRDPV---ILPSGHTYERSAIERWLEQ-------NGGTDPF--TRQPLSESD   53 (73)
T ss_dssp             GGGB-TTTSSB-SSEE---EETTSEEEEHHHHHHHHCT-------TSSB-TT--T-SB-SGGG
T ss_pred             cccCCcCcCcHhhCce---eCCcCCEEcHHHHHHHHHc-------CCCCCCC--CCCcCCccc
Confidence            4688999999887664   4678999999999999865       2457898  677776544

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 ....

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

Probab=96.28  E-value=0.0085  Score=50.18  Aligned_cols=111  Identities=20%  Similarity=0.442  Sum_probs=69.3

Q ss_pred             cccccc--ccccc---ccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhh---cC--C--
Q 045388           44 RSSCEI--CRERR---ENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKS---VL--S--  111 (214)
Q Consensus        44 ~~~C~i--C~~~~---~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~---~l--~--  111 (214)
                      ...||-  |....   +...+.....|.-+||.-|...|-      |. .  +     |+.... +.++-   .+  +  
T Consensus       273 v~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~H------G~-s--~-----Ck~~~~-~~~~l~~~~~~~d~a  337 (445)
T KOG1814|consen  273 VVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWH------GV-S--P-----CKVKAE-KLIELYLEYLEADEA  337 (445)
T ss_pred             cccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhc------CC-C--c-----ccCchH-HHHHHHHHHhhcCHH
Confidence            356665  44331   123344466888999999998884      22 2  2     554322 22221   11  1  


Q ss_pred             --HHHHHHHHHHHHHHHhc--------CCCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCC
Q 045388          112 --KNVLELWEKALSQELID--------ASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWH  175 (214)
Q Consensus       112 --~~~~~~~~~~~~~~~~~--------~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h  175 (214)
                        .++.++|-+++.+..++        ..+...||  .|...+...++-    +.+.|..|++.|||.|.....
T Consensus       338 ~k~ele~Ryg~rvve~~vn~~lsekwl~~N~krCP--~C~v~IEr~eGC----nKM~C~~c~~~fc~~c~~~l~  405 (445)
T KOG1814|consen  338 RKRELEKRYGKRVVEELVNDFLSEKWLESNSKRCP--KCKVVIERSEGC----NKMHCTKCGTYFCWICAELLY  405 (445)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHhcCCCCC--cccceeecCCCc----cceeeccccccceeehhhhcC
Confidence              24455565444443332        23556899  999999999875    889999999999999987544

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

Probab=95.87  E-value=0.008  Score=48.69  Aligned_cols=98  Identities=16%  Similarity=0.365  Sum_probs=58.0

Q ss_pred             cCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCHHHHHHHHHHHHHHHhcCCCCcccCccCCC
Q 045388           62 IESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCS  141 (214)
Q Consensus        62 ~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~  141 (214)
                      .-.|+-.||++|++.|-.-.-..+.  ..+ --..|...++...       ..-.+|+.....-  .+...+.||  .|.
T Consensus       339 ~~gCgf~FCR~C~e~yh~geC~~~~--~as-~t~tc~y~vde~~-------a~~arwd~as~~T--Ik~tTkpCP--kCh  404 (446)
T KOG0006|consen  339 EGGCGFAFCRECKEAYHEGECSAVF--EAS-GTTTCAYRVDERA-------AEQARWDAASKET--IKKTTKPCP--KCH  404 (446)
T ss_pred             CCCchhHhHHHHHhhhccccceeee--ccc-cccceeeecChhh-------hhhhhhhhhhhhh--hhhccCCCC--Ccc
Confidence            3459999999999998532111110  000 0012444443332       2334555544332  122345688  999


Q ss_pred             ceeeecCCCCCCcCcccCC--CCChhhccccCCCCCCC
Q 045388          142 AKLVYENDGEDVLSESECP--YCHRLFCAHCYVPWHPG  177 (214)
Q Consensus       142 ~~~~~~~~~~~~~~~~~C~--~C~~~~C~~C~~~~h~~  177 (214)
                      .....+.+-    ..+.|+  .||-.+||.|+.+|...
T Consensus       405 vptErnGGC----mHm~Ct~~~Cg~eWCw~C~tEW~r~  438 (446)
T KOG0006|consen  405 VPTERNGGC----MHMKCTQPQCGLEWCWNCGTEWNRV  438 (446)
T ss_pred             CccccCCce----EEeecCCCCCCceeEeccCChhhhh
Confidence            888777663    667785  59999999999999643

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

Probab=95.85  E-value=0.019  Score=45.69  Aligned_cols=55  Identities=27%  Similarity=0.587  Sum_probs=39.6

Q ss_pred             CCCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           38 PSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        38 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ....+...+|++|.+.-+.+-+  ...|+|.||-.|++.-....      ..++||.  |+....
T Consensus       233 ss~~t~~~~C~~Cg~~PtiP~~--~~~C~HiyCY~Ci~ts~~~~------asf~Cp~--Cg~~~~  287 (298)
T KOG2879|consen  233 SSTGTSDTECPVCGEPPTIPHV--IGKCGHIYCYYCIATSRLWD------ASFTCPL--CGENVE  287 (298)
T ss_pred             cccccCCceeeccCCCCCCCee--eccccceeehhhhhhhhcch------hhcccCc--cCCCCc
Confidence            3344567899999997665532  46799999999998875432      2479999  776553

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

Probab=95.77  E-value=0.0023  Score=54.25  Aligned_cols=102  Identities=17%  Similarity=0.405  Sum_probs=64.0

Q ss_pred             cccccccccccccc---cc--cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCHHHHHHH
Q 045388           44 RSSCEICRERREND---QM--FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELW  118 (214)
Q Consensus        44 ~~~C~iC~~~~~~~---~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~~~~~~~  118 (214)
                      ...|+.++......   +.  .....|+-.||.+|-..|-         ..           ++-++++.+.+.....  
T Consensus       238 ~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh---------~~-----------~sC~eykk~~~~~~~d--  295 (384)
T KOG1812|consen  238 YPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWH---------AN-----------LSCEEYKKLNPEEYVD--  295 (384)
T ss_pred             CCCchHhhhhhhhccchhhcccccccCCCceeecCCCcCC---------CC-----------CCHHHHHHhCCccccc--
Confidence            45677777754421   11  1144777788888844432         11           3345566655432222  


Q ss_pred             HHHHHHHHhcCCCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCC
Q 045388          119 EKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPG  177 (214)
Q Consensus       119 ~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~  177 (214)
                        ..+..++. ..++.||  .|...+....+-    +.++|. |+..||+.|...|..+
T Consensus       296 --~~~~~~la-~~wr~Cp--kC~~~ie~~~GC----nhm~Cr-C~~~fcy~C~~~~~~~  344 (384)
T KOG1812|consen  296 --DITLKYLA-KRWRQCP--KCKFMIELSEGC----NHMTCR-CGHQFCYMCGGDWKTH  344 (384)
T ss_pred             --HHHHHHHH-HhcCcCc--ccceeeeecCCc----ceEEee-ccccchhhcCcchhhC
Confidence              22222222 5778899  999999877764    889997 9999999999988654

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

Probab=95.30  E-value=0.011  Score=50.11  Aligned_cols=52  Identities=27%  Similarity=0.607  Sum_probs=39.7

Q ss_pred             CCCCCCccccccccccccccccc-ccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388           36 ASPSSPPSRSSCEICRERRENDQ-MFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS   99 (214)
Q Consensus        36 ~~~~~~~~~~~C~iC~~~~~~~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~   99 (214)
                      +.+.+..+..+|+||++..+.+. +.....|.|+|--.|+..|.          ..+||.  |..
T Consensus       167 ~~~~~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~----------~~scpv--cR~  219 (493)
T KOG0804|consen  167 EPPTGLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW----------DSSCPV--CRY  219 (493)
T ss_pred             CCCCCcccCCCcchhHhhcCccccceeeeecccccchHHHhhcc----------cCcChh--hhh
Confidence            45667788999999999876543 22356899999999999984          467777  543

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

Probab=95.26  E-value=0.014  Score=48.92  Aligned_cols=48  Identities=29%  Similarity=0.594  Sum_probs=37.2

Q ss_pred             ccccccccccccccc--ccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388           44 RSSCEICRERRENDQ--MFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS   99 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~--~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~   99 (214)
                      ..+|+||++.+..+-  -...+.|+|-|=.+|+++|+.      +.....||.  |..
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~------k~~~~~cp~--c~~   53 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG------KKTKMQCPL--CSG   53 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHh------hhhhhhCcc--cCC
Confidence            468999999986532  222689999999999999992      226789999  754

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

Probab=95.21  E-value=0.09  Score=43.04  Aligned_cols=120  Identities=22%  Similarity=0.485  Sum_probs=65.4

Q ss_pred             cccccccccccccc---cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCc--CcHHHHhhcCCHHHHHHH
Q 045388           44 RSSCEICRERREND---QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSV--LKFDACKSVLSKNVLELW  118 (214)
Q Consensus        44 ~~~C~iC~~~~~~~---~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~--l~~~~~~~~l~~~~~~~~  118 (214)
                      ...|.||-++|+..   ..+..+.|||.+|..|+...+.+       ..+.||.  |...  +....++.+-  ..|...
T Consensus         3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~-------~~i~cpf--cR~~~~~~~~~~~~l~--kNf~ll   71 (296)
T KOG4185|consen    3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGN-------SRILCPF--CRETTEIPDGDVKSLQ--KNFALL   71 (296)
T ss_pred             CCceeecCccccccCcccCCcccccCceehHhHHHHHhcC-------ceeeccC--CCCcccCCchhHhhhh--hhHHHH
Confidence            47899999998764   34447899999999999988643       4577888  7766  4444554442  222222


Q ss_pred             HHHHH--HHHhcCCCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCC-CCCC
Q 045388          119 EKALS--QELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVP-WHPG  177 (214)
Q Consensus       119 ~~~~~--~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~-~h~~  177 (214)
                      +....  ...+.......+| +.|..........  ....-.|+.....+|..|... .|.+
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~-~~c~~~~~nl~~~--vc~~~~~~~~~~~~c~t~~~~~~~~~  130 (296)
T KOG4185|consen   72 QAIEHMKKTTVEEKGEADSP-PKCKEHPYNLAEF--VCVEPDCSSKDKLMCRTCEEFGIHKG  130 (296)
T ss_pred             HHHHHHhcccccccCcccCC-cccccCcccccce--eecCCCcchhhhhhhhhccchhhhhh
Confidence            22111  1112222222333 1244222111110  111223666678899999874 4555

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

Probab=95.06  E-value=0.01  Score=48.36  Aligned_cols=47  Identities=30%  Similarity=0.793  Sum_probs=36.2

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL  101 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l  101 (214)
                      ...+|.+|-.-+-+...  ...|-|.||+.||-.|++.        ...||.  |+..+
T Consensus        14 ~~itC~LC~GYliDATT--I~eCLHTFCkSCivk~l~~--------~~~CP~--C~i~i   60 (331)
T KOG2660|consen   14 PHITCRLCGGYLIDATT--ITECLHTFCKSCIVKYLEE--------SKYCPT--CDIVI   60 (331)
T ss_pred             cceehhhccceeecchh--HHHHHHHHHHHHHHHHHHH--------hccCCc--cceec
Confidence            46899999887655433  5799999999999999986        247998  65433

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

Probab=94.97  E-value=0.018  Score=51.27  Aligned_cols=46  Identities=28%  Similarity=0.479  Sum_probs=35.5

Q ss_pred             ccccccccccccccccc--cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCC
Q 045388           43 SRSSCEICRERRENDQM--FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPD   96 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   96 (214)
                      ....|.||.+.+....-  ...+.|+|.|+..|++.|++.        .-.||.+.
T Consensus       290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er--------~qtCP~CR  337 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFER--------QQTCPTCR  337 (543)
T ss_pred             cCCeeeeechhhccccccccceeecccchHHHHHHHHHHH--------hCcCCcch
Confidence            36789999999866311  236899999999999999986        23688833

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

Probab=94.94  E-value=0.016  Score=38.00  Aligned_cols=52  Identities=31%  Similarity=0.628  Sum_probs=35.5

Q ss_pred             ccccccccccccc---------ccc-cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           44 RSSCEICRERREN---------DQM-FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        44 ~~~C~iC~~~~~~---------~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ...|+||...|..         ++- +..-.|+|.|...||.+|+.++-.     .-.||.  |...+.
T Consensus        21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~-----~~~CPm--CR~~w~   82 (85)
T PF12861_consen   21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSS-----KGQCPM--CRQPWK   82 (85)
T ss_pred             CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccC-----CCCCCC--cCCeee
Confidence            4578888877652         110 113479999999999999987522     237999  776553

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

Probab=94.79  E-value=0.014  Score=49.38  Aligned_cols=34  Identities=21%  Similarity=0.591  Sum_probs=28.5

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHH
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVA   79 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~   79 (214)
                      +...|+||..-|..+-   .+.|+|..|+.|.+..+.
T Consensus         3 eelkc~vc~~f~~epi---il~c~h~lc~~ca~~~~~   36 (699)
T KOG4367|consen    3 EELKCPVCGSFYREPI---ILPCSHNLCQACARNILV   36 (699)
T ss_pred             ccccCceehhhccCce---EeecccHHHHHHHHhhcc
Confidence            4678999999887765   589999999999997654

>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=94.65  E-value=0.0092  Score=35.20  Aligned_cols=32  Identities=41%  Similarity=0.969  Sum_probs=19.2

Q ss_pred             cCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCC
Q 045388          154 LSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCK  199 (214)
Q Consensus       154 ~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~  199 (214)
                      ....+|+.|+..||+.|..-.|+.              ...||.|.
T Consensus        19 ~~~y~C~~C~~~FC~dCD~fiHE~--------------LH~CPGC~   50 (51)
T PF07975_consen   19 SSRYRCPKCKNHFCIDCDVFIHET--------------LHNCPGCE   50 (51)
T ss_dssp             -EEE--TTTT--B-HHHHHTTTTT--------------S-SSSTT-
T ss_pred             CCeEECCCCCCccccCcChhhhcc--------------ccCCcCCC
Confidence            367899999999999998877743              56788774

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.

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

Probab=94.60  E-value=0.019  Score=43.45  Aligned_cols=38  Identities=29%  Similarity=0.579  Sum_probs=29.7

Q ss_pred             CCCCcccccccccccccccccccccCCCCccccHHHHHHHH
Q 045388           38 PSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHV   78 (214)
Q Consensus        38 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~   78 (214)
                      .+++.-.+.|.||-.+|..+.   ...|||.||..|+..-+
T Consensus       190 ~~~e~IPF~C~iCKkdy~spv---vt~CGH~FC~~Cai~~y  227 (259)
T COG5152         190 GPGEKIPFLCGICKKDYESPV---VTECGHSFCSLCAIRKY  227 (259)
T ss_pred             CCCCCCceeehhchhhccchh---hhhcchhHHHHHHHHHh
Confidence            344445689999999998764   47899999999976544

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

Probab=94.57  E-value=0.061  Score=52.08  Aligned_cols=67  Identities=21%  Similarity=0.388  Sum_probs=50.8

Q ss_pred             cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCC--cccccCCCCCCCCcCcHHHHhhcCCH
Q 045388           44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGI--ITPVTCPGPDCKSVLKFDACKSVLSK  112 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~--~~~i~CP~~~C~~~l~~~~~~~~l~~  112 (214)
                      .--|-|||.+.-.......++|+|.|...|.+..+++.-..-.  +.-|.||.  |...++--.++++|++
T Consensus      3486 DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPi--C~n~InH~~LkDLldP 3554 (3738)
T KOG1428|consen 3486 DDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPI--CKNKINHIVLKDLLDP 3554 (3738)
T ss_pred             CceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeeccc--ccchhhhHHHHHHHHH
Confidence            4569999988544333337899999999999998887665433  24589999  9998887777888764

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

Probab=94.47  E-value=0.042  Score=31.97  Aligned_cols=44  Identities=23%  Similarity=0.700  Sum_probs=20.5

Q ss_pred             ccccccccccc--cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCc
Q 045388           47 CEICRERREND--QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSV  100 (214)
Q Consensus        47 C~iC~~~~~~~--~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~  100 (214)
                      |++|.+++...  ++. --.|++++|+.|+.....    ++   .=+||.  |+..
T Consensus         1 cp~C~e~~d~~d~~~~-PC~Cgf~IC~~C~~~i~~----~~---~g~CPg--Cr~~   46 (48)
T PF14570_consen    1 CPLCDEELDETDKDFY-PCECGFQICRFCYHDILE----NE---GGRCPG--CREP   46 (48)
T ss_dssp             -TTTS-B--CCCTT---SSTTS----HHHHHHHTT----SS----SB-TT--T--B
T ss_pred             CCCcccccccCCCccc-cCcCCCcHHHHHHHHHHh----cc---CCCCCC--CCCC
Confidence            68888887443  333 348899999999987754    11   237998  7654

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

Probab=94.36  E-value=0.029  Score=45.21  Aligned_cols=52  Identities=23%  Similarity=0.500  Sum_probs=38.6

Q ss_pred             CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHH
Q 045388           41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFD  104 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~  104 (214)
                      .....+|.||+.+-..+   ..+.|+|.||.-|+++-+..    +   ...|+.  |..+++..
T Consensus         4 ~~~~~eC~IC~nt~n~P---v~l~C~HkFCyiCiKGsy~n----d---k~~Cav--CR~pids~   55 (324)
T KOG0824|consen    4 RTKKKECLICYNTGNCP---VNLYCFHKFCYICIKGSYKN----D---KKTCAV--CRFPIDST   55 (324)
T ss_pred             cccCCcceeeeccCCcC---ccccccchhhhhhhcchhhc----C---CCCCce--ecCCCCcc
Confidence            34567899999986554   26899999999999986542    1   235998  88777654

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

Probab=94.34  E-value=0.027  Score=48.36  Aligned_cols=53  Identities=25%  Similarity=0.560  Sum_probs=38.2

Q ss_pred             Ccccccccccccccccc----------ccc----ccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           41 PPSRSSCEICRERREND----------QMF----KIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~----------~~~----~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ...+..|.||+.+++.-          .++    -..+|.|.|.+.|+..|+..       +.+-||.  |..+|+
T Consensus       568 ~~~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~-------ykl~CPv--CR~pLP  634 (636)
T KOG0828|consen  568 VRRTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT-------YKLICPV--CRCPLP  634 (636)
T ss_pred             hhccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh-------hcccCCc--cCCCCC
Confidence            45678999999987531          111    14599999999999999853       3578999  555553

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

Probab=94.03  E-value=0.055  Score=31.74  Aligned_cols=42  Identities=17%  Similarity=0.536  Sum_probs=28.9

Q ss_pred             cccccccccccccccccCCCC-----ccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388           46 SCEICRERRENDQMFKIESCI-----HSFCSDCINKHVATKIQGGIITPVTCPG   94 (214)
Q Consensus        46 ~C~iC~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~~i~CP~   94 (214)
                      .|-||++..+..+.+ ..+|.     |.+..+||..|+...-      ..+||.
T Consensus         1 ~CrIC~~~~~~~~~l-~~PC~C~G~~~~vH~~Cl~~W~~~~~------~~~C~i   47 (49)
T smart00744        1 ICRICHDEGDEGDPL-VSPCRCKGSLKYVHQECLERWINESG------NKTCEI   47 (49)
T ss_pred             CccCCCCCCCCCCee-EeccccCCchhHHHHHHHHHHHHHcC------CCcCCC
Confidence            488999833333333 45674     7899999999997543      237887

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

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

Probab=93.96  E-value=0.088  Score=43.46  Aligned_cols=53  Identities=23%  Similarity=0.516  Sum_probs=37.5

Q ss_pred             CCCCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           37 SPSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        37 ~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ......+...|+||+..- ...+  ..+|+|+-|..|+..|+.+        .-+|..  |+..+.
T Consensus       415 ~~lp~sEd~lCpICyA~p-i~Av--f~PC~H~SC~~CI~qHlmN--------~k~CFf--CktTv~  467 (489)
T KOG4692|consen  415 KDLPDSEDNLCPICYAGP-INAV--FAPCSHRSCYGCITQHLMN--------CKRCFF--CKTTVI  467 (489)
T ss_pred             CCCCCcccccCcceeccc-chhh--ccCCCCchHHHHHHHHHhc--------CCeeeE--ecceee
Confidence            334456678899999863 3334  4799999999999999753        235666  776653

>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=93.72  E-value=0.037  Score=27.85  Aligned_cols=23  Identities=35%  Similarity=0.826  Sum_probs=16.5

Q ss_pred             ccCccCCCceeeecCCCCCCcCcccCCCCChhh
Q 045388          134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRLF  166 (214)
Q Consensus       134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~  166 (214)
                      .||  +|+..+....        ..||.||+.|
T Consensus         2 ~CP--~C~~~V~~~~--------~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCP--ECGAEVPESA--------KFCPHCGYDF   24 (26)
T ss_pred             cCC--CCcCCchhhc--------CcCCCCCCCC
Confidence            477  8888775543        3499999876

Several members are annotated as putative helicases.

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

Probab=93.60  E-value=0.068  Score=42.49  Aligned_cols=56  Identities=29%  Similarity=0.501  Sum_probs=41.3

Q ss_pred             cccccccccccccccc-------ccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHH
Q 045388           43 SRSSCEICRERRENDQ-------MFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC  106 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~-------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~  106 (214)
                      +...|.||...+..+.       =...++|+|.|...|+++|...    |+  .-.||-  |+..++...+
T Consensus       223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWciv----GK--kqtCPY--CKekVdl~rm  285 (328)
T KOG1734|consen  223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIV----GK--KQTCPY--CKEKVDLKRM  285 (328)
T ss_pred             CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheee----cC--CCCCch--HHHHhhHhhh
Confidence            4577999998876543       1226899999999999999642    33  468998  9887766544

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

Probab=93.56  E-value=0.062  Score=46.70  Aligned_cols=38  Identities=21%  Similarity=0.600  Sum_probs=29.3

Q ss_pred             CCcccCccCCCceeeecCCCCCCcCcccCCC--CChhhccccCCCC
Q 045388          131 QGIYCPFKDCSAKLVYENDGEDVLSESECPY--CHRLFCAHCYVPW  174 (214)
Q Consensus       131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~  174 (214)
                      +...||  .|...+..+.+.    +...|..  |+..||+.|...|
T Consensus       225 ntk~CP--~c~~~iek~~gc----~~~~~~~~~c~~~FCw~Cl~~~  264 (444)
T KOG1815|consen  225 NTKECP--KCKVPIEKDGGC----NHMTCKSASCKHEFCWVCLASL  264 (444)
T ss_pred             cCccCC--CcccchhccCCc----cccccccCCcCCeeceeeeccc
Confidence            444588  999998888764    5555654  9999999997776

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

Probab=93.48  E-value=0.062  Score=34.34  Aligned_cols=63  Identities=25%  Similarity=0.575  Sum_probs=25.9

Q ss_pred             CCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceecCCCCC
Q 045388          131 QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLH  210 (214)
Q Consensus       131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~GCnh  210 (214)
                      +...|.  -|+--+-.+..+   ...+.|..|+.-.|..|..             +......+.||+|++...+.-|+..
T Consensus         8 ~~qiCq--iCGD~VGl~~~G---e~FVAC~eC~fPvCr~CyE-------------YErkeg~q~CpqCkt~ykr~kgsp~   69 (80)
T PF14569_consen    8 NGQICQ--ICGDDVGLTENG---EVFVACHECAFPVCRPCYE-------------YERKEGNQVCPQCKTRYKRHKGSPR   69 (80)
T ss_dssp             SS-B-S--SS--B--B-SSS---SB--S-SSS-----HHHHH-------------HHHHTS-SB-TTT--B----TT---
T ss_pred             CCcccc--cccCccccCCCC---CEEEEEcccCCccchhHHH-------------HHhhcCcccccccCCCcccccCCCC
Confidence            444566  777666665544   3778899999999988853             5566788999999999988877654


Q ss_pred             e
Q 045388          211 M  211 (214)
Q Consensus       211 m  211 (214)
                      +
T Consensus        70 V   70 (80)
T PF14569_consen   70 V   70 (80)
T ss_dssp             -
T ss_pred             C
Confidence            3

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

Probab=93.35  E-value=0.13  Score=47.06  Aligned_cols=56  Identities=30%  Similarity=0.679  Sum_probs=43.6

Q ss_pred             Ccccccccccccccccc-cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388           41 PPSRSSCEICRERREND-QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS   99 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~   99 (214)
                      ....++|.||++.+... .++....|-|.|...||+.|.+..-.++. ..-+||.  |+.
T Consensus       188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~-~~WrCP~--Cqs  244 (950)
T KOG1952|consen  188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQ-DGWRCPA--CQS  244 (950)
T ss_pred             hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccC-ccccCCc--ccc
Confidence            34579999999998653 45556778999999999999988555555 5679998  763

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

Probab=93.35  E-value=0.039  Score=46.03  Aligned_cols=48  Identities=29%  Similarity=0.693  Sum_probs=34.9

Q ss_pred             cccccccccccccccccc-cCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCC
Q 045388           44 RSSCEICRERRENDQMFK-IESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCK   98 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~   98 (214)
                      ...|.||-+-++...-+. ...|||.|...|+..|++..-..     =.||.  |+
T Consensus         4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~-----R~cpi--c~   52 (465)
T KOG0827|consen    4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSN-----RGCPI--CQ   52 (465)
T ss_pred             cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCcc-----CCCCc--ee
Confidence            468999977666654333 34599999999999999754443     25888  65

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

Probab=93.34  E-value=0.16  Score=43.26  Aligned_cols=48  Identities=27%  Similarity=0.720  Sum_probs=36.3

Q ss_pred             cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ...+.|.||+..+..+.   .++|||.||..|+..    .+.    ....||.  |...+.
T Consensus        82 ~sef~c~vc~~~l~~pv---~tpcghs~c~~Cl~r----~ld----~~~~cp~--Cr~~l~  129 (398)
T KOG4159|consen   82 RSEFECCVCSRALYPPV---VTPCGHSFCLECLDR----SLD----QETECPL--CRDELV  129 (398)
T ss_pred             cchhhhhhhHhhcCCCc---cccccccccHHHHHH----Hhc----cCCCCcc--cccccc
Confidence            56799999999887654   469999999999766    222    2457888  877665

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

Probab=93.23  E-value=0.042  Score=46.04  Aligned_cols=46  Identities=35%  Similarity=0.798  Sum_probs=33.3

Q ss_pred             cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCC
Q 045388           44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCK   98 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~   98 (214)
                      ...|.||-+.-..   +...+|||..|..|+..|-..  .+|+    .||.+.|.
T Consensus       369 FeLCKICaendKd---vkIEPCGHLlCt~CLa~WQ~s--d~gq----~CPFCRcE  414 (563)
T KOG1785|consen  369 FELCKICAENDKD---VKIEPCGHLLCTSCLAAWQDS--DEGQ----TCPFCRCE  414 (563)
T ss_pred             HHHHHHhhccCCC---cccccccchHHHHHHHhhccc--CCCC----CCCceeeE
Confidence            4569999986433   446899999999999999422  1244    79996664

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

Probab=93.22  E-value=0.033  Score=39.68  Aligned_cols=36  Identities=25%  Similarity=0.530  Sum_probs=27.3

Q ss_pred             ccccccccccccccccccccCCCC------ccccHHHHHHHH
Q 045388           43 SRSSCEICRERRENDQMFKIESCI------HSFCSDCINKHV   78 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~------H~fC~~Cl~~~~   78 (214)
                      ...+|.||++.+...+-+....|+      |.||.+|++.|-
T Consensus        25 ~~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~   66 (134)
T PF05883_consen   25 CTVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWR   66 (134)
T ss_pred             cCeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence            368999999999873333334554      789999999994

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.

>TIGR00622 ssl1 transcription factor ssl1

Probab=93.15  E-value=0.11  Score=35.91  Aligned_cols=52  Identities=25%  Similarity=0.570  Sum_probs=35.5

Q ss_pred             cccCccCCCceeeecCC---C-CCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCc
Q 045388          133 IYCPFKDCSAKLVYEND---G-EDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKY  200 (214)
Q Consensus       133 ~~Cp~~~C~~~~~~~~~---~-~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~  200 (214)
                      ..|-  .|...+.....   + .....+..|+.|+..||..|..-+|+              ....||+|..
T Consensus        56 ~~C~--~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe--------------~Lh~CPGC~~  111 (112)
T TIGR00622        56 RFCF--GCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHE--------------SLHCCPGCIH  111 (112)
T ss_pred             Cccc--CcCCCCCCcccccccccccccceeCCCCCCccccccchhhhh--------------hccCCcCCCC
Confidence            4577  88876653211   0 12235678999999999999987774              3466888863

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

>PHA03096 p28-like protein; Provisional

Probab=93.12  E-value=0.18  Score=41.05  Aligned_cols=39  Identities=21%  Similarity=0.448  Sum_probs=30.7

Q ss_pred             ccccccccccccc----cccc-cCCCCccccHHHHHHHHHHHhh
Q 045388           45 SSCEICRERREND----QMFK-IESCIHSFCSDCINKHVATKIQ   83 (214)
Q Consensus        45 ~~C~iC~~~~~~~----~~~~-~~~C~H~fC~~Cl~~~~~~~i~   83 (214)
                      ..|+||++.....    ..+. +..|.|.||..|++.|..+...
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            7899999986543    1222 6699999999999999987764

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=93.03  E-value=0.059  Score=29.58  Aligned_cols=32  Identities=28%  Similarity=0.740  Sum_probs=22.2

Q ss_pred             cccCccCCCceeeecCCC-CCCcCcccCCCCChhh
Q 045388          133 IYCPFKDCSAKLVYENDG-EDVLSESECPYCHRLF  166 (214)
Q Consensus       133 ~~Cp~~~C~~~~~~~~~~-~~~~~~~~C~~C~~~~  166 (214)
                      +.||  +|+..+..++.. ......++|+.|+..|
T Consensus         3 i~CP--~C~~~f~v~~~~l~~~~~~vrC~~C~~~f   35 (37)
T PF13719_consen    3 ITCP--NCQTRFRVPDDKLPAGGRKVRCPKCGHVF   35 (37)
T ss_pred             EECC--CCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence            4688  999888776541 1334678888888765

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

Probab=93.01  E-value=0.036  Score=43.39  Aligned_cols=47  Identities=28%  Similarity=0.747  Sum_probs=34.1

Q ss_pred             cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcH
Q 045388           44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF  103 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~  103 (214)
                      .+.|..|+---. .+-+.++.|.|.||..|...-          .+-.||.  |+..+..
T Consensus         3 ~VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~----------~~~~C~l--Ckk~ir~   49 (233)
T KOG4739|consen    3 FVHCNKCFRFPS-QDPFFLTACRHVFCEPCLKAS----------SPDVCPL--CKKSIRI   49 (233)
T ss_pred             eEEeccccccCC-CCceeeeechhhhhhhhcccC----------Ccccccc--ccceeee
Confidence            467999988766 444558999999999996543          2228999  8876543

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

Probab=93.01  E-value=0.011  Score=48.53  Aligned_cols=46  Identities=33%  Similarity=0.812  Sum_probs=33.8

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS   99 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~   99 (214)
                      ..+.|+||++-+...-+  ...|.|+||.+||..-+..   .+.    .||-  |..
T Consensus        42 ~~v~c~icl~llk~tmt--tkeClhrfc~~ci~~a~r~---gn~----ecpt--cRk   87 (381)
T KOG0311|consen   42 IQVICPICLSLLKKTMT--TKECLHRFCFDCIWKALRS---GNN----ECPT--CRK   87 (381)
T ss_pred             hhhccHHHHHHHHhhcc--cHHHHHHHHHHHHHHHHHh---cCC----CCch--HHh
Confidence            46789999998876532  5799999999998876542   222    6887  654

>smart00647 IBR In Between Ring fingers

Probab=92.82  E-value=0.2  Score=30.69  Aligned_cols=26  Identities=38%  Similarity=0.823  Sum_probs=21.6

Q ss_pred             hCCCccCC--CCCccceecC--CCCCeecC
Q 045388          189 KKQLRKCP--NCKYHIERTG--GCLHMTCL  214 (214)
Q Consensus       189 ~~~~k~CP--~C~~~iek~~--GCnhm~C~  214 (214)
                      +.+++.||  +|+..|+..+  |.++++|+
T Consensus        15 ~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~   44 (64)
T smart00647       15 NPDLKWCPAPDCSAAIIVTEEEGCNRVTCP   44 (64)
T ss_pred             CCCccCCCCCCCcceEEecCCCCCCeeECC
Confidence            36789999  9999999874  88888883

the domains occurs between pairs og RING fingers

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=92.45  E-value=0.085  Score=28.75  Aligned_cols=32  Identities=28%  Similarity=0.663  Sum_probs=22.0

Q ss_pred             cccCccCCCceeeecCC-CCCCcCcccCCCCChhh
Q 045388          133 IYCPFKDCSAKLVYEND-GEDVLSESECPYCHRLF  166 (214)
Q Consensus       133 ~~Cp~~~C~~~~~~~~~-~~~~~~~~~C~~C~~~~  166 (214)
                      +.||  +|...+..++. -......++|+.|+..|
T Consensus         3 i~Cp--~C~~~y~i~d~~ip~~g~~v~C~~C~~~f   35 (36)
T PF13717_consen    3 ITCP--NCQAKYEIDDEKIPPKGRKVRCSKCGHVF   35 (36)
T ss_pred             EECC--CCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence            4688  99988777654 22344678888888765

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.40  E-value=0.072  Score=41.80  Aligned_cols=56  Identities=18%  Similarity=0.255  Sum_probs=42.7

Q ss_pred             ccccccccccccccccc-cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhh
Q 045388           43 SRSSCEICRERRENDQM-FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKS  108 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~  108 (214)
                      ..+.|++|-+.+++..- ..+.+|||.||.+|....|.        ..+.||.  ++.++..++|..
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir--------~D~v~pv--~d~plkdrdiI~  276 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR--------KDMVDPV--TDKPLKDRDIIG  276 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc--------ccccccC--CCCcCcccceEe
Confidence            67899999999876422 22679999999999999875        3567888  777777666543

>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate

Probab=91.64  E-value=0.17  Score=40.05  Aligned_cols=78  Identities=23%  Similarity=0.457  Sum_probs=45.8

Q ss_pred             CcccccccccccccccccccccCCCCcc-ccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCHHHHHHHH
Q 045388           41 PPSRSSCEICRERRENDQMFKIESCIHS-FCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWE  119 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~~~~~~~~  119 (214)
                      ....++|.+|...+..+.-.    =+|. -|..|-+..-...---|+ .-++||   |+-.|--                
T Consensus        62 ~~p~v~CrVCq~~I~i~gk~----~QhVVkC~~CnEATPIr~aPpGK-KYVRCP---CNCLLIC----------------  117 (256)
T PF09788_consen   62 GAPVVTCRVCQSLIDIEGKM----HQHVVKCSVCNEATPIRNAPPGK-KYVRCP---CNCLLIC----------------  117 (256)
T ss_pred             CCceEEeecCCceecccCcc----ceeeEECCCCCccccccCCCCCC-eeEecC---CceEEEe----------------
Confidence            33578999998877654311    1443 466665554322223344 457777   5543300                


Q ss_pred             HHHHHHHhcCCCCcccCccCCCceeeecCC
Q 045388          120 KALSQELIDASQGIYCPFKDCSAKLVYEND  149 (214)
Q Consensus       120 ~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~  149 (214)
                             .....++.||.|+|..++.....
T Consensus       118 -------k~sS~rIaCPRp~CkRiI~L~~~  140 (256)
T PF09788_consen  118 -------KSSSQRIACPRPNCKRIINLGPS  140 (256)
T ss_pred             -------ecccccccCCCCCCcceEEeCCc
Confidence                   02346778999999998877654

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

Probab=91.28  E-value=0.12  Score=43.28  Aligned_cols=76  Identities=18%  Similarity=0.457  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhhccccccCCCCCCCcccccccccccccccc-cccccCCCCccccHHHHHHHHHHHhhCCCc
Q 045388            9 AFATLAEELEIQEALMASTITSQMAKSASPSSPPSRSSCEICRERREND-QMFKIESCIHSFCSDCINKHVATKIQGGII   87 (214)
Q Consensus         9 ~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~   87 (214)
                      .++++++.+++++.+......+..-      .......|+.|.+.+... +-.+.++|.|.|...|+..+++.   +   
T Consensus       336 rla~iYrs~gl~d~~~~h~~ra~~~------~~e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---n---  403 (518)
T KOG1941|consen  336 RLASIYRSKGLQDELRAHVVRAHEC------VEETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---N---  403 (518)
T ss_pred             HHHHHHHhccchhHHHHHHHHHHHH------HHHHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---C---
Confidence            3566677776666666555443322      234468899999987643 23447899999999999999842   2   


Q ss_pred             ccccCCCCCCC
Q 045388           88 TPVTCPGPDCK   98 (214)
Q Consensus        88 ~~i~CP~~~C~   98 (214)
                      .+=+||.  |.
T Consensus       404 ~~rsCP~--Cr  412 (518)
T KOG1941|consen  404 GTRSCPN--CR  412 (518)
T ss_pred             CCCCCcc--HH
Confidence            2457998  65

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

Probab=91.23  E-value=0.2  Score=30.29  Aligned_cols=49  Identities=20%  Similarity=0.537  Sum_probs=32.4

Q ss_pred             cccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCc
Q 045388          133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKY  200 (214)
Q Consensus       133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~  200 (214)
                      -.|.  .|+..+...+..    ..+.||.||.+.=++|..=             -+..+.=.||+|+.
T Consensus        10 ~~Ct--SCg~~i~p~e~~----v~F~CPnCGe~~I~Rc~~C-------------Rk~g~~Y~Cp~CGF   58 (61)
T COG2888          10 PVCT--SCGREIAPGETA----VKFPCPNCGEVEIYRCAKC-------------RKLGNPYRCPKCGF   58 (61)
T ss_pred             ceec--cCCCEeccCCce----eEeeCCCCCceeeehhhhH-------------HHcCCceECCCcCc
Confidence            4577  888888555543    7888999996665555330             11345567999986

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

Probab=90.57  E-value=0.28  Score=41.96  Aligned_cols=38  Identities=21%  Similarity=0.549  Sum_probs=30.9

Q ss_pred             CcccccccccccccccccccccCCCCccccHHHHHHHHHH
Q 045388           41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVAT   80 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~   80 (214)
                      ......|++|...+..+..  ...|+|.||..|+..+...
T Consensus        18 ~~~~l~C~~C~~vl~~p~~--~~~cgh~fC~~C~~~~~~~   55 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDPVQ--TTTCGHRFCAGCLLESLSN   55 (391)
T ss_pred             CcccccCccccccccCCCC--CCCCCCcccccccchhhcc
Confidence            4567899999998876542  2599999999999999865

>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=90.32  E-value=0.16  Score=31.02  Aligned_cols=26  Identities=46%  Similarity=1.081  Sum_probs=14.9

Q ss_pred             hCCCccCCC--CCccceecCCCCC--eecC
Q 045388          189 KKQLRKCPN--CKYHIERTGGCLH--MTCL  214 (214)
Q Consensus       189 ~~~~k~CP~--C~~~iek~~GCnh--m~C~  214 (214)
                      +.+++.||+  |...|++.+|.++  |+|+
T Consensus        15 ~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~   44 (64)
T PF01485_consen   15 DPNIRWCPNPDCEYIIEKDDGCNSPIVTCP   44 (64)
T ss_dssp             ---CC--TTSST---ECS-SSTTS--CCTT
T ss_pred             CCCccCCCCCCCcccEEecCCCCCCeeECC
Confidence            446689988  9999999999999  8885

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.

>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=90.02  E-value=0.42  Score=38.55  Aligned_cols=52  Identities=27%  Similarity=0.757  Sum_probs=35.0

Q ss_pred             cccccccccc-cccccc-cCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHH
Q 045388           46 SCEICRERRE-NDQMFK-IESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC  106 (214)
Q Consensus        46 ~C~iC~~~~~-~~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~  106 (214)
                      .|++|-.+.- .++++- ...|+|..|.+|+-..+..       .+-.||.  |..+|-...+
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~-------g~~~Cpe--C~~iLRk~nf   55 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSL-------GPAQCPE--CMVILRKNNF   55 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhc-------CCCCCCc--ccchhhhccc
Confidence            4888877643 333322 4599999999999887642       3456995  9877754433

>PF04641 Rtf2: Rtf2 RING-finger

Probab=89.91  E-value=0.45  Score=38.30  Aligned_cols=71  Identities=13%  Similarity=0.284  Sum_probs=50.9

Q ss_pred             Ccccccccccccccccc-cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCC-HHHHHHH
Q 045388           41 PPSRSSCEICRERREND-QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLS-KNVLELW  118 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~-~~~~~~~  118 (214)
                      ....+.|||....+... .++.+.+|||+|....|...-     .    .-.||.  |+..+...+|-.|-+ .+.++.+
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~k-----~----~~~Cp~--c~~~f~~~DiI~Lnp~~ee~~~l  178 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKELK-----K----SKKCPV--CGKPFTEEDIIPLNPPEEELEKL  178 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhhc-----c----cccccc--cCCccccCCEEEecCCccHHHHH
Confidence            45678999999998543 455578999999999998871     1    234999  999998877766654 3344444


Q ss_pred             HHHH
Q 045388          119 EKAL  122 (214)
Q Consensus       119 ~~~~  122 (214)
                      ...+
T Consensus       179 ~~~~  182 (260)
T PF04641_consen  179 RERM  182 (260)
T ss_pred             HHHH
Confidence            4443

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

Probab=89.86  E-value=0.1  Score=30.97  Aligned_cols=45  Identities=24%  Similarity=0.574  Sum_probs=31.6

Q ss_pred             ccccccccccccccccccCCCCcc-ccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388           45 SSCEICRERRENDQMFKIESCIHS-FCSDCINKHVATKIQGGIITPVTCPGPDCKSVL  101 (214)
Q Consensus        45 ~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l  101 (214)
                      .+|.||++.-.++.   .-.|||. .|.+|-...+..    +   .-.||.  |..++
T Consensus         8 dECTICye~pvdsV---lYtCGHMCmCy~Cg~rl~~~----~---~g~CPi--CRapi   53 (62)
T KOG4172|consen    8 DECTICYEHPVDSV---LYTCGHMCMCYACGLRLKKA----L---HGCCPI--CRAPI   53 (62)
T ss_pred             cceeeeccCcchHH---HHHcchHHhHHHHHHHHHHc----c---CCcCcc--hhhHH
Confidence            78999999744332   3579998 899997776543    1   235888  77654

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

Probab=89.74  E-value=0.26  Score=40.80  Aligned_cols=47  Identities=28%  Similarity=0.651  Sum_probs=34.7

Q ss_pred             cccccccccccccccccccccCCCCcc-ccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388           42 PSRSSCEICRERRENDQMFKIESCIHS-FCSDCINKHVATKIQGGIITPVTCPGPDCKSVL  101 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l  101 (214)
                      ....+|.||+++.....   .++|.|. .|.+|.+..-   +..     =+||.  |...+
T Consensus       288 ~~gkeCVIClse~rdt~---vLPCRHLCLCs~Ca~~Lr---~q~-----n~CPI--CRqpi  335 (349)
T KOG4265|consen  288 ESGKECVICLSESRDTV---VLPCRHLCLCSGCAKSLR---YQT-----NNCPI--CRQPI  335 (349)
T ss_pred             cCCCeeEEEecCCcceE---EecchhhehhHhHHHHHH---Hhh-----cCCCc--cccch
Confidence            44789999999855432   6899998 9999987653   222     25999  87755

>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=89.21  E-value=0.073  Score=41.56  Aligned_cols=50  Identities=24%  Similarity=0.759  Sum_probs=36.8

Q ss_pred             cccccccccccc-ccc--cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388           45 SSCEICRERREN-DQM--FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL  101 (214)
Q Consensus        45 ~~C~iC~~~~~~-~~~--~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l  101 (214)
                      .-||+|..+.-. +++  .....|-|.+|..|+...++.       .+..||-.+|+..|
T Consensus        11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~-------GpAqCP~~gC~kIL   63 (314)
T COG5220          11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSR-------GPAQCPYKGCGKIL   63 (314)
T ss_pred             ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcC-------CCCCCCCccHHHHH
Confidence            469999988533 333  224569999999999887742       46789999998654

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

Probab=88.90  E-value=0.46  Score=28.81  Aligned_cols=45  Identities=22%  Similarity=0.769  Sum_probs=30.2

Q ss_pred             ccCccCCCceeeecCCCCCCcCcccCCCCChhh---ccccCCCCCCChHHHHHHHHHHhCCCccCCCCCc
Q 045388          134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRLF---CAHCYVPWHPGREELMMRELVKKKQLRKCPNCKY  200 (214)
Q Consensus       134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~---C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~  200 (214)
                      .|.  .|+..+...+..    ..+.||.||...   |.+|++                ..+.=.||+|+.
T Consensus         9 ~Ct--SCg~~i~~~~~~----~~F~CPnCG~~~I~RC~~CRk----------------~~~~Y~CP~CGF   56 (59)
T PRK14890          9 KCT--SCGIEIAPREKA----VKFLCPNCGEVIIYRCEKCRK----------------QSNPYTCPKCGF   56 (59)
T ss_pred             ccc--CCCCcccCCCcc----CEeeCCCCCCeeEeechhHHh----------------cCCceECCCCCC
Confidence            566  788777655432    788899999874   555543                234567898885

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

Probab=88.25  E-value=0.47  Score=27.25  Aligned_cols=28  Identities=25%  Similarity=0.745  Sum_probs=19.8

Q ss_pred             cccCccCCCceeeecCCCCCCcCcccCCCCChhh
Q 045388          133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLF  166 (214)
Q Consensus       133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~  166 (214)
                      +.|+  +|+..+..++..    ..++||.||..+
T Consensus         4 y~C~--~CG~~~~~~~~~----~~~~Cp~CG~~~   31 (46)
T PRK00398          4 YKCA--RCGREVELDEYG----TGVRCPYCGYRI   31 (46)
T ss_pred             EECC--CCCCEEEECCCC----CceECCCCCCeE
Confidence            4578  888888777653    267788887654

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=88.22  E-value=0.26  Score=26.99  Aligned_cols=32  Identities=19%  Similarity=0.519  Sum_probs=18.3

Q ss_pred             cccCccCCCceeeecCCCC-CCcCcccCCCCChhh
Q 045388          133 IYCPFKDCSAKLVYENDGE-DVLSESECPYCHRLF  166 (214)
Q Consensus       133 ~~Cp~~~C~~~~~~~~~~~-~~~~~~~C~~C~~~~  166 (214)
                      +.||  .|+..+..++... .....++|+.|+..|
T Consensus         3 ~~CP--~C~~~~~v~~~~~~~~~~~v~C~~C~~~~   35 (38)
T TIGR02098         3 IQCP--NCKTSFRVVDSQLGANGGKVRCGKCGHVW   35 (38)
T ss_pred             EECC--CCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence            4577  8887766654311 122356777777643

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.

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

Probab=87.95  E-value=0.12  Score=47.01  Aligned_cols=41  Identities=7%  Similarity=0.404  Sum_probs=22.4

Q ss_pred             cccccccccccccc----ccccccCCCCccccHHHHHHHHHHHhh
Q 045388           43 SRSSCEICRERREN----DQMFKIESCIHSFCSDCINKHVATKIQ   83 (214)
Q Consensus        43 ~~~~C~iC~~~~~~----~~~~~~~~C~H~fC~~Cl~~~~~~~i~   83 (214)
                      ...+|.+|.-++..    ..+.....|+|.+|..||..|....+.
T Consensus        95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~  139 (1134)
T KOG0825|consen   95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEE  139 (1134)
T ss_pred             cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhc
Confidence            34555555555443    111113347777777777777655544

>PRK14714 DNA polymerase II large subunit; Provisional

Probab=87.94  E-value=0.52  Score=45.44  Aligned_cols=48  Identities=27%  Similarity=0.748  Sum_probs=32.5

Q ss_pred             cccCccCCCceeeecCCCCCCcCcccCCCCChhh-----ccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccce
Q 045388          133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLF-----CAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIE  203 (214)
Q Consensus       133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~-----C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~ie  203 (214)
                      +.||  +|+....          ..+||.||...     |..|+.....+           ......||+|++.+.
T Consensus       668 rkCP--kCG~~t~----------~~fCP~CGs~te~vy~CPsCGaev~~d-----------es~a~~CP~CGtplv  720 (1337)
T PRK14714        668 RRCP--SCGTETY----------ENRCPDCGTHTEPVYVCPDCGAEVPPD-----------ESGRVECPRCDVELT  720 (1337)
T ss_pred             EECC--CCCCccc----------cccCcccCCcCCCceeCccCCCccCCC-----------ccccccCCCCCCccc
Confidence            5899  9997532          23699998664     99998864433           122567999998653

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

Probab=87.72  E-value=3.3  Score=29.54  Aligned_cols=56  Identities=29%  Similarity=0.574  Sum_probs=42.5

Q ss_pred             CCcccccccccccccccccccc-cCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           40 SPPSRSSCEICRERRENDQMFK-IESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        40 ~~~~~~~C~iC~~~~~~~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      .+...++|.||.+.-.++.+.. ..-||-+.|..|....|...-     .-.+||+  |+..+.
T Consensus        76 ~d~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~-----~ypvCPv--CkTSFK  132 (140)
T PF05290_consen   76 LDPKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCN-----LYPVCPV--CKTSFK  132 (140)
T ss_pred             cCCCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcc-----cCCCCCc--cccccc
Confidence            3447899999999877766554 456899999999999886543     2468999  876653

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

Probab=87.65  E-value=0.39  Score=38.90  Aligned_cols=45  Identities=16%  Similarity=0.401  Sum_probs=36.3

Q ss_pred             CCCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHh
Q 045388           38 PSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKI   82 (214)
Q Consensus        38 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i   82 (214)
                      +..+.....|.||+--|...+-|....|.|.|...||..|+...+
T Consensus       109 T~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~  153 (368)
T KOG4445|consen  109 TENNHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECL  153 (368)
T ss_pred             ccCCCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHH
Confidence            334555678999998888877666789999999999999986554

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

Probab=87.56  E-value=0.64  Score=43.05  Aligned_cols=46  Identities=22%  Similarity=0.478  Sum_probs=34.9

Q ss_pred             CCCCCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHh
Q 045388           36 ASPSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKI   82 (214)
Q Consensus        36 ~~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i   82 (214)
                      +....-...-.|.+|.-.+-...++ ..+|||.|.++|+..++....
T Consensus       809 ~ry~v~ep~d~C~~C~~~ll~~pF~-vf~CgH~FH~~Cl~~~v~~~~  854 (911)
T KOG2034|consen  809 QRYRVLEPQDSCDHCGRPLLIKPFY-VFPCGHCFHRDCLIRHVLSLL  854 (911)
T ss_pred             cceEEecCccchHHhcchhhcCcce-eeeccchHHHHHHHHHHHccc
Confidence            3344445567899999988777655 579999999999999875433

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

Probab=87.54  E-value=0.28  Score=45.74  Aligned_cols=51  Identities=25%  Similarity=0.634  Sum_probs=36.6

Q ss_pred             cccccccccccccc-c-ccc--ccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388           43 SRSSCEICRERREN-D-QMF--KIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL  101 (214)
Q Consensus        43 ~~~~C~iC~~~~~~-~-~~~--~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l  101 (214)
                      ...+|+|||.-+.. + ..+  ....|.|.|...|+-+|+...-      .-+||.  |...+
T Consensus      1468 G~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~------~s~CPl--CRsei 1522 (1525)
T COG5219        1468 GHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSA------RSNCPL--CRSEI 1522 (1525)
T ss_pred             CcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcC------CCCCCc--ccccc
Confidence            35689999987652 1 111  1678999999999999997533      247999  77654

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

Probab=87.35  E-value=0.32  Score=26.30  Aligned_cols=28  Identities=29%  Similarity=0.676  Sum_probs=18.2

Q ss_pred             cccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388          133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRL  165 (214)
Q Consensus       133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~  165 (214)
                      ++||  .|+..+....+..   ....|..|++.
T Consensus         2 ~FCp--~C~nlL~p~~~~~---~~~~C~~C~Y~   29 (35)
T PF02150_consen    2 RFCP--ECGNLLYPKEDKE---KRVACRTCGYE   29 (35)
T ss_dssp             -BET--TTTSBEEEEEETT---TTEEESSSS-E
T ss_pred             eeCC--CCCccceEcCCCc---cCcCCCCCCCc
Confidence            5799  9999998876532   11268878764

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 ....

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

Probab=87.27  E-value=0.59  Score=37.58  Aligned_cols=57  Identities=28%  Similarity=0.681  Sum_probs=42.3

Q ss_pred             CCCcccccccccccccccccccccCC-CCccccHHHHHHHHHHHhhCCCcccccCCC-CCCC
Q 045388           39 SSPPSRSSCEICRERRENDQMFKIES-CIHSFCSDCINKHVATKIQGGIITPVTCPG-PDCK   98 (214)
Q Consensus        39 ~~~~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~-~~C~   98 (214)
                      .......-|.+|.+.+++..+++... =.|.||..|-+..|..+-..|   .++||. ..|.
T Consensus       263 ~A~~apLcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSResIK~Qg~sg---evYCPSGdkCP  321 (352)
T KOG3579|consen  263 AAPSAPLCCTLCHERLEDTHFVQCPSVPSHKFCFPCSRESIKQQGASG---EVYCPSGDKCP  321 (352)
T ss_pred             cCCCCceeehhhhhhhccCceeecCCCcccceecccCHHHHHhhcCCC---ceeCCCCCcCc
Confidence            33445689999999998887665221 169999999999998876655   478888 3564

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

Probab=87.24  E-value=0.11  Score=42.47  Aligned_cols=32  Identities=34%  Similarity=0.918  Sum_probs=24.9

Q ss_pred             cCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCC
Q 045388          154 LSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCK  199 (214)
Q Consensus       154 ~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~  199 (214)
                      ...++|..|+.+||..|..-.|+.              ...||.|.
T Consensus       343 ~~~y~C~~Ck~~FCldCDv~iHes--------------Lh~CpgCe  374 (378)
T KOG2807|consen  343 SGRYRCESCKNVFCLDCDVFIHES--------------LHNCPGCE  374 (378)
T ss_pred             CCcEEchhccceeeccchHHHHhh--------------hhcCCCcC
Confidence            367889999999999998866632              35688776

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

Probab=86.76  E-value=0.36  Score=25.90  Aligned_cols=31  Identities=26%  Similarity=0.573  Sum_probs=14.9

Q ss_pred             cccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388          133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRL  165 (214)
Q Consensus       133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~  165 (214)
                      ++||  .|+..+...-...+...+..|+.|+..
T Consensus         1 kfC~--~CG~~l~~~ip~gd~r~R~vC~~Cg~I   31 (34)
T PF14803_consen    1 KFCP--QCGGPLERRIPEGDDRERLVCPACGFI   31 (34)
T ss_dssp             -B-T--TT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred             Cccc--cccChhhhhcCCCCCccceECCCCCCE
Confidence            3788  899776554222234577889988863

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

Probab=86.63  E-value=0.99  Score=37.10  Aligned_cols=62  Identities=29%  Similarity=0.544  Sum_probs=43.6

Q ss_pred             CCCCCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhc
Q 045388           36 ASPSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSV  109 (214)
Q Consensus        36 ~~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~  109 (214)
                      +.+........|++|+....++.+.  ..-|-.||-.|+..|+.   +.|     +||..++.  ...+++.++
T Consensus       292 e~e~l~~~~~~CpvClk~r~Nptvl--~vSGyVfCY~Ci~~Yv~---~~~-----~CPVT~~p--~~v~~l~rl  353 (357)
T KOG0826|consen  292 ESELLPPDREVCPVCLKKRQNPTVL--EVSGYVFCYPCIFSYVV---NYG-----HCPVTGYP--ASVDHLIRL  353 (357)
T ss_pred             ccccCCCccccChhHHhccCCCceE--EecceEEeHHHHHHHHH---hcC-----CCCccCCc--chHHHHHHH
Confidence            5566666788999999988776543  33488999999999986   222     59996554  444555443

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=86.18  E-value=1  Score=37.14  Aligned_cols=53  Identities=21%  Similarity=0.536  Sum_probs=37.1

Q ss_pred             cccccccccccc--ccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh
Q 045388           45 SSCEICRERREN--DQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK  107 (214)
Q Consensus        45 ~~C~iC~~~~~~--~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~  107 (214)
                      -.|++|.+++..  ..++. -+||-++|+-||...-+. +      .=+||+  |......+.|+
T Consensus        15 d~cplcie~mditdknf~p-c~cgy~ic~fc~~~irq~-l------ngrcpa--crr~y~denv~   69 (480)
T COG5175          15 DYCPLCIEPMDITDKNFFP-CPCGYQICQFCYNNIRQN-L------NGRCPA--CRRKYDDENVR   69 (480)
T ss_pred             ccCcccccccccccCCccc-CCcccHHHHHHHHHHHhh-c------cCCChH--hhhhcccccee
Confidence            349999998653  45554 589999999998765332 3      237999  88766665554

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

Probab=85.80  E-value=0.55  Score=37.90  Aligned_cols=46  Identities=26%  Similarity=0.532  Sum_probs=34.4

Q ss_pred             cccccccccccccc-cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388           44 RSSCEICRERREND-QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS   99 (214)
Q Consensus        44 ~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~   99 (214)
                      ...||+|.+.+... ..+..+.|+|..-..|++.++..       . .+||.  |..
T Consensus       158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~-------~-y~CP~--C~~  204 (276)
T KOG1940|consen  158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICE-------G-YTCPI--CSK  204 (276)
T ss_pred             cCCCchhHHHhccccccCCccCcccchHHHHHHHHhcc-------C-CCCCc--ccc
Confidence            34499999986543 22337899999999999998642       2 68999  877

>PLN02189 cellulose synthase

Probab=85.26  E-value=0.74  Score=43.68  Aligned_cols=63  Identities=25%  Similarity=0.578  Sum_probs=48.7

Q ss_pred             CCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceecCCCCC
Q 045388          131 QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLH  210 (214)
Q Consensus       131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~GCnh  210 (214)
                      +...|.  -|+..+-.+..+   ...+-|..|+.-.|.-|..             +.++...+.||+|++...+.-|++.
T Consensus        33 ~~~~C~--iCgd~vg~~~~g---~~fvaC~~C~fpvCr~Cye-------------yer~eg~q~CpqCkt~Y~r~kgs~~   94 (1040)
T PLN02189         33 DGQVCE--ICGDEIGLTVDG---DLFVACNECGFPVCRPCYE-------------YERREGTQNCPQCKTRYKRLKGSPR   94 (1040)
T ss_pred             cCcccc--ccccccCcCCCC---CEEEeeccCCCccccchhh-------------hhhhcCCccCcccCCchhhccCCCC
Confidence            444677  788777766554   2778999999999999974             3456678999999999987777765


Q ss_pred             e
Q 045388          211 M  211 (214)
Q Consensus       211 m  211 (214)
                      +
T Consensus        95 v   95 (1040)
T PLN02189         95 V   95 (1040)
T ss_pred             c
Confidence            4

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=85.16  E-value=0.4  Score=23.26  Aligned_cols=22  Identities=36%  Similarity=1.008  Sum_probs=12.1

Q ss_pred             ccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388          134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRL  165 (214)
Q Consensus       134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~  165 (214)
                      +||  .|+.-+..+.        ..|+.||..
T Consensus         1 ~Cp--~CG~~~~~~~--------~fC~~CG~~   22 (23)
T PF13240_consen    1 YCP--NCGAEIEDDA--------KFCPNCGTP   22 (23)
T ss_pred             CCc--ccCCCCCCcC--------cchhhhCCc
Confidence            466  7776664322        236666653

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=84.79  E-value=0.44  Score=23.82  Aligned_cols=23  Identities=30%  Similarity=0.940  Sum_probs=13.1

Q ss_pred             cccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388          133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRL  165 (214)
Q Consensus       133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~  165 (214)
                      +.||  +|+..+..+.        ..|+.||+.
T Consensus         3 ~~Cp--~Cg~~~~~~~--------~fC~~CG~~   25 (26)
T PF13248_consen    3 MFCP--NCGAEIDPDA--------KFCPNCGAK   25 (26)
T ss_pred             CCCc--ccCCcCCccc--------ccChhhCCC
Confidence            4577  8887443322        237777653

>PRK04023 DNA polymerase II large subunit; Validated

Probab=84.72  E-value=0.89  Score=42.91  Aligned_cols=45  Identities=22%  Similarity=0.642  Sum_probs=30.1

Q ss_pred             CCcccCccCCCceeeecCCCCCCcCcccCCCCCh-----hhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccce
Q 045388          131 QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHR-----LFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIE  203 (214)
Q Consensus       131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~-----~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~ie  203 (214)
                      ..++||  .|+...          ..++||.||.     .||..|.....                ...||+|+..+.
T Consensus       625 g~RfCp--sCG~~t----------~~frCP~CG~~Te~i~fCP~CG~~~~----------------~y~CPKCG~El~  674 (1121)
T PRK04023        625 GRRKCP--SCGKET----------FYRRCPFCGTHTEPVYRCPRCGIEVE----------------EDECEKCGREPT  674 (1121)
T ss_pred             cCccCC--CCCCcC----------CcccCCCCCCCCCcceeCccccCcCC----------------CCcCCCCCCCCC
Confidence            456899  888663          4456999984     58888865322                245888887553

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

Probab=84.71  E-value=0.26  Score=38.44  Aligned_cols=37  Identities=27%  Similarity=0.728  Sum_probs=27.3

Q ss_pred             CcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCcccee
Q 045388          155 SESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIER  204 (214)
Q Consensus       155 ~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek  204 (214)
                      +.+++  ||+.|||-|.-.|-           ....+.+.||-|+..|..
T Consensus        60 PVvTl--CGHLFCWpClyqWl-----------~~~~~~~~cPVCK~~Vs~   96 (230)
T KOG0823|consen   60 PVVTL--CGHLFCWPCLYQWL-----------QTRPNSKECPVCKAEVSI   96 (230)
T ss_pred             CEEee--cccceehHHHHHHH-----------hhcCCCeeCCcccccccc
Confidence            66665  99999999986552           224567889999986643

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=84.61  E-value=0.69  Score=27.08  Aligned_cols=28  Identities=21%  Similarity=0.542  Sum_probs=18.3

Q ss_pred             ccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388          134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRL  165 (214)
Q Consensus       134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~  165 (214)
                      +||  .|+..+...+..  ....+.|+.|++.
T Consensus         2 FCp--~Cg~~l~~~~~~--~~~~~vC~~Cg~~   29 (52)
T smart00661        2 FCP--KCGNMLIPKEGK--EKRRFVCRKCGYE   29 (52)
T ss_pred             CCC--CCCCccccccCC--CCCEEECCcCCCe
Confidence            688  898877666432  1136678888753

>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit

Probab=84.59  E-value=0.75  Score=43.77  Aligned_cols=63  Identities=27%  Similarity=0.572  Sum_probs=48.7

Q ss_pred             CCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceecCCCCC
Q 045388          131 QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLH  210 (214)
Q Consensus       131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~GCnh  210 (214)
                      +..-|.  -|+..+-.+..+   ...+-|..|+.-.|.-|..             +.+....+.||+|++...+.-|++.
T Consensus        16 ~~qiCq--ICGD~vg~~~~G---e~FVAC~eC~FPVCrpCYE-------------YEr~eG~q~CPqCktrYkr~kgspr   77 (1079)
T PLN02638         16 GGQVCQ--ICGDNVGKTVDG---EPFVACDVCAFPVCRPCYE-------------YERKDGNQSCPQCKTKYKRHKGSPA   77 (1079)
T ss_pred             CCceee--ecccccCcCCCC---CEEEEeccCCCccccchhh-------------hhhhcCCccCCccCCchhhhcCCCC
Confidence            334577  788777666555   3778999999999999974             4456778999999999988778775


Q ss_pred             e
Q 045388          211 M  211 (214)
Q Consensus       211 m  211 (214)
                      +
T Consensus        78 v   78 (1079)
T PLN02638         78 I   78 (1079)
T ss_pred             c
Confidence            4

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=84.41  E-value=0.83  Score=41.57  Aligned_cols=13  Identities=31%  Similarity=0.723  Sum_probs=8.1

Q ss_pred             CCccCCCCCccce
Q 045388          191 QLRKCPNCKYHIE  203 (214)
Q Consensus       191 ~~k~CP~C~~~ie  203 (214)
                      +.+.||+||..+.
T Consensus        40 ~~~fC~~CG~~~~   52 (645)
T PRK14559         40 DEAHCPNCGAETG   52 (645)
T ss_pred             ccccccccCCccc
Confidence            4567777776543

>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=84.09  E-value=0.96  Score=23.72  Aligned_cols=28  Identities=25%  Similarity=0.552  Sum_probs=15.7

Q ss_pred             CcccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388          132 GIYCPFKDCSAKLVYENDGEDVLSESECPYCHRL  165 (214)
Q Consensus       132 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~  165 (214)
                      ..+|+  .|+........+    ....|+.|+..
T Consensus         3 ~rfC~--~CG~~t~~~~~g----~~r~C~~Cg~~   30 (32)
T PF09297_consen    3 HRFCG--RCGAPTKPAPGG----WARRCPSCGHE   30 (32)
T ss_dssp             TSB-T--TT--BEEE-SSS----S-EEESSSS-E
T ss_pred             CcccC--cCCccccCCCCc----CEeECCCCcCE
Confidence            45788  888888777664    56678888753

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

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

Probab=83.91  E-value=3.6  Score=34.81  Aligned_cols=59  Identities=20%  Similarity=0.353  Sum_probs=43.2

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhh
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKS  108 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~  108 (214)
                      +.+.|||=-+.-+.++.+..+.|||..+++=+.....    +|. ..++||=  |+..-...+.+.
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~----ng~-~sfKCPY--CP~e~~~~~~kq  391 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSK----NGS-QSFKCPY--CPVEQLASDTKQ  391 (394)
T ss_pred             ceeecccchhhccCCCCCeeeeccceecHHHHHHHhh----CCC-eeeeCCC--CCcccCHHhccc
Confidence            4678999777666666556899999999998877653    444 4789998  887666655443

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=83.87  E-value=0.15  Score=38.81  Aligned_cols=63  Identities=22%  Similarity=0.517  Sum_probs=35.5

Q ss_pred             CCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChH--HHHHHHHHHhCCCccCCCCCcccee
Q 045388          130 SQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGRE--ELMMRELVKKKQLRKCPNCKYHIER  204 (214)
Q Consensus       130 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~--~~~~~~~~~~~~~k~CP~C~~~iek  204 (214)
                      .+.+.||  =|...+..        +.+  ..||+.||+.|...|.....  ......+....+...||.|+..|..
T Consensus        16 ~~~~~Cp--ICld~~~d--------PVv--T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~   80 (193)
T PLN03208         16 GGDFDCN--ICLDQVRD--------PVV--TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE   80 (193)
T ss_pred             CCccCCc--cCCCcCCC--------cEE--cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence            3456777  66654311        222  26899999999887742100  0001111123445789999998854

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

Probab=82.86  E-value=0.73  Score=26.12  Aligned_cols=42  Identities=26%  Similarity=0.560  Sum_probs=20.6

Q ss_pred             ccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388           47 CEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPG   94 (214)
Q Consensus        47 C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~   94 (214)
                      |.+|.+-+.....-...+|+-++...|++.|++.+-      ..+||.
T Consensus         1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~------~~~CP~   42 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRS------NPKCPN   42 (43)
T ss_dssp             -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-S------S-B-TT
T ss_pred             CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCC------CCCCcC
Confidence            566766655444333457899999999999986432      227886

; PDB: 3NW0_A 2CT0_A.

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=82.66  E-value=0.39  Score=28.70  Aligned_cols=46  Identities=24%  Similarity=0.586  Sum_probs=29.8

Q ss_pred             cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHH
Q 045388           44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFD  104 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~  104 (214)
                      ...|-.|...-..   -..++|+|.+|..||...          .---||.  |+..+...
T Consensus         7 ~~~~~~~~~~~~~---~~~~pCgH~I~~~~f~~~----------rYngCPf--C~~~~~~~   52 (55)
T PF14447_consen    7 EQPCVFCGFVGTK---GTVLPCGHLICDNCFPGE----------RYNGCPF--CGTPFEFD   52 (55)
T ss_pred             ceeEEEccccccc---cccccccceeeccccChh----------hccCCCC--CCCcccCC
Confidence            3455555443222   226899999999998654          1236999  88877644

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

Probab=82.55  E-value=0.73  Score=34.51  Aligned_cols=30  Identities=33%  Similarity=0.960  Sum_probs=22.3

Q ss_pred             CCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCcccee
Q 045388          161 YCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIER  204 (214)
Q Consensus       161 ~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek  204 (214)
                      +||++||..|-+            ...  .+...||-|+..|.+
T Consensus       150 kCGHvFC~~Cik------------~al--k~~~~CP~C~kkIt~  179 (187)
T KOG0320|consen  150 KCGHVFCSQCIK------------DAL--KNTNKCPTCRKKITH  179 (187)
T ss_pred             ccchhHHHHHHH------------HHH--HhCCCCCCcccccch
Confidence            789999999953            222  356899999987643

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

Probab=82.17  E-value=2.2  Score=31.96  Aligned_cols=57  Identities=19%  Similarity=0.428  Sum_probs=36.6

Q ss_pred             ccccccccccccc----ccccccCCCCccccHHHHHHHHHHHhhCCCcccc---cCCCCCCCCcCc
Q 045388           44 RSSCEICRERREN----DQMFKIESCIHSFCSDCINKHVATKIQGGIITPV---TCPGPDCKSVLK  102 (214)
Q Consensus        44 ~~~C~iC~~~~~~----~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i---~CP~~~C~~~l~  102 (214)
                      ...|+|||.---.    +......+|+..|..-||..|++.-+-.++.+.|   .||-  |..++.
T Consensus       165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPY--CS~Pia  228 (234)
T KOG3268|consen  165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPY--CSDPIA  228 (234)
T ss_pred             hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCC--CCCcce
Confidence            4456666653211    1122256899999999999999887766554443   6777  766553

>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=82.02  E-value=1.7  Score=29.55  Aligned_cols=32  Identities=25%  Similarity=0.600  Sum_probs=25.9

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHH
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCIN   75 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~   75 (214)
                      ....|.+|...+..+. |...+|||.|...|++
T Consensus        77 ~~~~C~vC~k~l~~~~-f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   77 ESTKCSVCGKPLGNSV-FVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCCccCcCCcCCCce-EEEeCCCeEEeccccc
Confidence            3566999999998755 4467999999999975

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 [].

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=81.97  E-value=1.8  Score=34.42  Aligned_cols=58  Identities=21%  Similarity=0.583  Sum_probs=41.0

Q ss_pred             Ccccccccccccccccccccc-cCCCC-----ccccHHHHHHHHHHHhhCCCcccccCCCCCCCCc
Q 045388           41 PPSRSSCEICRERRENDQMFK-IESCI-----HSFCSDCINKHVATKIQGGIITPVTCPGPDCKSV  100 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~-~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~  100 (214)
                      ......|-|||.+-++...-. .-+|.     |-+...|+..|+.++-.....-++.||+  |+..
T Consensus        17 ~e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~Q--CqTE   80 (293)
T KOG3053|consen   17 QELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQ--CQTE   80 (293)
T ss_pred             cccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechh--hcch
Confidence            344578999999865543211 33553     6699999999998877655557899999  8753

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

Probab=81.87  E-value=1.3  Score=36.30  Aligned_cols=49  Identities=22%  Similarity=0.430  Sum_probs=33.7

Q ss_pred             CCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           39 SSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        39 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ....+.++||||++.+..+. ++ -+=||..|..|-..           ..-+||.  |...+.
T Consensus        43 ~~~~~lleCPvC~~~l~~Pi-~Q-C~nGHlaCssC~~~-----------~~~~CP~--Cr~~~g   91 (299)
T KOG3002|consen   43 LLDLDLLDCPVCFNPLSPPI-FQ-CDNGHLACSSCRTK-----------VSNKCPT--CRLPIG   91 (299)
T ss_pred             ccchhhccCchhhccCcccc-ee-cCCCcEehhhhhhh-----------hcccCCc--cccccc
Confidence            34556899999999988764 32 23489999999641           2346777  665554

>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins

Probab=81.10  E-value=1.7  Score=25.81  Aligned_cols=41  Identities=20%  Similarity=0.449  Sum_probs=23.5

Q ss_pred             cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      .++||.|...++...               |..++...=.... ..+.||.  |...+.
T Consensus         2 ~f~CP~C~~~~~~~~---------------L~~H~~~~H~~~~-~~v~CPi--C~~~~~   42 (54)
T PF05605_consen    2 SFTCPYCGKGFSESS---------------LVEHCEDEHRSES-KNVVCPI--CSSRVT   42 (54)
T ss_pred             CcCCCCCCCccCHHH---------------HHHHHHhHCcCCC-CCccCCC--chhhhh
Confidence            578999988544322               3444433322333 4689999  876443

Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.

>PLN02436 cellulose synthase A

Probab=80.95  E-value=1.4  Score=42.00  Aligned_cols=63  Identities=25%  Similarity=0.590  Sum_probs=47.7

Q ss_pred             CCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceecCCCCC
Q 045388          131 QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLH  210 (214)
Q Consensus       131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~GCnh  210 (214)
                      +..-|.  =|+-.+-.+..+   ...+-|..|+.-.|.-|..             +.++...+.||+|++...+.-|++.
T Consensus        35 ~~~iCq--ICGD~Vg~t~dG---e~FVACn~C~fpvCr~Cye-------------yer~eg~~~Cpqckt~Y~r~kgs~~   96 (1094)
T PLN02436         35 SGQTCQ--ICGDEIELTVDG---EPFVACNECAFPVCRPCYE-------------YERREGNQACPQCKTRYKRIKGSPR   96 (1094)
T ss_pred             CCcccc--ccccccCcCCCC---CEEEeeccCCCccccchhh-------------hhhhcCCccCcccCCchhhccCCCC
Confidence            334677  788776665554   2788999999999999974             3456678999999999887777765


Q ss_pred             e
Q 045388          211 M  211 (214)
Q Consensus       211 m  211 (214)
                      +
T Consensus        97 ~   97 (1094)
T PLN02436         97 V   97 (1094)
T ss_pred             c
Confidence            4

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

Probab=80.89  E-value=1.3  Score=27.41  Aligned_cols=19  Identities=21%  Similarity=0.543  Sum_probs=13.4

Q ss_pred             cccHHHHHHHHHHHhhCCC
Q 045388           68 SFCSDCINKHVATKIQGGI   86 (214)
Q Consensus        68 ~fC~~Cl~~~~~~~i~~~~   86 (214)
                      -||++||..|+...-.+..
T Consensus        11 gFCRNCLskWy~~aA~~~g   29 (68)
T PF06844_consen   11 GFCRNCLSKWYREAAEERG   29 (68)
T ss_dssp             S--HHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHHHhcC
Confidence            4999999999988776543

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

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

Probab=80.68  E-value=0.63  Score=37.66  Aligned_cols=45  Identities=27%  Similarity=0.483  Sum_probs=33.6

Q ss_pred             cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388           44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL  101 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l  101 (214)
                      .+-|.||-..|..+.   ...|+|.||..|....++        ..-+|++  |+...
T Consensus       241 Pf~c~icr~~f~~pV---vt~c~h~fc~~ca~~~~q--------k~~~c~v--C~~~t  285 (313)
T KOG1813|consen  241 PFKCFICRKYFYRPV---VTKCGHYFCEVCALKPYQ--------KGEKCYV--CSQQT  285 (313)
T ss_pred             Cccccccccccccch---hhcCCceeehhhhccccc--------cCCccee--ccccc
Confidence            467999999987764   478999999999776653        2347887  76533

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

Probab=80.22  E-value=2.5  Score=34.37  Aligned_cols=44  Identities=30%  Similarity=0.816  Sum_probs=32.6

Q ss_pred             ccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC
Q 045388           45 SSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS   99 (214)
Q Consensus        45 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~   99 (214)
                      ..|++|..-+..+  +....|+|.||.+||..-+.    +   ..+.||.  |..
T Consensus       275 LkCplc~~Llrnp--~kT~cC~~~fc~eci~~al~----d---sDf~Cpn--C~r  318 (427)
T COG5222         275 LKCPLCHCLLRNP--MKTPCCGHTFCDECIGTALL----D---SDFKCPN--CSR  318 (427)
T ss_pred             ccCcchhhhhhCc--ccCccccchHHHHHHhhhhh----h---ccccCCC--ccc
Confidence            7899998876544  23468999999999876543    2   4579999  753

---

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	214
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	7e-15
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	8e-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 = 66.4 bits (162), Expect = 7e-15
 Identities = 19/86 (22%), Positives = 43/86 (50%), Gaps = 2/86 (2%)

Query: 47  CEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS--VLKFD 104
           C++C      +QM  I  C   FC+ C+ ++V   I+ G+ T ++CP   C     L+ +
Sbjct: 8   CKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQEN 67

Query: 105 ACKSVLSKNVLELWEKALSQELIDAS 130
             + +++  +++ ++K   +    +S
Sbjct: 68  EIECMVAAEIMQRYKKLQFERSGPSS 93

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

 Score = 38.6 bits (90), Expect = 8e-05
 Identities = 11/21 (52%), Positives = 14/21 (66%)

Query: 193 RKCPNCKYHIERTGGCLHMTC 213
           ++CP C   IE+ GGC HM C
Sbjct: 7   KECPKCHVTIEKDGGCNHMVC 27

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	214
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.79
2jmo_A	80	Parkin; IBR, E3 ligase, zinc binding domain, RBR;	99.25
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.16
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	99.11
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	99.09
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	98.93
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	98.9
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.9
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	98.89
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	98.89
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	98.84
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	98.84
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	98.81
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	98.78
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	98.77
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	98.77
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	98.77
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.77
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	98.76
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	98.76
2ect_A	78	Ring finger protein 126; metal binding protein, st	98.74
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	98.74
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	98.72
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	98.72
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	98.72
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	98.71
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	98.7
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	98.67
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	98.67
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	98.66
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	98.66
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	98.66
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.65
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	98.64
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	98.62
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	98.59
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	98.59
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	98.58
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.58
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	98.5
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	98.49
1z6u_A	150	NP95-like ring finger protein isoform B; structura	98.46
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.43
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	98.41
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	98.4
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.38
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.37
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.36
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	98.33
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.3
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	98.23
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.21
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.19
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.18
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	98.17
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	98.14
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	98.07
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.04
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.02
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	97.96
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	97.96
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	97.93
2ea5_A	68	Cell growth regulator with ring finger domain prot	97.88
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	97.84
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	97.82
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	97.64
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	97.56
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	97.47
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	97.32
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	97.1
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	96.9
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	96.86
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	96.39
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	96.38
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	96.19
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	95.96
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	95.87
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	93.67
3nw0_A	238	Non-structural maintenance of chromosomes element	91.34
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	90.25
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	88.73
1z60_A	59	TFIIH basal transcription factor complex P44 subun	87.8
3qt1_I	133	DNA-directed RNA polymerases I, II, and III subun;	86.44
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	86.13
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	85.99
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	85.33
2d8v_A	67	Zinc finger FYVE domain-containing protein 19; zfy	85.05
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	84.38
2hu9_A	130	MERP, mercuric transport protein periplasmic compo	83.08
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	82.9
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	82.5
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	82.1
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	81.48
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	80.18

>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=99.79  E-value=1.1e-19  Score=122.84  Aligned_cols=88  Identities=22%  Similarity=0.503  Sum_probs=78.4

Q ss_pred             cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCc--CcHHHHhhcCCHHHHHHHH
Q 045388           42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSV--LKFDACKSVLSKNVLELWE  119 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~--l~~~~~~~~l~~~~~~~~~  119 (214)
                      .+.++|+||+++++.+.++.+..|+|.||++||+.|+..++.+|.+.+++||..+|...  +..+.++.+|+++++++|+
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            45789999999998887766668999999999999999999888756899999999999  9999999999999999999


Q ss_pred             HHHHHHHhcC
Q 045388          120 KALSQELIDA  129 (214)
Q Consensus       120 ~~~~~~~~~~  129 (214)
                      +++.+.++..
T Consensus        83 ~~~~~~~v~~   92 (94)
T 1wim_A           83 KLQFERSGPS   92 (94)
T ss_dssp             HHHHHSSCSS
T ss_pred             HHHHHhhhcc
Confidence            9888876654

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

Probab=99.25  E-value=4.1e-14  Score=91.99  Aligned_cols=64  Identities=23%  Similarity=0.510  Sum_probs=56.3

Q ss_pred             cCCHHHHHHHHHHHHHHHhcCCCCcccCccCCCceeeecCCCCCCcCcccCC-----CCChhhccccCCCCCC
Q 045388          109 VLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECP-----YCHRLFCAHCYVPWHP  176 (214)
Q Consensus       109 ~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~-----~C~~~~C~~C~~~~h~  176 (214)
                      +|+++++++|++++.++++..++.+|||.|+|++++..+..    ...+.|+     .|+..||+.|+.+||.
T Consensus         2 ~l~~~~~~rY~~~~~e~~v~~~~~~~CP~p~C~~~v~~~~~----~~~v~C~~~~~~~C~~~FC~~C~~~wH~   70 (80)
T 2jmo_A            2 HMGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPD----QRKVTCEGGNGLGCGFAFCRECKEAYHE   70 (80)
T ss_dssp             CCCCCCCCSCCCSSSCCSSCCCSSCCCCSSSCCCCCCCCSC----TTSBCTTSSSTTCCSCCEETTTTEECCS
T ss_pred             CCCHHHHHHHHHHHHHHHhhhCCcEECCCCCCCcccEECCC----CCcCCCCCCCCCCCCCeeccccCccccC
Confidence            57788899999999998888777999999999999987753    2668898     9999999999999997

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

Probab=99.16  E-value=5.2e-12  Score=90.02  Aligned_cols=117  Identities=23%  Similarity=0.561  Sum_probs=79.7

Q ss_pred             ccccccccccccccc----cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCHHHHHHH
Q 045388           43 SRSSCEICRERREND----QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELW  118 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~~~~~~~  118 (214)
                      +..+|+||++.+..+    .....+.|||.||.+||..|+..        ...||.  |...+....+..+.        
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~--------~~~CP~--Cr~~~~~~~l~~l~--------   67 (133)
T 4ap4_A            6 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN--------ANTCPT--CRKKINHKRYHPIY--------   67 (133)
T ss_dssp             CSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTT--------CSBCTT--TCCBCTTTCEEECB--------
T ss_pred             CCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHh--------CCCCCC--CCCcCccccccccc--------
Confidence            468999999998654    22236799999999999999852        248999  98888665544331        


Q ss_pred             HHHHHHHHhcCCCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCC
Q 045388          119 EKALSQELIDASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNC  198 (214)
Q Consensus       119 ~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C  198 (214)
                               ...+...|+  -|...+......   ........||..||..|...|            .+.  .+.||.|
T Consensus        68 ---------i~~~~~~C~--iC~~~~~~~~~~---~~~~~~~~CgH~fc~~Ci~~~------------~~~--~~~CP~C  119 (133)
T 4ap4_A           68 ---------IGSGTVSCP--ICMDGYSEIVQN---GRLIVSTECGHVFCSQCLRDS------------LKN--ANTCPTC  119 (133)
T ss_dssp             ---------CSSSSCBCT--TTCCBHHHHHHT---TCCEEEETTSBEEEHHHHHHH------------HHH--CSBCTTT
T ss_pred             ---------cCCCCCCCC--CCCCcccccccc---CcceEeCCCCChhhHHHHHHH------------HHc--CCCCCCC
Confidence                     124556788  787665432111   012223468999999996543            332  3699999


Q ss_pred             Cccceec
Q 045388          199 KYHIERT  205 (214)
Q Consensus       199 ~~~iek~  205 (214)
                      +..|.++
T Consensus       120 r~~~~~~  126 (133)
T 4ap4_A          120 RKKINHK  126 (133)
T ss_dssp             CCBCCGG
T ss_pred             CCcCChh
Confidence            9998765

>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=99.11  E-value=1e-12  Score=86.72  Aligned_cols=72  Identities=28%  Similarity=0.676  Sum_probs=58.7

Q ss_pred             HHHHHHHHHHHHHHHhcC-CCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCC---CCChHHHHHHHHH
Q 045388          112 KNVLELWEKALSQELIDA-SQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPW---HPGREELMMRELV  187 (214)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~---h~~~~~~~~~~~~  187 (214)
                      ++++++|++++.++++.. ++.+|||  +|+++++.+..    ...+.|+.|+..||+.|+.+|   |.+.....++.|.
T Consensus         4 ~~~~e~y~~~l~e~~v~~~~~~~wCP--~C~~~~~~~~~----~~~v~C~~C~~~FC~~C~~~w~~~H~~~sC~~~~~w~   77 (86)
T 2ct7_A            4 GSSGALFHKKLTEGVLMRDPKFLWCA--QCSFGFIYERE----QLEATCPQCHQTFCVRCKRQWEEQHRGRSCEDFQNWK   77 (86)
T ss_dssp             CCCCCSSSSCCCCSCCCSCCCEECCS--SSCCCEECCCS----CSCEECTTTCCEECSSSCSBCCTTTTTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCEeECc--CCCchheecCC----CCceEeCCCCCccccccCCchhhcCCCCChHHHHHHH
Confidence            455677888888887765 4566999  99999887654    366899999999999999999   9998888888877


Q ss_pred             Hh
Q 045388          188 KK  189 (214)
Q Consensus       188 ~~  189 (214)
                      +.
T Consensus        78 ~~   79 (86)
T 2ct7_A           78 RM   79 (86)
T ss_dssp             HH
T ss_pred             Hh
Confidence            64

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

Probab=99.09  E-value=2.9e-11  Score=73.72  Aligned_cols=26  Identities=42%  Similarity=1.085  Sum_probs=23.9

Q ss_pred             hCCCccCCCCCccceecCCCCCeecC
Q 045388          189 KKQLRKCPNCKYHIERTGGCLHMTCL  214 (214)
Q Consensus       189 ~~~~k~CP~C~~~iek~~GCnhm~C~  214 (214)
                      ..++|+||+|+++|||++|||||+|+
T Consensus         3 ~~~~k~CP~C~~~Iek~~GCnhmtC~   28 (60)
T 1wd2_A            3 AANTKECPKCHVTIEKDGGCNHMVCR   28 (60)
T ss_dssp             CCCCCCCTTTCCCCSSCCSCCSSSCC
T ss_pred             cccceECcCCCCeeEeCCCCCcEEEC
Confidence            35789999999999999999999995

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

Probab=98.93  E-value=7.4e-10  Score=73.11  Aligned_cols=64  Identities=27%  Similarity=0.609  Sum_probs=47.7

Q ss_pred             CCCcccccccccccccccccc-cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhc
Q 045388           39 SSPPSRSSCEICRERRENDQM-FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSV  109 (214)
Q Consensus        39 ~~~~~~~~C~iC~~~~~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~  109 (214)
                      ....+..+|+||++.+...+. ...+.|+|.||..|+..|+...    . ..+.||.  |...+...++..+
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~----~-~~~~CP~--Cr~~~~~~~i~~l   74 (88)
T 2ct2_A           10 DALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASS----I-NGVRCPF--CSKITRITSLTQL   74 (88)
T ss_dssp             CCCCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHC----S-SCBCCTT--TCCCBCCSSTTTS
T ss_pred             hhccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcC----C-CCcCCCC--CCCcccchhHHHH
Confidence            344557899999999876432 3357999999999999999754    1 3579999  8887766655443

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

Probab=98.90  E-value=9.8e-10  Score=71.93  Aligned_cols=60  Identities=22%  Similarity=0.478  Sum_probs=47.2

Q ss_pred             CCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHH
Q 045388           40 SPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC  106 (214)
Q Consensus        40 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~  106 (214)
                      ...+..+|+||++.+..+.   .+.|+|.||..|+..|+......+.  .+.||.  |...+..+++
T Consensus        15 ~~~~~~~C~IC~~~~~~p~---~~~CgH~fC~~Ci~~~~~~~~~~~~--~~~CP~--Cr~~~~~~~~   74 (85)
T 2ecv_A           15 NVKEEVTCPICLELLTQPL---SLDCGHSFCQACLTANHKKSMLDKG--ESSCPV--CRISYQPENI   74 (85)
T ss_dssp             CCCCCCCCTTTCSCCSSCB---CCSSSCCBCTTHHHHHHHHHHHTTS--CCCCTT--TCCSSCSSSC
T ss_pred             HccCCCCCCCCCcccCCce---eCCCCCHHHHHHHHHHHHHhhcCCC--CCcCCC--CCCccCHHhc
Confidence            3445789999999987653   4689999999999999988765544  689999  8887765443

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

Probab=98.90  E-value=5.7e-10  Score=82.94  Aligned_cols=85  Identities=25%  Similarity=0.423  Sum_probs=59.4

Q ss_pred             CCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCHHHHHHHH
Q 045388           40 SPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWE  119 (214)
Q Consensus        40 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~~~~~~~~  119 (214)
                      ...+.+.|+||++.+..+.   .+.|||.||..||..|+...       ..+||.  |...+..+++.   ....++   
T Consensus        14 ~~~~~~~C~IC~~~~~~pv---~~~CgH~fC~~Ci~~~~~~~-------~~~CP~--Cr~~~~~~~~~---~~~~~~---   75 (170)
T 3hcs_A           14 PLESKYECPICLMALREAV---QTPCGHRFCKACIIKSIRDA-------GHKCPV--DNEILLENQLF---PDNFAK---   75 (170)
T ss_dssp             CCCGGGBCTTTCSBCSSEE---ECTTSCEEEHHHHHHHHHHH-------CSBCTT--TCCBCCGGGCE---ECHHHH---
T ss_pred             CCCCCCCCCCCChhhcCcE---ECCCCCHHHHHHHHHHHHhC-------CCCCCC--CccCcchhhhh---hhHHHH---
Confidence            3456789999999987653   36899999999999998643       238999  88888665422   211111   


Q ss_pred             HHHHHHHhcCCCCcccCccCCCceeeecC
Q 045388          120 KALSQELIDASQGIYCPFKDCSAKLVYEN  148 (214)
Q Consensus       120 ~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~  148 (214)
                           +.+. .-.++||+.+|...+....
T Consensus        76 -----~~i~-~l~v~C~n~GC~~~~~~~~   98 (170)
T 3hcs_A           76 -----REIL-SLMVKCPNEGCLHKMELRH   98 (170)
T ss_dssp             -----HHHH-TSEEECCSTTCCCEEEGGG
T ss_pred             -----HHHh-hcccCCCCCCCCceecHhH
Confidence                 1111 3457899999998887665

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

Probab=98.89  E-value=2.7e-10  Score=72.61  Aligned_cols=56  Identities=25%  Similarity=0.533  Sum_probs=42.5

Q ss_pred             CCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHH
Q 045388           39 SSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFD  104 (214)
Q Consensus        39 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~  104 (214)
                      ....+..+|+||++.+..+.   .+.|+|.||..|+..|+..    .. ....||.  |...+..+
T Consensus        15 ~~~~~~~~C~IC~~~~~~~~---~~~CgH~fC~~Ci~~~~~~----~~-~~~~CP~--Cr~~~~~~   70 (73)
T 2ysl_A           15 NKLQEEVICPICLDILQKPV---TIDCGHNFCLKCITQIGET----SC-GFFKCPL--CKTSVRKN   70 (73)
T ss_dssp             CCCCCCCBCTTTCSBCSSEE---ECTTCCEEEHHHHHHHCSS----SC-SCCCCSS--SCCCCCCC
T ss_pred             HhCccCCEeccCCcccCCeE---EcCCCChhhHHHHHHHHHc----CC-CCCCCCC--CCCcCCcc
Confidence            33456789999999887543   4599999999999999751    12 3679999  88877544

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

Probab=98.89  E-value=1.5e-09  Score=67.04  Aligned_cols=48  Identities=25%  Similarity=0.486  Sum_probs=37.2

Q ss_pred             CCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388           39 SSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPG   94 (214)
Q Consensus        39 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~   94 (214)
                      ....+..+|+||++.+..+.   .+.|+|.||..||..|+..   .+  ...+||.
T Consensus        15 ~~~~~~~~C~IC~~~~~~p~---~~~CgH~fC~~Ci~~~~~~---~~--~~~~CP~   62 (63)
T 2ysj_A           15 NKLQEEVICPICLDILQKPV---TIDCGHNFCLKCITQIGET---SC--GFFKCPL   62 (63)
T ss_dssp             CCCCCCCBCTTTCSBCSSCE---ECTTSSEECHHHHHHHHHH---CS--SCCCCSC
T ss_pred             HhCccCCCCCcCCchhCCeE---EeCCCCcchHHHHHHHHHc---CC--CCCcCcC
Confidence            34456789999999987653   4699999999999999974   12  2568987

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

Probab=98.84  E-value=2.2e-09  Score=66.95  Aligned_cols=53  Identities=21%  Similarity=0.550  Sum_probs=41.8

Q ss_pred             CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHH
Q 045388           41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDA  105 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~  105 (214)
                      ..+..+|+||++.+..+.   .+.|||.||..|+..|+.    .   ....||.  |+..+..++
T Consensus        12 ~~~~~~C~IC~~~~~~p~---~~~CgH~fC~~Ci~~~~~----~---~~~~CP~--Cr~~~~~~~   64 (66)
T 2ecy_A           12 VEDKYKCEKCHLVLCSPK---QTECGHRFCESCMAALLS----S---SSPKCTA--CQESIVKDK   64 (66)
T ss_dssp             CCCCEECTTTCCEESSCC---CCSSSCCCCHHHHHHHHT----T---SSCCCTT--TCCCCCTTT
T ss_pred             CCcCCCCCCCChHhcCee---ECCCCCHHHHHHHHHHHH----h---CcCCCCC--CCcCCChhh
Confidence            345789999999987654   369999999999999985    1   2468999  888776543

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

Probab=98.84  E-value=1.9e-09  Score=70.49  Aligned_cols=59  Identities=25%  Similarity=0.542  Sum_probs=45.7

Q ss_pred             CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHH
Q 045388           41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC  106 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~  106 (214)
                      ..+..+|+||++.+..+.   .+.|+|.||..|+..|+......+  ....||.  |...+..+++
T Consensus        16 ~~~~~~C~IC~~~~~~p~---~~~CgH~fC~~Ci~~~~~~~~~~~--~~~~CP~--Cr~~~~~~~~   74 (85)
T 2ecw_A           16 IKEEVTCPICLELLKEPV---SADCNHSFCRACITLNYESNRNTD--GKGNCPV--CRVPYPFGNL   74 (85)
T ss_dssp             CCTTTSCTTTCSCCSSCE---ECTTSCCBCHHHHHHHHHHSBCTT--SCBCCTT--TCCCCCTTCC
T ss_pred             CccCCCCcCCChhhCcce---eCCCCCHHHHHHHHHHHHhccCCC--CCCCCCC--CCCcCCHHhC
Confidence            345789999999987654   468999999999999998755323  3689999  8888766543

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

Probab=98.81  E-value=4.6e-10  Score=72.61  Aligned_cols=60  Identities=23%  Similarity=0.453  Sum_probs=45.4

Q ss_pred             CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHH
Q 045388           41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC  106 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~  106 (214)
                      ..+..+|+||++.+..+.   .+.|||.||..|+..|+........ ....||.  |...+...++
T Consensus         9 ~~~~~~C~IC~~~~~~p~---~l~CgH~fC~~Ci~~~~~~~~~~~~-~~~~CP~--Cr~~~~~~~l   68 (79)
T 2egp_A            9 VQEEVTCPICLELLTEPL---SLDCGHSLCRACITVSNKEAVTSMG-GKSSCPV--CGISYSFEHL   68 (79)
T ss_dssp             CCCCCEETTTTEECSSCC---CCSSSCCCCHHHHSCCCCCCSSSCC-CCCCCSS--SCCCCCSSGG
T ss_pred             cccCCCCcCCCcccCCee---ECCCCCHHHHHHHHHHHHhcccCCC-CCCcCCC--CCCcCCHhhC
Confidence            345789999999987654   4689999999999999865433323 4689999  8887765544

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

Probab=98.78  E-value=4.3e-09  Score=66.82  Aligned_cols=55  Identities=27%  Similarity=0.646  Sum_probs=42.5

Q ss_pred             CCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHH
Q 045388           40 SPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC  106 (214)
Q Consensus        40 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~  106 (214)
                      ...+..+|+||++.+..+.  ....|+|.||..|+..|+..        ...||.  |...+...++
T Consensus        11 ~~~~~~~C~IC~~~~~~p~--~~~~CgH~fC~~Ci~~~~~~--------~~~CP~--Cr~~~~~~~~   65 (72)
T 2djb_A           11 ELTPYILCSICKGYLIDAT--TITECLHTFCKSCIVRHFYY--------SNRCPK--CNIVVHQTQP   65 (72)
T ss_dssp             CCCGGGSCTTTSSCCSSCE--ECSSSCCEECHHHHHHHHHH--------CSSCTT--TCCCCCSSCS
T ss_pred             hcCCCCCCCCCChHHHCcC--EECCCCCHHHHHHHHHHHHc--------CCcCCC--cCcccCcccc
Confidence            3456789999999887643  23599999999999999964        357999  8887765543

>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=98.77  E-value=3.9e-09  Score=72.83  Aligned_cols=71  Identities=25%  Similarity=0.439  Sum_probs=51.2

Q ss_pred             cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhh-cCCHHHHHHHHHHH
Q 045388           44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKS-VLSKNVLELWEKAL  122 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~-~l~~~~~~~~~~~~  122 (214)
                      ...|+||++.+..+.   .+.|||.||..|+..|+...    . ..+.||.  |...+...++.. ....++.+.+.+.+
T Consensus        21 ~~~C~IC~~~~~~p~---~~~CgH~fC~~Ci~~~~~~~----~-~~~~CP~--Cr~~~~~~~~~~~~~l~~~~~~~~~~~   90 (112)
T 1jm7_A           21 ILECPICLELIKEPV---STKCDHIFCKFCMLKLLNQK----K-GPSQCPL--CKNDITKRSLQESTRFSQLVEELLKII   90 (112)
T ss_dssp             HTSCSSSCCCCSSCC---BCTTSCCCCSHHHHHHHHSS----S-SSCCCTT--TSCCCCTTTCBCCCSSSHHHHHHHHHH
T ss_pred             CCCCcccChhhcCeE---ECCCCCHHHHHHHHHHHHhC----C-CCCCCcC--CCCcCCHhhcCccHHHHHHHHHHHHHH
Confidence            478999999886653   46899999999999998743    2 3478999  988887766543 33355566665554


Q ss_pred             HH
Q 045388          123 SQ  124 (214)
Q Consensus       123 ~~  124 (214)
                      ..
T Consensus        91 ~~   92 (112)
T 1jm7_A           91 CA   92 (112)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

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

Probab=98.77  E-value=1.6e-09  Score=68.53  Aligned_cols=57  Identities=26%  Similarity=0.688  Sum_probs=43.5

Q ss_pred             Ccccccccccccccccc----cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh
Q 045388           41 PPSRSSCEICRERREND----QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK  107 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~  107 (214)
                      ..+..+|+||++.+..+    .....+.|+|.||..|+..|+...        ..||.  |...+...++.
T Consensus         7 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~--------~~CP~--Cr~~~~~~~~~   67 (71)
T 3ng2_A            7 PSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA--------NTCPT--CRKKINHKRYH   67 (71)
T ss_dssp             CTTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHC--------SBCTT--TCCBCCCCSCC
T ss_pred             CCCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcC--------CCCCC--CCCccChhhee
Confidence            34568999999998654    223368999999999999998632        48999  88887655544

>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=98.77  E-value=5.6e-09  Score=62.52  Aligned_cols=51  Identities=22%  Similarity=0.483  Sum_probs=39.4

Q ss_pred             cccccccccccccccc-cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           42 PSRSSCEICRERREND-QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~-~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ....+|+||++.+... ..+..+.|+|.||..|+..|+...        .+||.  |...+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~--------~~CP~--Cr~~~~   54 (55)
T 2ecm_A            3 SGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEG--------YRCPL--CSGPSS   54 (55)
T ss_dssp             SCCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHT--------CCCTT--SCCSSC
T ss_pred             CCCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcC--------CcCCC--CCCcCC
Confidence            3467899999998542 234468999999999999998753        57999  877653

>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=98.77  E-value=3.2e-09  Score=73.88  Aligned_cols=83  Identities=29%  Similarity=0.538  Sum_probs=57.9

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCHHHHHHHHHHH
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWEKAL  122 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~~~~~~~~~~~  122 (214)
                      +.+.|+||++.+..+.   .+.|||.||..|+..|+...       ...||.  |...+...++... ...+.    +.+
T Consensus        22 ~~~~C~IC~~~~~~p~---~~~CgH~fC~~Ci~~~~~~~-------~~~CP~--Cr~~~~~~~~~~~-~~~l~----~~i   84 (116)
T 1rmd_A           22 KSISCQICEHILADPV---ETSCKHLFCRICILRCLKVM-------GSYCPS--CRYPCFPTDLESP-VKSFL----NIL   84 (116)
T ss_dssp             HHTBCTTTCSBCSSEE---ECTTSCEEEHHHHHHHHHHT-------CSBCTT--TCCBCCGGGCBCC-CHHHH----HHH
T ss_pred             CCCCCCCCCcHhcCcE---EcCCCCcccHHHHHHHHhHC-------cCcCCC--CCCCCCHhhcccc-HHHHH----HHH
Confidence            4688999999987653   36999999999999998752       347999  9988877654432 11111    111


Q ss_pred             HHHHhcCCCCcccCccCCCceeeecC
Q 045388          123 SQELIDASQGIYCPFKDCSAKLVYEN  148 (214)
Q Consensus       123 ~~~~~~~~~~~~Cp~~~C~~~~~~~~  148 (214)
                            ..-.++||+.+|+..+...+
T Consensus        85 ------~~l~v~C~~~gC~~~~~~~~  104 (116)
T 1rmd_A           85 ------NSLMVKCPAQDCNEEVSLEK  104 (116)
T ss_dssp             ------HHCEEECCSTTCCCEEEHHH
T ss_pred             ------HHhcCCCCCCCCcchhhHhH
Confidence                  12456899889998776543

>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=98.76  E-value=1.1e-08  Score=64.27  Aligned_cols=53  Identities=23%  Similarity=0.574  Sum_probs=40.9

Q ss_pred             CCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           40 SPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        40 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ......+|+||++.+.....+..+.|+|.||..|+..|+..        ..+||.  |...+.
T Consensus        10 ~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~--------~~~CP~--Cr~~~~   62 (69)
T 2kiz_A           10 EEDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLIT--------NKKCPI--CRVDIE   62 (69)
T ss_dssp             STTCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHH--------CSBCTT--TCSBSC
T ss_pred             cCCCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHc--------CCCCcC--cCcccc
Confidence            34456889999999865544556899999999999999864        135999  876654

>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=98.76  E-value=1.4e-08  Score=70.84  Aligned_cols=86  Identities=24%  Similarity=0.423  Sum_probs=60.0

Q ss_pred             CCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCHHHHHHHH
Q 045388           40 SPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKNVLELWE  119 (214)
Q Consensus        40 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~~~~~~~~  119 (214)
                      ...+.+.|+||++.+..+.   .+.|||.||..|+..|+...       ...||.  |...+...++   .....++   
T Consensus        14 ~~~~~~~C~IC~~~~~~p~---~~~CgH~fC~~Ci~~~~~~~-------~~~CP~--Cr~~~~~~~~---~~~~~l~---   75 (118)
T 3hct_A           14 PLESKYECPICLMALREAV---QTPCGHRFCKACIIKSIRDA-------GHKCPV--DNEILLENQL---FPDNFAK---   75 (118)
T ss_dssp             CCCGGGBCTTTCSBCSSEE---ECTTSCEEEHHHHHHHHHHH-------CSBCTT--TCCBCCGGGC---EECHHHH---
T ss_pred             CCCCCCCCCcCChhhcCeE---ECCcCChhhHHHHHHHHhhC-------CCCCCC--CCCCcCHHhc---ccCHHHH---
Confidence            3455789999999887653   46899999999999998753       238999  8888866432   2221111   


Q ss_pred             HHHHHHHhcCCCCcccCccCCCceeeecCC
Q 045388          120 KALSQELIDASQGIYCPFKDCSAKLVYEND  149 (214)
Q Consensus       120 ~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~  149 (214)
                           +.+. .-.++||+.+|...+...+.
T Consensus        76 -----~~i~-~l~v~C~n~gC~~~~~~~~l   99 (118)
T 3hct_A           76 -----REIL-SLMVKCPNEGCLHKMELRHL   99 (118)
T ss_dssp             -----HHHH-TSEEECSSTTCCCEEEGGGS
T ss_pred             -----HHHc-cceeECCCCCCCCEEeeHHH
Confidence                 1122 34578999999988877654

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

Probab=98.74  E-value=5.2e-09  Score=67.46  Aligned_cols=57  Identities=23%  Similarity=0.473  Sum_probs=44.0

Q ss_pred             CCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHH
Q 045388           39 SSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDA  105 (214)
Q Consensus        39 ~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~  105 (214)
                      .......+|+||++.+.....+..+.|+|.||..|+..|+..        ...||.  |...+....
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~--------~~~CP~--Cr~~~~~~~   66 (78)
T 2ect_A           10 EHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQ--------HDSCPV--CRKSLTGQN   66 (78)
T ss_dssp             TTSSSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTT--------TCSCTT--TCCCCCCSC
T ss_pred             ccCCCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHc--------CCcCcC--cCCccCCcc
Confidence            334557899999999877655556799999999999999842        247999  887776543

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

Probab=98.74  E-value=1.2e-08  Score=65.03  Aligned_cols=52  Identities=23%  Similarity=0.522  Sum_probs=41.0

Q ss_pred             CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      .....+|+||++.+.....+..+.|+|.||..|+..|+...        ..||.  |...+.
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~--------~~CP~--Cr~~~~   63 (74)
T 2ep4_A           12 LNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVR--------KVCPL--CNMPVL   63 (74)
T ss_dssp             CCCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHC--------SBCTT--TCCBCS
T ss_pred             CCCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcC--------CcCCC--cCcccc
Confidence            34467899999998876655556899999999999998642        37999  876653

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

Probab=98.72  E-value=6.3e-09  Score=67.04  Aligned_cols=66  Identities=24%  Similarity=0.408  Sum_probs=48.1

Q ss_pred             cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh-hcCCHHHHHHHH
Q 045388           42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK-SVLSKNVLELWE  119 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~-~~l~~~~~~~~~  119 (214)
                      .+.+.|+||++.+..+.   .+.|||.||+.|+..|+..    +   ..+||.  |+..+...++. +....+.++.|.
T Consensus         6 ~~~~~C~IC~~~~~~Pv---~~~CgH~fc~~Ci~~~~~~----~---~~~CP~--C~~~~~~~~l~~n~~l~~~i~~~~   72 (78)
T 1t1h_A            6 PEYFRCPISLELMKDPV---IVSTGQTYERSSIQKWLDA----G---HKTCPK--SQETLLHAGLTPNYVLKSLIALWC   72 (78)
T ss_dssp             SSSSSCTTTSCCCSSEE---EETTTEEEEHHHHHHHHTT----T---CCBCTT--TCCBCSSCCCEECTTTHHHHHHHH
T ss_pred             cccCCCCCccccccCCE---EcCCCCeecHHHHHHHHHH----C---cCCCCC--CcCCCChhhCccCHHHHHHHHHHH
Confidence            45789999999887653   3689999999999999852    1   468999  88887655432 344455555554

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

Probab=98.72  E-value=1.2e-08  Score=64.00  Aligned_cols=54  Identities=28%  Similarity=0.717  Sum_probs=41.1

Q ss_pred             CCCcccccccccccccccc----cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           39 SSPPSRSSCEICRERREND----QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        39 ~~~~~~~~C~iC~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      .......+|+||++.+..+    ..+..+.|+|.||..|+..|+..        ...||.  |...+.
T Consensus        10 ~~~~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~--------~~~CP~--Cr~~~~   67 (69)
T 2ea6_A           10 LRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN--------ANTCPT--CRKKIN   67 (69)
T ss_dssp             CCTTCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHH--------CSSCTT--TCCCCC
T ss_pred             cCCCCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHc--------CCCCCC--CCCccC
Confidence            3445678999999998754    22236899999999999999874        247999  877664

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

Probab=98.72  E-value=6.1e-09  Score=65.90  Aligned_cols=56  Identities=21%  Similarity=0.409  Sum_probs=43.7

Q ss_pred             CCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhh
Q 045388           40 SPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKS  108 (214)
Q Consensus        40 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~  108 (214)
                      ......+|+||++.+....   .+.|+|.||..|+..|+..        ...||.  |...+..+++..
T Consensus        11 ~~~~~~~C~IC~~~~~~~~---~~~CgH~fC~~Ci~~~~~~--------~~~CP~--Cr~~~~~~~~~~   66 (71)
T 2d8t_A           11 PSLTVPECAICLQTCVHPV---SLPCKHVFCYLCVKGASWL--------GKRCAL--CRQEIPEDFLDS   66 (71)
T ss_dssp             SSSSCCBCSSSSSBCSSEE---EETTTEEEEHHHHHHCTTC--------SSBCSS--SCCBCCHHHHSC
T ss_pred             cCCCCCCCccCCcccCCCE---EccCCCHHHHHHHHHHHHC--------CCcCcC--cCchhCHhhccC
Confidence            3455789999999886543   4689999999999999742        258999  999888776643

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

Probab=98.71  E-value=2.6e-09  Score=65.99  Aligned_cols=56  Identities=25%  Similarity=0.655  Sum_probs=42.7

Q ss_pred             ccccccccccccccc----cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhh
Q 045388           43 SRSSCEICRERREND----QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKS  108 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~  108 (214)
                      +..+|+||++.+..+    +.+..+.|+|.||.+|+..|+..        ...||.  |...+..+++..
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~--------~~~CP~--Cr~~~~~~~~~~   61 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN--------ANTCPT--CRKKINHKRYHP   61 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHH--------CSBCTT--TCCBCTTTCEEE
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHc--------CCCCCC--CCccCCccceee
Confidence            357899999998654    22236799999999999999874        248999  888887655443

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

Probab=98.70  E-value=6.9e-09  Score=69.04  Aligned_cols=50  Identities=26%  Similarity=0.656  Sum_probs=39.4

Q ss_pred             CcccccccccccccccccccccCC-CCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388           41 PPSRSSCEICRERRENDQMFKIES-CIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL  101 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l  101 (214)
                      ..+.++|+||++.+..+.   .+. |||.||..||..|+...      ....||.  |...+
T Consensus        10 ~~~~~~C~IC~~~~~~p~---~~~~CgH~fC~~Ci~~~~~~~------~~~~CP~--Cr~~~   60 (92)
T 3ztg_A           10 IPDELLCLICKDIMTDAV---VIPCCGNSYCDECIRTALLES------DEHTCPT--CHQND   60 (92)
T ss_dssp             CCTTTEETTTTEECSSCE---ECTTTCCEECHHHHHHHHHHC------TTCCCTT--TCCSS
T ss_pred             CCcCCCCCCCChhhcCce---ECCCCCCHHHHHHHHHHHHhc------CCCcCcC--CCCcC
Confidence            345789999999887653   456 99999999999998632      1368999  88775

>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=98.67  E-value=1.5e-08  Score=68.51  Aligned_cols=55  Identities=22%  Similarity=0.570  Sum_probs=43.5

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhh
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKS  108 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~  108 (214)
                      +.++|+||++.+..+.  ..+.|||.||..||..|+...       ...||.  |...+..+++..
T Consensus        21 ~~~~C~IC~~~~~~p~--~~~~CgH~FC~~Ci~~~~~~~-------~~~CP~--Cr~~~~~~~l~~   75 (100)
T 3lrq_A           21 EVFRCFICMEKLRDAR--LCPHCSKLCCFSCIRRWLTEQ-------RAQCPH--CRAPLQLRELVN   75 (100)
T ss_dssp             HHTBCTTTCSBCSSEE--ECTTTCCEEEHHHHHHHHHHT-------CSBCTT--TCCBCCGGGCEE
T ss_pred             CCCCCccCCccccCcc--ccCCCCChhhHHHHHHHHHHC-------cCCCCC--CCCcCCHHHhHh
Confidence            4688999999987543  237999999999999998753       258999  998887766543

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

Probab=98.67  E-value=2e-08  Score=63.99  Aligned_cols=52  Identities=25%  Similarity=0.637  Sum_probs=40.2

Q ss_pred             CCCcccccccccccccccccccccCC-CCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388           39 SSPPSRSSCEICRERRENDQMFKIES-CIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL  101 (214)
Q Consensus        39 ~~~~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l  101 (214)
                      ......+.|+||++.+..+.   .+. |+|.||..||..|+...   +   ...||.  |...+
T Consensus        10 ~~~~~~~~C~IC~~~~~~p~---~~~~CgH~fC~~Ci~~~~~~~---~---~~~CP~--Cr~~~   62 (74)
T 2yur_A           10 DPIPDELLCLICKDIMTDAV---VIPCCGNSYCDECIRTALLES---D---EHTCPT--CHQND   62 (74)
T ss_dssp             CCSCGGGSCSSSCCCCTTCE---ECSSSCCEECTTHHHHHHHHS---S---SSCCSS--SCCSS
T ss_pred             ccCCCCCCCcCCChHHhCCe---EcCCCCCHHHHHHHHHHHHhc---C---CCcCCC--CCCcC
Confidence            34456789999999987653   356 99999999999999752   1   368999  87653

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

Probab=98.66  E-value=4.3e-09  Score=65.39  Aligned_cols=57  Identities=19%  Similarity=0.574  Sum_probs=42.3

Q ss_pred             ccccccccc-cccccccc-ccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhc
Q 045388           44 RSSCEICRE-RRENDQMF-KIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSV  109 (214)
Q Consensus        44 ~~~C~iC~~-~~~~~~~~-~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~  109 (214)
                      ..+|+||++ .+..+... ..+.|||.||..|+..|+..       ...+||.  |+..+..++++..
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~-------~~~~CP~--Cr~~~~~~~~~~~   61 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR-------GAGNCPE--CGTPLRKSNFRVQ   61 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHT-------TSSSCTT--TCCCCSSCCCEEE
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHc-------CCCcCCC--CCCccccccceee
Confidence            478999999 66655321 24799999999999999752       1468999  9888876655443

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

Probab=98.66  E-value=2.8e-08  Score=64.48  Aligned_cols=50  Identities=26%  Similarity=0.554  Sum_probs=40.4

Q ss_pred             CCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           40 SPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        40 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      .....+.|+||++.+..+.   .+.|+|.||..|+..|+..        ...||.  |...+.
T Consensus        11 ~~~~~~~C~IC~~~~~~p~---~~~CgH~fC~~Ci~~~~~~--------~~~CP~--Cr~~~~   60 (81)
T 2csy_A           11 EEEIPFRCFICRQAFQNPV---VTKCRHYFCESCALEHFRA--------TPRCYI--CDQPTG   60 (81)
T ss_dssp             CCCCCSBCSSSCSBCCSEE---ECTTSCEEEHHHHHHHHHH--------CSBCSS--SCCBCC
T ss_pred             cCCCCCCCcCCCchhcCee---EccCCCHhHHHHHHHHHHC--------CCcCCC--cCcccc
Confidence            3445789999999986643   4799999999999999863        358999  888775

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

Probab=98.66  E-value=1.3e-08  Score=64.99  Aligned_cols=52  Identities=25%  Similarity=0.647  Sum_probs=41.5

Q ss_pred             CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      .....+|+||++.+...+.+..+.|+|.||..|+..|+...        ..||.  |...+.
T Consensus        20 ~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~--------~~CP~--Cr~~~~   71 (75)
T 1x4j_A           20 QSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKAN--------RTCPI--CRADSG   71 (75)
T ss_dssp             SSSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHC--------SSCTT--TCCCCC
T ss_pred             cCCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcC--------CcCcC--cCCcCC
Confidence            34567899999998876655567899999999999998642        37999  877664

>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=1.7e-08  Score=67.55  Aligned_cols=59  Identities=19%  Similarity=0.422  Sum_probs=44.9

Q ss_pred             cccccccccccccccccccccC-CCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCc-CcHHH
Q 045388           42 PSRSSCEICRERRENDQMFKIE-SCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSV-LKFDA  105 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~-~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~-l~~~~  105 (214)
                      ...+.|+||++.+..+.   .+ .|||.||+.||..|+...-..+  ...+||..+|... +...+
T Consensus         5 ~~~~~CPI~~~~~~dPV---~~~~cGh~f~r~cI~~~l~~~~~~~--~~~~CP~tgc~~~~l~~~~   65 (94)
T 2yu4_A            5 SSGFTCPITKEEMKKPV---KNKVCGHTYEEDAIVRMIESRQKRK--KKAYCPQIGCSHTDIRKSD   65 (94)
T ss_dssp             SSCCBCTTTCSBCSSEE---EESSSCCEEEHHHHHHHHHHHHTTT--CCBCCCSTTCCCCCBCGGG
T ss_pred             CcEeECcCcCchhcCCE---EcCCCCCeecHHHHHHHHHHccCcC--CCCCCCcCcCcccccCHhh
Confidence            45689999999887654   34 5999999999999997643222  3578999999876 65543

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

Probab=98.64  E-value=2.4e-08  Score=64.27  Aligned_cols=55  Identities=22%  Similarity=0.423  Sum_probs=39.8

Q ss_pred             Ccccccccccccccccccccc-cCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHH
Q 045388           41 PPSRSSCEICRERRENDQMFK-IESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFD  104 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~  104 (214)
                      ..+..+|+||++.+...+... .+.|||.||+.||..++..       ...+||.  |...+...
T Consensus         8 ~~~~~~CpICle~~~~~d~~~~p~~CGH~fC~~Cl~~~~~~-------~~~~CP~--CR~~~~~~   63 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTD-------ENGLCPA--CRKPYPED   63 (78)
T ss_dssp             CCCCCBCTTTCCBCCTTTTTCCSSTTSCCCCHHHHHHHTTS-------SCSBCTT--TCCBCSSC
T ss_pred             cccCCcCCccCccCccccccccccCCCCCcCHHHHHHHHhc-------CCCCCCC--CCCccCCC
Confidence            345689999999886443221 2359999999999988642       2468999  88877654

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

Probab=98.62  E-value=3.2e-08  Score=59.78  Aligned_cols=47  Identities=28%  Similarity=0.596  Sum_probs=35.9

Q ss_pred             CCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCC
Q 045388           40 SPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPG   94 (214)
Q Consensus        40 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~   94 (214)
                      ...+...|+||++.+..+.   .+.|+|.||..|+..|+...    . ...+||.
T Consensus        11 ~~~~~~~C~IC~~~~~~p~---~~~CgH~fC~~Ci~~~~~~~----~-~~~~CP~   57 (58)
T 2ecj_A           11 NLQVEASCSVCLEYLKEPV---IIECGHNFCKACITRWWEDL----E-RDFPCPV   57 (58)
T ss_dssp             CSCCCCBCSSSCCBCSSCC---CCSSCCCCCHHHHHHHTTSS----C-CSCCCSC
T ss_pred             ccccCCCCccCCcccCccE---eCCCCCccCHHHHHHHHHhc----C-CCCCCCC
Confidence            3445789999999987653   47899999999999997531    1 3468887

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

Probab=98.59  E-value=1.7e-08  Score=68.16  Aligned_cols=66  Identities=24%  Similarity=0.487  Sum_probs=46.1

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh-hcCCHHHHHHHHH
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK-SVLSKNVLELWEK  120 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~-~~l~~~~~~~~~~  120 (214)
                      +..+|+||++.+..+.+  ...|||.||..|+..|+..        ...||.  |+..+...++. +....++++.|..
T Consensus        21 ~~~~C~IC~~~~~~p~~--~~~CgH~fC~~Ci~~~~~~--------~~~CP~--Cr~~~~~~~l~~n~~l~~~i~~~~~   87 (99)
T 2y43_A           21 DLLRCGICFEYFNIAMI--IPQCSHNYCSLCIRKFLSY--------KTQCPT--CCVTVTEPDLKNNRILDELVKSLNF   87 (99)
T ss_dssp             HHTBCTTTCSBCSSEEE--CTTTCCEEEHHHHHHHHTT--------CCBCTT--TCCBCCGGGCEECHHHHHHHHHHHH
T ss_pred             CCCCcccCChhhCCcCE--ECCCCCHhhHHHHHHHHHC--------CCCCCC--CCCcCChhhCCcCHHHHHHHHHHHH
Confidence            35789999999876532  3489999999999999862        258999  98888764432 2222444444443

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

Probab=98.59  E-value=3.5e-08  Score=65.54  Aligned_cols=52  Identities=21%  Similarity=0.505  Sum_probs=40.9

Q ss_pred             CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      .....+|+||++.+...+.+..+.|+|.||..|+..|+..        ...||.  |...+.
T Consensus        37 ~~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~--------~~~CP~--Cr~~~~   88 (91)
T 2l0b_A           37 VGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQK--------SGTCPV--CRCMFP   88 (91)
T ss_dssp             SSSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTT--------TCBCTT--TCCBSS
T ss_pred             cCCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHc--------CCcCcC--cCccCC
Confidence            4456889999999877555556789999999999999842        237999  877664

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

Probab=98.58  E-value=1.7e-08  Score=60.33  Aligned_cols=49  Identities=22%  Similarity=0.651  Sum_probs=37.6

Q ss_pred             ccccccccccccccccccccCC-CCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388           43 SRSSCEICRERRENDQMFKIES-CIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL  101 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l  101 (214)
                      +..+|+||++.+...+....+. |+|.||.+|+..|+..        ...||.  |...+
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~--------~~~CP~--Cr~~~   53 (55)
T 1iym_A            4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGS--------HSTCPL--CRLTV   53 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTT--------CCSCSS--SCCCS
T ss_pred             CCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHc--------CCcCcC--CCCEe
Confidence            4578999999987754444454 9999999999999742        347999  87655

>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=98.58  E-value=2.7e-09  Score=76.78  Aligned_cols=91  Identities=20%  Similarity=0.464  Sum_probs=56.5

Q ss_pred             cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhhcCCHH-HHHHHHH
Q 045388           42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKSVLSKN-VLELWEK  120 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~~l~~~-~~~~~~~  120 (214)
                      .+.++|+||++.+..+.   .+.|||.||..||..|+..       ....||.  |...+..+....+++.+ ++   ..
T Consensus        29 ~~~~~C~IC~~~~~~pv---~~~CgH~FC~~Ci~~~~~~-------~~~~CP~--Cr~~~~~~~~~~~l~~~~~~---~d   93 (141)
T 3knv_A           29 EAKYLCSACRNVLRRPF---QAQCGHRYCSFCLASILSS-------GPQNCAA--CVHEGIYEEGISILESSSAF---PD   93 (141)
T ss_dssp             CGGGBCTTTCSBCSSEE---ECTTSCEEEHHHHHHHGGG-------SCEECHH--HHHTTCCCTTTTEECGGGCE---EC
T ss_pred             CcCcCCCCCChhhcCcE---ECCCCCccCHHHHHHHHhc-------CCCCCCC--CCCcccccccccccchhhhc---cc
Confidence            45789999999887663   4699999999999999841       2358998  76654333222222110 00   00


Q ss_pred             HHHHHHhcCCCCcccCccCCCceeeecC
Q 045388          121 ALSQELIDASQGIYCPFKDCSAKLVYEN  148 (214)
Q Consensus       121 ~~~~~~~~~~~~~~Cp~~~C~~~~~~~~  148 (214)
                      ...++.+. .-.++||+.+|...+...+
T Consensus        94 ~~~~~~i~-~L~v~Cpn~GC~~~~~l~~  120 (141)
T 3knv_A           94 NAARREVE-SLPAVCPSDGCTWKGTLKE  120 (141)
T ss_dssp             HHHHHHHH-TSEEECCSTTCCCEEEHHH
T ss_pred             HHHHHHHc-ccccccCCCCCCCEeEHHH
Confidence            11112222 3557899889998776654

>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=98.50  E-value=3.3e-08  Score=69.52  Aligned_cols=49  Identities=24%  Similarity=0.613  Sum_probs=39.4

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcH
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF  103 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~  103 (214)
                      ..++|+||++.+..+.   .++|||.||..|+..|+.     .  ....||.  |...+..
T Consensus        51 ~~~~C~IC~~~~~~p~---~~~CgH~fC~~Ci~~~~~-----~--~~~~CP~--Cr~~~~~   99 (124)
T 3fl2_A           51 ETFQCICCQELVFRPI---TTVCQHNVCKDCLDRSFR-----A--QVFSCPA--CRYDLGR   99 (124)
T ss_dssp             HHTBCTTTSSBCSSEE---ECTTSCEEEHHHHHHHHH-----T--TCCBCTT--TCCBCCT
T ss_pred             cCCCCCcCChHHcCcE---EeeCCCcccHHHHHHHHh-----H--CcCCCCC--CCccCCC
Confidence            4578999999987653   469999999999999987     1  2468999  8877754

>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=98.49  E-value=1.1e-07  Score=65.72  Aligned_cols=54  Identities=22%  Similarity=0.555  Sum_probs=39.5

Q ss_pred             ccccccccccccccc---------------ccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           44 RSSCEICRERRENDQ---------------MFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~---------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ..+|+||++.+....               +...+.|+|.||..||..|+...-..   ....||.  |...+.
T Consensus        25 ~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~---~~~~CP~--CR~~~~   93 (114)
T 1v87_A           25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKD---GSLQCPS--CKTIYG   93 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCS---SCCBCTT--TCCBSS
T ss_pred             CCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCC---CCCcCCC--CCCccC
Confidence            358999999986532               22257899999999999998543211   3568999  877664

>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=98.46  E-value=2e-08  Score=73.04  Aligned_cols=50  Identities=24%  Similarity=0.658  Sum_probs=40.5

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHH
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFD  104 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~  104 (214)
                      +.+.|+||++.+..+.   .+.|+|.||..|+..|+..       ....||.  |...+...
T Consensus        77 ~~~~C~IC~~~~~~pv---~~~CgH~fC~~Ci~~~~~~-------~~~~CP~--Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVYQPV---TTECFHNVCKDCLQRSFKA-------QVFSCPA--CRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCSSEE---ECTTSCEEEHHHHHHHHHT-------TCCBCTT--TCCBCCTT
T ss_pred             cCCEeecCChhhcCCE---EcCCCCchhHHHHHHHHHh-------CCCcCCC--CCccCCCC
Confidence            4678999999887654   4799999999999999963       2468999  88877654

>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=98.43  E-value=6.8e-08  Score=66.93  Aligned_cols=52  Identities=25%  Similarity=0.588  Sum_probs=40.8

Q ss_pred             CCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcH
Q 045388           40 SPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF  103 (214)
Q Consensus        40 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~  103 (214)
                      ...+.++|+||++.+..+.   .+.|||.||..|+..|+..       ....||.  |...+..
T Consensus        11 ~~~~~~~C~iC~~~~~~p~---~~~CgH~fC~~Ci~~~~~~-------~~~~CP~--Cr~~~~~   62 (115)
T 3l11_A           11 PSLSECQCGICMEILVEPV---TLPCNHTLCKPCFQSTVEK-------ASLCCPF--CRRRVSS   62 (115)
T ss_dssp             CCHHHHBCTTTCSBCSSCE---ECTTSCEECHHHHCCCCCT-------TTSBCTT--TCCBCHH
T ss_pred             CCCCCCCCccCCcccCcee---EcCCCCHHhHHHHHHHHhH-------CcCCCCC--CCcccCc
Confidence            3445789999999887653   4699999999999988741       2468999  9888865

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

Probab=98.41  E-value=1.4e-07  Score=58.92  Aligned_cols=48  Identities=33%  Similarity=0.742  Sum_probs=37.6

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ...+|+||++.+..+.  ..++|+|.||..|+..|+..        ...||.  |...+.
T Consensus         4 ~~~~C~IC~~~~~~~~--~~~~C~H~fc~~Ci~~~~~~--------~~~CP~--Cr~~~~   51 (68)
T 1chc_A            4 VAERCPICLEDPSNYS--MALPCLHAFCYVCITRWIRQ--------NPTCPL--CKVPVE   51 (68)
T ss_dssp             CCCCCSSCCSCCCSCE--EETTTTEEESTTHHHHHHHH--------SCSTTT--TCCCCC
T ss_pred             CCCCCeeCCccccCCc--EecCCCCeeHHHHHHHHHhC--------cCcCcC--CChhhH
Confidence            3578999999986542  25789999999999999853        247999  877664

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

Probab=98.40  E-value=9.6e-08  Score=68.40  Aligned_cols=46  Identities=37%  Similarity=0.775  Sum_probs=36.5

Q ss_pred             cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ..+|+||++.+..+.   .++|||.||..|+..|+..        ...||.  |...+.
T Consensus        53 ~~~C~iC~~~~~~~~---~~~CgH~fc~~Ci~~~~~~--------~~~CP~--Cr~~~~   98 (138)
T 4ayc_A           53 ELQCIICSEYFIEAV---TLNCAHSFCSYCINEWMKR--------KIECPI--CRKDIK   98 (138)
T ss_dssp             HSBCTTTCSBCSSEE---EETTSCEEEHHHHHHHTTT--------CSBCTT--TCCBCC
T ss_pred             cCCCcccCcccCCce---ECCCCCCccHHHHHHHHHc--------CCcCCC--CCCcCC
Confidence            468999999986643   4689999999999999742        357999  876664

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

Probab=98.38  E-value=3.4e-07  Score=59.90  Aligned_cols=51  Identities=12%  Similarity=0.004  Sum_probs=41.3

Q ss_pred             cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHH
Q 045388           42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDA  105 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~  105 (214)
                      .+.+.|+||++.+..+.   .+.|||.||+.||..|+..        ..+||.  |+..+...+
T Consensus        12 p~~~~CpI~~~~m~dPV---~~~cGhtf~r~~I~~~l~~--------~~~cP~--~~~~l~~~~   62 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTDPV---RLPSGTVMDRSIILRHLLN--------SPTDPF--NRQMLTESM   62 (85)
T ss_dssp             CTTTBCTTTCSBCSSEE---ECTTSCEEEHHHHHHHHHH--------CSBCTT--TCCBCCGGG
T ss_pred             chheECcccCchhcCCe---ECCCCCEECHHHHHHHHhc--------CCCCCC--CcCCCChHh
Confidence            45799999999887764   4679999999999999973        247999  888887654

>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=98.37  E-value=3.7e-08  Score=68.52  Aligned_cols=46  Identities=24%  Similarity=0.603  Sum_probs=37.5

Q ss_pred             cccccccccccccccccccC-CCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHH
Q 045388           44 RSSCEICRERRENDQMFKIE-SCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFD  104 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~-~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~  104 (214)
                      .++|+||++.+..+.   .+ .|||.||..|+..|+.          ..||.  |...+...
T Consensus        22 ~~~C~IC~~~~~~pv---~~~~CgH~fC~~Ci~~~~~----------~~CP~--Cr~~~~~~   68 (117)
T 1jm7_B           22 LLRCSRCTNILREPV---CLGGCEHIFCSNCVSDCIG----------TGCPV--CYTPAWIQ   68 (117)
T ss_dssp             TTSCSSSCSCCSSCB---CCCSSSCCBCTTTGGGGTT----------TBCSS--SCCBCSCS
T ss_pred             CCCCCCCChHhhCcc---EeCCCCCHHHHHHHHHHhc----------CCCcC--CCCcCccc
Confidence            589999999987653   35 8999999999999864          57999  88777543

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

Probab=98.36  E-value=9.5e-08  Score=57.41  Aligned_cols=45  Identities=22%  Similarity=0.705  Sum_probs=35.6

Q ss_pred             cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      .+..+|+||++.+..+.   .++|+|.||..|+..           ..+.||.  |...+.
T Consensus         4 ~~~~~C~IC~~~~~~p~---~l~CgH~fC~~Ci~~-----------~~~~CP~--Cr~~~~   48 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCPK---LLPCLHTLCSGCLEA-----------SGMQCPI--CQAPWP   48 (56)
T ss_dssp             CCCSSCSSSCSSCBCCS---CSTTSCCSBTTTCSS-----------SSSSCSS--CCSSSS
T ss_pred             ccCCCceEeCCccCCeE---EcCCCCcccHHHHcc-----------CCCCCCc--CCcEee
Confidence            35688999999987653   578999999999866           1468999  876654

>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=98.33  E-value=1.8e-07  Score=64.03  Aligned_cols=49  Identities=29%  Similarity=0.644  Sum_probs=38.4

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcH
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF  103 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~  103 (214)
                      +..+|+||++.+..+.  ....|||.||..|+..|+..        ...||.  |...+..
T Consensus        14 ~~~~C~IC~~~~~~p~--~~~~CgH~fC~~Ci~~~~~~--------~~~CP~--Cr~~~~~   62 (108)
T 2ckl_A           14 PHLMCVLCGGYFIDAT--TIIECLHSFCKTCIVRYLET--------SKYCPI--CDVQVHK   62 (108)
T ss_dssp             GGTBCTTTSSBCSSEE--EETTTCCEEEHHHHHHHHTS--------CSBCTT--TCCBSCS
T ss_pred             CcCCCccCChHHhCcC--EeCCCCChhhHHHHHHHHHh--------CCcCcC--CCccccc
Confidence            4689999999987643  23499999999999999853        268999  8776653

>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=98.30  E-value=2.3e-07  Score=62.41  Aligned_cols=51  Identities=16%  Similarity=0.040  Sum_probs=41.0

Q ss_pred             cccccccccccccccccccccCCCC-ccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHH
Q 045388           42 PSRSSCEICRERRENDQMFKIESCI-HSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDA  105 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~~C~-H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~  105 (214)
                      .+.+.|+||++.+..+.   .+.|| |.||+.||..|+..        ..+||.  |+..+..++
T Consensus        20 p~~~~CpI~~~~m~dPV---~~~cG~htf~r~cI~~~l~~--------~~~cP~--~~~~l~~~~   71 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCDPV---VLPSSRVTVDRSTIARHLLS--------DQTDPF--NRSPLTMDQ   71 (98)
T ss_dssp             CTTTBCTTTCSBCSSEE---ECTTTCCEEEHHHHHHHTTT--------SCBCTT--TCSBCCTTT
T ss_pred             cHhcCCcCccccccCCe---ECCCCCeEECHHHHHHHHHh--------CCCCCC--CCCCCChhh
Confidence            45789999999887764   46899 99999999999863        237999  888887543

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

Probab=98.23  E-value=1e-07  Score=59.88  Aligned_cols=48  Identities=33%  Similarity=0.776  Sum_probs=37.4

Q ss_pred             CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      .....+|+||++.+..    ..+.|+|.||..|+..|+.        ....||.  |...+.
T Consensus        12 ~~~~~~C~IC~~~~~~----~~~~CgH~fc~~Ci~~~~~--------~~~~CP~--Cr~~~~   59 (70)
T 2ecn_A           12 LTDEEECCICMDGRAD----LILPCAHSFCQKCIDKWSD--------RHRNCPI--CRLQMT   59 (70)
T ss_dssp             CCCCCCCSSSCCSCCS----EEETTTEEECHHHHHHSSC--------CCSSCHH--HHHCTT
T ss_pred             CCCCCCCeeCCcCccC----cccCCCCcccHHHHHHHHH--------CcCcCCC--cCCccc
Confidence            3456899999999866    2578999999999999875        1457998  765554

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

Probab=98.21  E-value=2.3e-06  Score=68.06  Aligned_cols=54  Identities=19%  Similarity=0.126  Sum_probs=42.0

Q ss_pred             CCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHH
Q 045388           40 SPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDA  105 (214)
Q Consensus        40 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~  105 (214)
                      .....+.|+||++.+..+.   .++|||+||+.||..|+..   .+    ..||.  |+..+...+
T Consensus       204 ~~~~~~~c~i~~~~~~dPv---~~~~gh~f~~~~i~~~~~~---~~----~~cP~--~~~~~~~~~  257 (281)
T 2c2l_A          204 DIPDYLCGKISFELMREPC---ITPSGITYDRKDIEEHLQR---VG----HFNPV--TRSPLTQEQ  257 (281)
T ss_dssp             CCCSTTBCTTTCSBCSSEE---ECSSCCEEETTHHHHHHHH---TC----SSCTT--TCCCCCGGG
T ss_pred             CCCcccCCcCcCCHhcCCe---ECCCCCEECHHHHHHHHHH---CC----CCCcC--CCCCCchhc
Confidence            3446789999999987764   4679999999999999864   12    23999  888886543

>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=98.19  E-value=5e-07  Score=70.61  Aligned_cols=57  Identities=23%  Similarity=0.362  Sum_probs=44.5

Q ss_pred             cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHH
Q 045388           42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC  106 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~  106 (214)
                      ...+.|+||++.+..+.  ....|||.||+.||..|+..    +  ....||..||...+...++
T Consensus       179 ~~el~CPIcl~~f~DPV--ts~~CGHsFcR~cI~~~~~~----~--~~~~CPvtGCr~~l~~~dL  235 (267)
T 3htk_C          179 KIELTCPITCKPYEAPL--ISRKCNHVFDRDGIQNYLQG----Y--TTRDCPQAACSQVVSMRDF  235 (267)
T ss_dssp             BCCSBCTTTSSBCSSEE--EESSSCCEEEHHHHHHHSTT----C--SCEECSGGGCSCEECGGGE
T ss_pred             ceeeECcCccCcccCCe--eeCCCCCcccHHHHHHHHHh----C--CCCCCCcccccCcCchhhC
Confidence            34678999999987663  23589999999999999863    1  2468999999988876543

>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=98.18  E-value=5.5e-07  Score=60.73  Aligned_cols=50  Identities=12%  Similarity=-0.008  Sum_probs=40.3

Q ss_pred             cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHH
Q 045388           42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFD  104 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~  104 (214)
                      .+.+.|+||++.+..+.   .++|||.||+.||..|+..        ..+||.  |+..+...
T Consensus        27 p~~~~CpI~~~~m~dPV---~~~cGhtf~r~~I~~~l~~--------~~~cP~--~~~~l~~~   76 (100)
T 2kre_A           27 PDEFRDPLMDTLMTDPV---RLPSGTIMDRSIILRHLLN--------SPTDPF--NRQTLTES   76 (100)
T ss_dssp             STTTBCTTTCSBCSSEE---EETTTEEEEHHHHHHHTTS--------CSBCSS--SCCBCCTT
T ss_pred             cHhhCCcCccCcccCCe---ECCCCCEEchHHHHHHHHc--------CCCCCC--CCCCCChh
Confidence            45789999999887764   4679999999999999852        247999  88888654

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

Probab=98.17  E-value=9.9e-07  Score=57.08  Aligned_cols=52  Identities=25%  Similarity=0.537  Sum_probs=37.6

Q ss_pred             ccccccccccccccc-----------cc-ccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcH
Q 045388           42 PSRSSCEICRERREN-----------DQ-MFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF  103 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~-----------~~-~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~  103 (214)
                      .+..+|+||++++..           .+ ......|+|.|+.+||..|+..        .-.||.  |...+..
T Consensus        13 ~~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~--------~~~CP~--CR~~~~~   76 (81)
T 2ecl_A           13 VECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQ--------NNRCPL--CQQDWVV   76 (81)
T ss_dssp             CCCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTT--------CCBCTT--TCCBCCE
T ss_pred             CCCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHh--------CCCCCC--cCCCcch
Confidence            356779999998854           12 2334579999999999999753        137999  8877653

>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=98.14  E-value=1.3e-06  Score=64.40  Aligned_cols=49  Identities=33%  Similarity=0.784  Sum_probs=38.6

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ..+.|+||++.+..+.  ....|||.||..|+..|+..       ....||.  |...+.
T Consensus        53 ~~~~C~IC~~~~~~p~--~~~~CgH~fC~~Ci~~~~~~-------~~~~CP~--Cr~~~~  101 (165)
T 2ckl_B           53 SELMCPICLDMLKNTM--TTKECLHRFCADCIITALRS-------GNKECPT--CRKKLV  101 (165)
T ss_dssp             HHHBCTTTSSBCSSEE--EETTTCCEEEHHHHHHHHHT-------TCCBCTT--TCCBCC
T ss_pred             CCCCCcccChHhhCcC--EeCCCCChhHHHHHHHHHHh-------CcCCCCC--CCCcCC
Confidence            4579999999987643  23599999999999999862       1467999  887774

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

Probab=98.07  E-value=3.8e-06  Score=54.11  Aligned_cols=57  Identities=21%  Similarity=0.553  Sum_probs=42.7

Q ss_pred             CCCCcccccccccccccccccccccCCCC-----ccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcH
Q 045388           38 PSSPPSRSSCEICRERRENDQMFKIESCI-----HSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF  103 (214)
Q Consensus        38 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~-----H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~  103 (214)
                      .........|.||++++...+.+ .++|.     |.|+.+||..|+...      ....||.  |...+..
T Consensus         9 s~~~~~~~~C~IC~~~~~~~~~l-~~pC~C~Gs~h~fH~~Cl~~Wl~~~------~~~~Cpl--Cr~~~~~   70 (80)
T 2d8s_A            9 SITPSSQDICRICHCEGDDESPL-ITPCHCTGSLHFVHQACLQQWIKSS------DTRCCEL--CKYEFIM   70 (80)
T ss_dssp             CCCCTTSCCCSSSCCCCCSSSCE-ECSSSCCSSSCCEETTHHHHHHHHH------CCSBCSS--SCCBCCC
T ss_pred             CCCCCCCCCCeEcCccccCCCee-EeccccCCcCCeeCHHHHHHHHhhC------CCCCCCC--CCCeeec
Confidence            34445567899999988655444 47886     999999999999753      1368999  8876653

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

Probab=98.04  E-value=1.2e-05  Score=59.65  Aligned_cols=54  Identities=20%  Similarity=0.137  Sum_probs=42.5

Q ss_pred             CCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHH
Q 045388           40 SPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDA  105 (214)
Q Consensus        40 ~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~  105 (214)
                      .....+.|+||++.+..+.   .++|||.||+.||..|+...   +.    .||.  |+..+...+
T Consensus       102 ~ip~~f~CPI~~elm~DPV---~~~~Ghtfer~~I~~~l~~~---~~----tcP~--t~~~l~~~~  155 (179)
T 2f42_A          102 EIPDYLCGKISFELMREPC---ITPSGITYDRKDIEEHLQRV---GH----FDPV--TRSPLTQDQ  155 (179)
T ss_dssp             CCCGGGBCTTTCSBCSSEE---ECTTSCEEEHHHHHHHHHHT---CS----BCTT--TCCBCCGGG
T ss_pred             CCcHhhcccCccccCCCCe---ECCCCCEECHHHHHHHHHhC---CC----CCCC--CcCCCChhh
Confidence            3456899999999887654   46899999999999999752   22    6999  888887653

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

Probab=98.02  E-value=1.5e-06  Score=61.30  Aligned_cols=58  Identities=24%  Similarity=0.630  Sum_probs=44.1

Q ss_pred             Ccccccccccccccccc----cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhh
Q 045388           41 PPSRSSCEICRERREND----QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKS  108 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~----~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~  108 (214)
                      +.....|+||++.+...    .....+.|+|.||..|+..|+..        ...||.  |...+..+++..
T Consensus        69 ~~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~--------~~~CP~--Cr~~~~~~~~~~  130 (133)
T 4ap4_A           69 GSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN--------ANTCPT--CRKKINHKRYHP  130 (133)
T ss_dssp             SSSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHH--------CSBCTT--TCCBCCGGGEEE
T ss_pred             CCCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHc--------CCCCCC--CCCcCChhccee
Confidence            34578899999988653    11235799999999999999864        248999  998887776544

>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=97.96  E-value=4.6e-06  Score=51.20  Aligned_cols=51  Identities=20%  Similarity=0.511  Sum_probs=37.2

Q ss_pred             CcccccccccccccccccccccCCCCcc-ccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           41 PPSRSSCEICRERRENDQMFKIESCIHS-FCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ......|.||++......++ ..+|||. ||.+|+..+...        .-+||.  |...+.
T Consensus         4 ~~~~~~C~IC~~~~~~~~~~-~~pCgH~~~C~~C~~~~~~~--------~~~CPi--CR~~i~   55 (63)
T 2vje_B            4 QNLLKPCSLCEKRPRDGNII-HGRTGHLVTCFHCARRLKKA--------GASCPI--CKKEIQ   55 (63)
T ss_dssp             GGGGSBCTTTSSSBSCEEEE-ETTEEEEEECHHHHHHHHHT--------TCBCTT--TCCBCC
T ss_pred             CCcCCCCcccCCcCCCeEEE-ecCCCCHhHHHHHHHHHHHh--------CCcCCC--cCchhh
Confidence            44567899999976544322 3599998 999999987642        247999  877663

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

Probab=97.96  E-value=1.6e-06  Score=55.04  Aligned_cols=42  Identities=29%  Similarity=0.668  Sum_probs=33.4

Q ss_pred             cccccccccccccccccccCCCCcc-ccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           44 RSSCEICRERRENDQMFKIESCIHS-FCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ...|.||++.+....   .++|||. ||..|+..|            ..||.  |...+.
T Consensus        24 ~~~C~iC~~~~~~~~---~~pCgH~~~C~~C~~~~------------~~CP~--Cr~~i~   66 (74)
T 4ic3_A           24 EKLCKICMDRNIAIV---FVPCGHLVTCKQCAEAV------------DKCPM--CYTVIT   66 (74)
T ss_dssp             HTBCTTTSSSBCCEE---EETTCCBCCCHHHHTTC------------SBCTT--TCCBCS
T ss_pred             CCCCCCCCCCCCCEE---EcCCCChhHHHHhhhcC------------ccCCC--cCcCcc
Confidence            478999999876543   4699999 999998766            57999  877664

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

Probab=97.93  E-value=4.4e-06  Score=53.11  Aligned_cols=42  Identities=29%  Similarity=0.670  Sum_probs=32.6

Q ss_pred             cccccccccccccccccccCCCCcc-ccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           44 RSSCEICRERRENDQMFKIESCIHS-FCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ..+|+||++.+....   .++|+|. ||..|+..            ...||.  |...+.
T Consensus        25 ~~~C~IC~~~~~~~~---~~pCgH~~~C~~C~~~------------~~~CP~--Cr~~i~   67 (75)
T 2ecg_A           25 EKLCKICMDRNIAIV---FVPCGHLVTCKQCAEA------------VDKCPM--CYTVIT   67 (75)
T ss_dssp             HHSCSSSCSSCCCBC---CSSSCCCCBCHHHHHH------------CSBCTT--TCCBCC
T ss_pred             CCCCCcCCCCCCCEE---EecCCCHHHHHHHhhC------------CCCCcc--CCceec
Confidence            468999999876543   5799999 99999842            257999  877664

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

Probab=97.88  E-value=1.1e-05  Score=50.28  Aligned_cols=50  Identities=22%  Similarity=0.632  Sum_probs=37.3

Q ss_pred             CCCCCCcccccccccccccccccccccCCCCcc-ccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           36 ASPSSPPSRSSCEICRERRENDQMFKIESCIHS-FCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        36 ~~~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      +.+....+...|.||++.....   .+++|+|. ||..|+..            ...||.  |...+.
T Consensus         7 e~e~~~~~~~~C~IC~~~~~~~---v~~pCgH~~~C~~C~~~------------~~~CP~--CR~~i~   57 (68)
T 2ea5_A            7 GVEPSEENSKDCVVCQNGTVNW---VLLPCRHTCLCDGCVKY------------FQQCPM--CRQFVQ   57 (68)
T ss_dssp             CCCCSCCCSSCCSSSSSSCCCC---EETTTTBCCSCTTHHHH------------CSSCTT--TCCCCC
T ss_pred             cccccCCCCCCCCCcCcCCCCE---EEECCCChhhhHHHHhc------------CCCCCC--CCcchh
Confidence            4455566678999999976543   25899999 99999883            147999  877653

>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=97.84  E-value=9.2e-06  Score=55.22  Aligned_cols=49  Identities=24%  Similarity=0.492  Sum_probs=37.1

Q ss_pred             cccccccccccccccc---------------cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           44 RSSCEICRERRENDQM---------------FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~---------------~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ..+|.||++.+...-.               +..+.|+|.|+..||..|+..        ...||.  |...+.
T Consensus        37 ~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~--------~~~CP~--Cr~~~~  100 (106)
T 3dpl_R           37 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT--------RQVCPL--DNREWE  100 (106)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTT--------CSBCSS--SCSBCC
T ss_pred             CCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHc--------CCcCcC--CCCcce
Confidence            4679999999875411               224789999999999999753        247999  887654

>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=97.82  E-value=8.9e-06  Score=50.03  Aligned_cols=50  Identities=24%  Similarity=0.510  Sum_probs=36.5

Q ss_pred             cccccccccccccccccccccCCCCcc-ccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           42 PSRSSCEICRERRENDQMFKIESCIHS-FCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      .+..+|.||++......+. .++|||. ||.+|+..+...        .-+||.  |...+.
T Consensus         6 ~~~~~C~IC~~~~~~~~~~-~~pCgH~~~C~~C~~~~~~~--------~~~CPi--CR~~i~   56 (64)
T 2vje_A            6 NAIEPCVICQGRPKNGCIV-HGKTGHLMACFTCAKKLKKR--------NKPCPV--CRQPIQ   56 (64)
T ss_dssp             GGGSCCTTTSSSCSCEEEE-ETTEEEEEECHHHHHHHHHT--------TCCCTT--TCCCCC
T ss_pred             CCcCCCCcCCCCCCCEEEE-CCCCCChhhHHHHHHHHHHc--------CCcCCC--cCcchh
Confidence            3567899999986554321 2499999 899999988741        237999  877663

>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=97.64  E-value=3.1e-05  Score=64.12  Aligned_cols=47  Identities=30%  Similarity=0.725  Sum_probs=37.2

Q ss_pred             ccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcH
Q 045388           45 SSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF  103 (214)
Q Consensus        45 ~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~  103 (214)
                      .+|+||++.+..+.   .++|||.||..|+..|+..       ....||.  |...+..
T Consensus       333 ~~C~ICle~~~~pv---~lpCGH~FC~~Ci~~wl~~-------~~~~CP~--CR~~i~~  379 (389)
T 2y1n_A          333 QLCKICAENDKDVK---IEPCGHLMCTSCLTSWQES-------EGQGCPF--CRCEIKG  379 (389)
T ss_dssp             SBCTTTSSSBCCEE---EETTCCEECHHHHHHHHHH-------TCSBCTT--TCCBCCE
T ss_pred             CCCCccCcCCCCeE---EeCCCChhhHHHHHHHHhc-------CCCCCCC--CCCccCC
Confidence            68999999875542   5799999999999999863       1358999  8876654

>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=97.56  E-value=1.2e-05  Score=51.63  Aligned_cols=43  Identities=28%  Similarity=0.707  Sum_probs=33.1

Q ss_pred             cccccccccccccccccccCCCCcc-ccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcH
Q 045388           44 RSSCEICRERRENDQMFKIESCIHS-FCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF  103 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~  103 (214)
                      ...|.||++......   .++|||. ||..|+..+            ..||.  |...+..
T Consensus        18 ~~~C~IC~~~~~~~v---~~pCgH~~~C~~C~~~~------------~~CP~--Cr~~i~~   61 (79)
T 2yho_A           18 AMLCMVCCEEEINST---FCPCGHTVCCESCAAQL------------QSCPV--CRSRVEH   61 (79)
T ss_dssp             HTBCTTTSSSBCCEE---EETTCBCCBCHHHHTTC------------SBCTT--TCCBCCE
T ss_pred             CCEeEEeCcccCcEE---EECCCCHHHHHHHHHhc------------CcCCC--CCchhhC
Confidence            368999999865432   5799999 999998754            28999  8876654

>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=97.47  E-value=1.9e-05  Score=54.51  Aligned_cols=49  Identities=27%  Similarity=0.532  Sum_probs=0.0

Q ss_pred             cccccccccccccc---------------ccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcH
Q 045388           45 SSCEICRERRENDQ---------------MFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF  103 (214)
Q Consensus        45 ~~C~iC~~~~~~~~---------------~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~  103 (214)
                      .+|.||++.+...-               .+..+.|+|.|+..||..|+..        .-.||.  |...+..
T Consensus        49 d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~--------~~~CP~--Cr~~~~~  112 (117)
T 4a0k_B           49 DNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT--------RQVCPL--DNREWEF  112 (117)
T ss_dssp             --------------------------------------------------------------------------
T ss_pred             CcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHc--------CCcCCC--CCCeeee
Confidence            58999999986531               1113589999999999999864        237998  8776543

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

Probab=97.32  E-value=0.00023  Score=44.82  Aligned_cols=55  Identities=22%  Similarity=0.468  Sum_probs=40.8

Q ss_pred             CCCCcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           38 PSSPPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        38 ~~~~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ........+|.||++.+...+  ....|+|.|...||..|++.+    .  .-+||.  |+..+.
T Consensus         9 ~~y~~~i~~C~IC~~~i~~g~--~C~~C~h~fH~~Ci~kWl~~~----~--~~~CP~--Cr~~w~   63 (74)
T 2ct0_A            9 ETYPDAVKICNICHSLLIQGQ--SCETCGIRMHLPCVAKYFQSN----A--EPRCPH--CNDYWP   63 (74)
T ss_dssp             CCCSSSSCBCSSSCCBCSSSE--ECSSSCCEECHHHHHHHSTTC----S--SCCCTT--TCSCCC
T ss_pred             hhccCCCCcCcchhhHcccCC--ccCCCCchhhHHHHHHHHHhc----C--CCCCCC--CcCcCC
Confidence            334455789999999987543  245999999999999998532    1  247999  877664

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

Probab=97.10  E-value=0.00039  Score=56.35  Aligned_cols=60  Identities=22%  Similarity=0.448  Sum_probs=43.6

Q ss_pred             ccccccccccccccc-cccc----ccCCCCccccHHHHHHHHHHHhhCCCccc---ccCCCCCCCCcCcH
Q 045388           42 PSRSSCEICRERREN-DQMF----KIESCIHSFCSDCINKHVATKIQGGIITP---VTCPGPDCKSVLKF  103 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~-~~~~----~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~---i~CP~~~C~~~l~~  103 (214)
                      ....+|+|||+.+.. ..+.    ....|+|.|...|+..|+...-.....+.   =.||.  |...+.-
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPy--Cr~pIs~  373 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPF--CKAKLST  373 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTT--TCCEEEG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCC--CCCcCCc
Confidence            457789999998775 2222    14589999999999999987665443222   27998  8887753

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

Probab=96.90  E-value=0.00061  Score=41.04  Aligned_cols=40  Identities=25%  Similarity=0.718  Sum_probs=34.3

Q ss_pred             CCCcccCccCCCceeeecCCCCCCcCcccCCC--CChhhccccCCCCC
Q 045388          130 SQGIYCPFKDCSAKLVYENDGEDVLSESECPY--CHRLFCAHCYVPWH  175 (214)
Q Consensus       130 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~h  175 (214)
                      .+.+.||  +|...+..+++-    +.++|..  |+..||+.|..+|.
T Consensus         4 ~~~k~CP--~C~~~Iek~~GC----nhmtC~~~~C~~~FCw~C~~~~~   45 (60)
T 1wd2_A            4 ANTKECP--KCHVTIEKDGGC----NHMVCRNQNCKAEFCWVCLGPWE   45 (60)
T ss_dssp             CCCCCCT--TTCCCCSSCCSC----CSSSCCSSGGGSCCSSSSCSCSG
T ss_pred             ccceECc--CCCCeeEeCCCC----CcEEECCCCcCCEEeeCcCCCcc
Confidence            3557899  999999998774    7889987  99999999999874

>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=96.86  E-value=0.00016  Score=59.19  Aligned_cols=42  Identities=24%  Similarity=0.763  Sum_probs=33.3

Q ss_pred             cccccccccccccccccccCCCCcc-ccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           44 RSSCEICRERRENDQMFKIESCIHS-FCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~-fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ...|+||++.+....   .++|||. ||..|+..+            ..||.  |...+.
T Consensus       295 ~~~C~IC~~~~~~~v---~lpCgH~~fC~~C~~~~------------~~CP~--CR~~i~  337 (345)
T 3t6p_A          295 ERTCKVCMDKEVSVV---FIPCGHLVVCQECAPSL------------RKCPI--CRGIIK  337 (345)
T ss_dssp             TCBCTTTSSSBCCEE---EETTCCEEECTTTGGGC------------SBCTT--TCCBCC
T ss_pred             CCCCCccCCcCCceE---EcCCCChhHhHHHHhcC------------CcCCC--CCCCcc
Confidence            468999999876543   4699999 999998755            47999  877664

>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=96.39  E-value=0.009  Score=37.46  Aligned_cols=56  Identities=29%  Similarity=0.629  Sum_probs=42.2

Q ss_pred             CCcccccccccccccccccccccCC-CCccccHHHHHHHHHHHhhCCCcccccCCCC-CCC
Q 045388           40 SPPSRSSCEICRERRENDQMFKIES-CIHSFCSDCINKHVATKIQGGIITPVTCPGP-DCK   98 (214)
Q Consensus        40 ~~~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~-~C~   98 (214)
                      .+.....|.+|.+.++...+++..+ =.|.||..|-+.+|+.+-..+   .+.||.. .|.
T Consensus        11 ~~~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~q~~~~---EvyCPSG~kCp   68 (93)
T 2cs3_A           11 ANSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKAQGATG---EVYCPSGEKCP   68 (93)
T ss_dssp             CSCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHHHHSSS---CCCCTTSSCCB
T ss_pred             CCCCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHhcCCCC---cEECCCCCccc
Confidence            3566899999999999888766222 269999999999999876543   5777773 443

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

Probab=96.38  E-value=0.0017  Score=43.35  Aligned_cols=34  Identities=21%  Similarity=0.694  Sum_probs=26.7

Q ss_pred             cccccccccccccccccccCCCCccccHHHHHHH
Q 045388           44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKH   77 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~   77 (214)
                      ...|+||.+++..+.+...+.|+|.||..|++.+
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            4789999986544444445899999999999983

>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=96.19  E-value=0.0017  Score=39.21  Aligned_cols=51  Identities=14%  Similarity=0.179  Sum_probs=38.4

Q ss_pred             cccccccccccccccccccC-CCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh
Q 045388           44 RSSCEICRERRENDQMFKIE-SCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK  107 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~-~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~  107 (214)
                      .+.|+|+++.+..+.   .. .+||.|++.++..|+...   +     +||.  .+..|..+++.
T Consensus         3 ~~~CpIs~~~m~dPV---~~~~sG~~yer~~I~~~l~~~---~-----~cP~--t~~~L~~~~Li   54 (61)
T 2bay_A            3 HMLCAISGKVPRRPV---LSPKSRTIFEKSLLEQYVKDT---G-----NDPI--TNEPLSIEEIV   54 (61)
T ss_dssp             -CCCTTTCSCCSSEE---EETTTTEEEEHHHHHHHHHHH---S-----BCTT--TCCBCCGGGCE
T ss_pred             eEEecCCCCCCCCCE---EeCCCCcEEcHHHHHHHHHhC---C-----CCcC--CcCCCChhhcE
Confidence            478999999887653   34 899999999999999742   1     3898  66777665543

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

Probab=95.96  E-value=0.016  Score=34.71  Aligned_cols=49  Identities=20%  Similarity=0.496  Sum_probs=35.4

Q ss_pred             ccccccccccccccccccccCCC--Cc---cccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           43 SRSSCEICRERRENDQMFKIESC--IH---SFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C--~H---~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      +...|.||+++...+ +  .++|  .|   .|..+||..|+...-      ..+||.  |+..+.
T Consensus         5 ~~~~CrIC~~~~~~~-l--~~PC~C~gs~~~~H~~Cl~~W~~~~~------~~~C~~--C~~~~~   58 (60)
T 1vyx_A            5 DVPVCWICNEELGNE-R--FRACGCTGELENVHRSCLSTWLTISR------NTACQI--CGVVYN   58 (60)
T ss_dssp             SCCEETTTTEECSCC-C--CCSCCCSSGGGSCCHHHHHHHHHHHT------CSBCTT--TCCBCC
T ss_pred             CCCEeEEeecCCCCc-e--ecCcCCCCchhhhHHHHHHHHHHhCC------CCccCC--CCCeee
Confidence            457899999985433 3  3554  45   899999999997532      368999  887664

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

Probab=95.87  E-value=0.0046  Score=40.79  Aligned_cols=32  Identities=28%  Similarity=0.573  Sum_probs=23.1

Q ss_pred             cccccccccccccccccCCCCccccHHHHHHHHH
Q 045388           46 SCEICRERRENDQMFKIESCIHSFCSDCINKHVA   79 (214)
Q Consensus        46 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~   79 (214)
                      .|++|--+  ...-..+.+|.|.||.+|+..|..
T Consensus         3 fC~~C~~P--i~iygRmIPCkHvFCydCa~~~~~   34 (101)
T 3vk6_A            3 FCDKCGLP--IKVYGRMIPCKHVFCYDCAILHEK   34 (101)
T ss_dssp             BCTTTCSB--CSEEEEEETTCCEEEHHHHHHHHH
T ss_pred             ecCccCCC--eEEEeeeccccccHHHHHHHHHHh
Confidence            47777443  333344789999999999999864

>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=93.67  E-value=0.08  Score=33.91  Aligned_cols=61  Identities=25%  Similarity=0.595  Sum_probs=45.1

Q ss_pred             CcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceecCCCCC
Q 045388          132 GIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLH  210 (214)
Q Consensus       132 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~GCnh  210 (214)
                      ...|.  -|+--+-.+..+   ...+.|..|+.-.|.-|..             +.+....+.||+|++...+.-|...
T Consensus        16 ~qiCq--iCGD~VG~~~~G---e~FVAC~eC~FPvCrpCyE-------------YErkeG~q~CpqCktrYkr~kgsp~   76 (93)
T 1weo_A           16 GQFCE--ICGDQIGLTVEG---DLFVACNECGFPACRPCYE-------------YERREGTQNCPQCKTRYKRLRGSPR   76 (93)
T ss_dssp             SCBCS--SSCCBCCBCSSS---SBCCSCSSSCCCCCHHHHH-------------HHHHTSCSSCTTTCCCCCCCTTCCC
T ss_pred             CCccc--cccCccccCCCC---CEEEeeeccCChhhHHHHH-------------HHHhccCccccccCCccccccCCCC
Confidence            34566  677666555544   2778899999999988853             5567788999999999987666543

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

Probab=91.34  E-value=0.14  Score=39.53  Aligned_cols=52  Identities=21%  Similarity=0.459  Sum_probs=39.0

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHH
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFD  104 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~  104 (214)
                      ....|.+|.+.+....  ....|+|.|...|+..|++.     . ...+||.  |+..++.+
T Consensus       179 ~i~~C~iC~~iv~~g~--~C~~C~~~~H~~C~~~~~~~-----~-~~~~CP~--C~~~W~~~  230 (238)
T 3nw0_A          179 AVKICNICHSLLIQGQ--SCETCGIRMHLPCVAKYFQS-----N-AEPRCPH--CNDYWPHE  230 (238)
T ss_dssp             TCCBCTTTCSBCSSCE--ECSSSCCEECHHHHHHHTTT-----C-SSCBCTT--TCCBCCSC
T ss_pred             CCCcCcchhhHHhCCc--ccCccChHHHHHHHHHHHHh-----C-CCCCCCC--CCCCCCCC
Confidence            3678999999887543  24469999999999999853     1 2468998  88766543

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

Probab=90.25  E-value=0.18  Score=31.04  Aligned_cols=33  Identities=21%  Similarity=0.654  Sum_probs=24.0

Q ss_pred             CCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCcccee
Q 045388          160 PYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIER  204 (214)
Q Consensus       160 ~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek  204 (214)
                      +.||+.||..|..            .|.+......||.|+..+.+
T Consensus        32 ~~CgH~fC~~Ci~------------~~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A           32 PCCGNSYCDECIR------------TALLESDEHTCPTCHQNDVS   64 (74)
T ss_dssp             SSSCCEECTTHHH------------HHHHHSSSSCCSSSCCSSCC
T ss_pred             CCCCCHHHHHHHH------------HHHHhcCCCcCCCCCCcCCC
Confidence            3489999999953            34444456799999997543

>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=88.73  E-value=0.21  Score=32.89  Aligned_cols=48  Identities=27%  Similarity=0.718  Sum_probs=31.9

Q ss_pred             cccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCcccee
Q 045388          133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIER  204 (214)
Q Consensus       133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek  204 (214)
                      ..||  -|...+..         .+.+..||+.||..|...            |..... ..||.|+..+..
T Consensus        23 ~~C~--IC~~~~~~---------p~~~~~CgH~FC~~Ci~~------------~~~~~~-~~CP~Cr~~~~~   70 (100)
T 3lrq_A           23 FRCF--ICMEKLRD---------ARLCPHCSKLCCFSCIRR------------WLTEQR-AQCPHCRAPLQL   70 (100)
T ss_dssp             TBCT--TTCSBCSS---------EEECTTTCCEEEHHHHHH------------HHHHTC-SBCTTTCCBCCG
T ss_pred             CCCc--cCCccccC---------ccccCCCCChhhHHHHHH------------HHHHCc-CCCCCCCCcCCH
Confidence            4577  77665531         233567999999999643            333322 689999998754

>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=87.80  E-value=0.14  Score=30.42  Aligned_cols=44  Identities=32%  Similarity=0.802  Sum_probs=30.6

Q ss_pred             cccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCC
Q 045388          133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCK  199 (214)
Q Consensus       133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~  199 (214)
                      ..|-  .|...+..       ....+|+.|+..||..|..-.|+              ....||.|.
T Consensus        16 ~~C~--~C~~~~~~-------~~~y~C~~C~~~FC~dCD~fiHe--------------~Lh~CPgC~   59 (59)
T 1z60_A           16 RFCY--GCQGELKD-------QHVYVCAVCQNVFCVDCDVFVHD--------------SLHSCPGCI   59 (59)
T ss_dssp             CEET--TTTEECTT-------SEEECCTTTTCCBCHHHHHTTTT--------------TSCSSSTTC
T ss_pred             Cccc--ccCcccCC-------CccEECCccCcCcccchhHHHHh--------------hccCCcCCC
Confidence            3466  67666521       12367999999999999887774              356788773

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

Probab=86.44  E-value=0.53  Score=32.84  Aligned_cols=37  Identities=24%  Similarity=0.387  Sum_probs=26.5

Q ss_pred             cCCCCcccCccCCCceeeecCCCCCCcCcccCCCCChhh
Q 045388          128 DASQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLF  166 (214)
Q Consensus       128 ~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~  166 (214)
                      ......+||  .|+..+....+.......+.|+.|++..
T Consensus        20 ~~~~~~FCP--eCgNmL~pked~~~~~l~~~CrtCgY~~   56 (133)
T 3qt1_I           20 HMTTFRFCR--DCNNMLYPREDKENNRLLFECRTCSYVE   56 (133)
T ss_dssp             --CCCCBCT--TTCCBCBCCBCTTTCCBCCBCSSSCCBC
T ss_pred             cccCCeeCC--CCCCEeeECccCCCceeEEECCCCCCcE
Confidence            345678999  9999998876532334678899998754

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

Probab=86.13  E-value=0.27  Score=32.34  Aligned_cols=32  Identities=34%  Similarity=0.859  Sum_probs=24.6

Q ss_pred             CCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceec
Q 045388          161 YCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERT  205 (214)
Q Consensus       161 ~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~  205 (214)
                      -|+.+||..|..             .....+.+.||.|+..|++.
T Consensus        19 PCkHvFCydCa~-------------~~~~~~~k~Cp~C~~~V~rV   50 (101)
T 3vk6_A           19 PCKHVFCYDCAI-------------LHEKKGDKMCPGCSDPVQRI   50 (101)
T ss_dssp             TTCCEEEHHHHH-------------HHHHTTCCBCTTTCCBCSEE
T ss_pred             cccccHHHHHHH-------------HHHhccCCCCcCcCCeeeee
Confidence            578999999953             22345679999999998775

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

Probab=85.99  E-value=0.34  Score=31.08  Aligned_cols=49  Identities=18%  Similarity=0.554  Sum_probs=31.7

Q ss_pred             CCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccc
Q 045388          131 QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHI  202 (214)
Q Consensus       131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~i  202 (214)
                      +...||  -|...+..        + +.-+.||+.||..|..            .+....+...||.|+..+
T Consensus        12 ~~~~C~--IC~~~~~~--------p-~~~~~CgH~fC~~Ci~------------~~~~~~~~~~CP~Cr~~~   60 (92)
T 3ztg_A           12 DELLCL--ICKDIMTD--------A-VVIPCCGNSYCDECIR------------TALLESDEHTCPTCHQND   60 (92)
T ss_dssp             TTTEET--TTTEECSS--------C-EECTTTCCEECHHHHH------------HHHHHCTTCCCTTTCCSS
T ss_pred             cCCCCC--CCChhhcC--------c-eECCCCCCHHHHHHHH------------HHHHhcCCCcCcCCCCcC
Confidence            345677  77755531        1 1223489999999954            344444557999999976

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

Probab=85.33  E-value=0.48  Score=29.08  Aligned_cols=33  Identities=30%  Similarity=0.669  Sum_probs=24.1

Q ss_pred             CCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceecCC
Q 045388          161 YCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGG  207 (214)
Q Consensus       161 ~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~G  207 (214)
                      .|+..||..|...            |.+..  ..||.|+..|....|
T Consensus        43 ~C~H~fh~~Ci~~------------w~~~~--~~CP~Cr~~~~~~~g   75 (75)
T 1x4j_A           43 PCNHEFHAKCVDK------------WLKAN--RTCPICRADSGPSSG   75 (75)
T ss_dssp             TTTEEEETTHHHH------------HHHHC--SSCTTTCCCCCCCCC
T ss_pred             CCCCHhHHHHHHH------------HHHcC--CcCcCcCCcCCCCCC
Confidence            4899999999643            33332  589999999877665

>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=85.05  E-value=0.44  Score=28.68  Aligned_cols=35  Identities=20%  Similarity=0.574  Sum_probs=27.5

Q ss_pred             CCcccccccccccccccccccccCCC-CccccHHHHHHHH
Q 045388           40 SPPSRSSCEICRERRENDQMFKIESC-IHSFCSDCINKHV   78 (214)
Q Consensus        40 ~~~~~~~C~iC~~~~~~~~~~~~~~C-~H~fC~~Cl~~~~   78 (214)
                      .+.+..-|.||.++-    .+..+.| +..||..||+..-
T Consensus         4 ~~ee~pWC~ICneDA----tlrC~gCdgDLYC~rC~rE~H   39 (67)
T 2d8v_A            4 GSSGLPWCCICNEDA----TLRCAGCDGDLYCARCFREGH   39 (67)
T ss_dssp             SCCCCSSCTTTCSCC----CEEETTTTSEEECSSHHHHHT
T ss_pred             cCcCCCeeEEeCCCC----eEEecCCCCceehHHHHHHHc
Confidence            345677899999963    3457899 7899999999976

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

Probab=84.38  E-value=0.47  Score=29.60  Aligned_cols=37  Identities=22%  Similarity=0.555  Sum_probs=24.7

Q ss_pred             CCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceec
Q 045388          161 YCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERT  205 (214)
Q Consensus       161 ~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~  205 (214)
                      .|++.||..|...|        +...........||.|+..+...
T Consensus        36 ~CgH~fC~~Ci~~~--------~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecv_A           36 DCGHSFCQACLTAN--------HKKSMLDKGESSCPVCRISYQPE   72 (85)
T ss_dssp             SSSCCBCTTHHHHH--------HHHHHHTTSCCCCTTTCCSSCSS
T ss_pred             CCCCHHHHHHHHHH--------HHHhhcCCCCCcCCCCCCccCHH
Confidence            58999999996432        11111234578999999988754

>2hu9_A MERP, mercuric transport protein periplasmic component; copper chaperone, iron-sufur protein, COPZ, ATX1, ATOX1, metal transport; 1.78A {Archaeoglobus fulgidus}

Probab=83.08  E-value=0.69  Score=32.07  Aligned_cols=46  Identities=13%  Similarity=0.317  Sum_probs=33.1

Q ss_pred             ccCCCCCCC---CcCcHHHHhhcCCHHHHHHHHHHHHHHHhcCCCCcccCccCCCceeeec
Q 045388           90 VTCPGPDCK---SVLKFDACKSVLSKNVLELWEKALSQELIDASQGIYCPFKDCSAKLVYE  147 (214)
Q Consensus        90 i~CP~~~C~---~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~  147 (214)
                      ..||.  |+   ..+....|+++|.++.++          +...++.+|++|+|...++..
T Consensus         2 ~~CP~--Cg~~G~~V~~~Tvk~ll~~~~~~----------~~~~~y~~C~~~~C~VvYf~~   50 (130)
T 2hu9_A            2 MRCPE--CSTEGWRVLPLTVGAHVKEGLWS----------KIKGDFYFCSLESCEVVYFNE   50 (130)
T ss_dssp             CBCTT--TCCBCEEECHHHHHHHBCGGGGG----------GCCSCEEECCCTTCSEEEECS
T ss_pred             CcCCC--CCCcCcCccHHHHHHHhhHHHhc----------cCCCCEEeECCCCCCEEEECC
Confidence            46998  65   466788888888765432          344678899999999766543

>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=82.90  E-value=0.5  Score=31.90  Aligned_cols=46  Identities=22%  Similarity=0.465  Sum_probs=29.6

Q ss_pred             CcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCcccee
Q 045388          132 GIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIER  204 (214)
Q Consensus       132 ~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek  204 (214)
                      ...||  -|...+..        +.. -..||+.||..|...|-.                ..||.|+..+..
T Consensus        22 ~~~C~--IC~~~~~~--------pv~-~~~CgH~fC~~Ci~~~~~----------------~~CP~Cr~~~~~   67 (117)
T 1jm7_B           22 LLRCS--RCTNILRE--------PVC-LGGCEHIFCSNCVSDCIG----------------TGCPVCYTPAWI   67 (117)
T ss_dssp             TTSCS--SSCSCCSS--------CBC-CCSSSCCBCTTTGGGGTT----------------TBCSSSCCBCSC
T ss_pred             CCCCC--CCChHhhC--------ccE-eCCCCCHHHHHHHHHHhc----------------CCCcCCCCcCcc
Confidence            45687  77655532        111 115899999999876532                678888887743

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

Probab=82.50  E-value=0.59  Score=26.63  Aligned_cols=29  Identities=21%  Similarity=0.668  Sum_probs=18.2

Q ss_pred             CCcccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388          131 QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRL  165 (214)
Q Consensus       131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~  165 (214)
                      ...+||  .|+..++..+..    .+..|+.||..
T Consensus        18 ~~k~CP--~CG~~~fm~~~~----~R~~C~kCG~t   46 (50)
T 3j20_Y           18 KNKFCP--RCGPGVFMADHG----DRWACGKCGYT   46 (50)
T ss_dssp             SSEECS--SSCSSCEEEECS----SEEECSSSCCE
T ss_pred             ecccCC--CCCCceEEecCC----CeEECCCCCCE
Confidence            345899  898733332222    56788888864

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

Probab=82.10  E-value=0.36  Score=29.77  Aligned_cols=27  Identities=33%  Similarity=0.653  Sum_probs=21.8

Q ss_pred             CCChh-hccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceec
Q 045388          161 YCHRL-FCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERT  205 (214)
Q Consensus       161 ~C~~~-~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~  205 (214)
                      .||+. ||..|...|                  +.||-|+..|.+.
T Consensus        41 pCgH~~~C~~C~~~~------------------~~CP~Cr~~i~~~   68 (74)
T 4ic3_A           41 PCGHLVTCKQCAEAV------------------DKCPMCYTVITFK   68 (74)
T ss_dssp             TTCCBCCCHHHHTTC------------------SBCTTTCCBCSEE
T ss_pred             CCCChhHHHHhhhcC------------------ccCCCcCcCccCc
Confidence            57888 999996643                  8999999988653

>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=81.48  E-value=0.43  Score=32.03  Aligned_cols=30  Identities=20%  Similarity=0.604  Sum_probs=23.9

Q ss_pred             CCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccce
Q 045388          161 YCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIE  203 (214)
Q Consensus       161 ~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~ie  203 (214)
                      .||+.||..|...|...             ....||.|+..+.
T Consensus        32 ~CgH~fC~~Ci~~~~~~-------------~~~~CP~Cr~~~~   61 (115)
T 3l11_A           32 PCNHTLCKPCFQSTVEK-------------ASLCCPFCRRRVS   61 (115)
T ss_dssp             TTSCEECHHHHCCCCCT-------------TTSBCTTTCCBCH
T ss_pred             CCCCHHhHHHHHHHHhH-------------CcCCCCCCCcccC
Confidence            58999999999877632             2378999999775

>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=80.18  E-value=0.87  Score=30.36  Aligned_cols=35  Identities=20%  Similarity=0.475  Sum_probs=24.8

Q ss_pred             CCCChhhccccCCCCCCChHHHHHHHHHHh---CCCccCCCCCccceecC
Q 045388          160 PYCHRLFCAHCYVPWHPGREELMMRELVKK---KQLRKCPNCKYHIERTG  206 (214)
Q Consensus       160 ~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~---~~~k~CP~C~~~iek~~  206 (214)
                      ..|++.||..|...            |...   .....||-|+..+.+..
T Consensus        59 ~~C~H~Fh~~Ci~~------------wl~~~~~~~~~~CP~CR~~~~~~~   96 (114)
T 1v87_A           59 TKCSHAFHLLCLLA------------MYCNGNKDGSLQCPSCKTIYGEKT   96 (114)
T ss_dssp             SSSCCEECHHHHHH------------HHHHTCCSSCCBCTTTCCBSSSCS
T ss_pred             CCCCCcccHHHHHH------------HHHcccCCCCCcCCCCCCccCCCC
Confidence            46899999999643            3332   34568999999876543

---

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	214
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	3e-10
d1wd2a_	60	g.44.1.1 (A:) Ariadne-1 protein homolog {Human (Ho	2e-04
d2ct7a1	73	g.44.1.4 (A:8-80) Ring finger protein 31 {Human (H	4e-04

>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 = 53.2 bits (127), Expect = 3e-10
 Identities = 20/88 (22%), Positives = 44/88 (50%), Gaps = 2/88 (2%)

Query: 45  SSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCK--SVLK 102
           S C++C      +QM  I  C   FC+ C+ ++V   I+ G+ T ++CP   C     L+
Sbjct: 6   SGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQ 65

Query: 103 FDACKSVLSKNVLELWEKALSQELIDAS 130
            +  + +++  +++ ++K   +    +S
Sbjct: 66  ENEIECMVAAEIMQRYKKLQFERSGPSS 93

>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 = 36.0 bits (83), Expect = 2e-04
 Identities = 11/25 (44%), Positives = 14/25 (56%)

Query: 189 KKQLRKCPNCKYHIERTGGCLHMTC 213
               ++CP C   IE+ GGC HM 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 = 35.8 bits (82), Expect = 4e-04
 Identities = 6/30 (20%), Positives = 10/30 (33%)

Query: 184 RELVKKKQLRKCPNCKYHIERTGGCLHMTC 213
             L++  +   C  C +        L  TC
Sbjct: 10  GVLMRDPKFLWCAQCSFGFIYEREQLEATC 39

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	214
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	99.79
d1wd2a_	60	Ariadne-1 protein homolog {Human (Homo sapiens) [T	99.11
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	99.05
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	98.86
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	98.8
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	98.72
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	98.64
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	98.64
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	98.58
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	98.56
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	98.56
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.56
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	98.46
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	98.45
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	98.42
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.4
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.26
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	97.79
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	97.67
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	97.63
d1wd2a_	60	Ariadne-1 protein homolog {Human (Homo sapiens) [T	96.89
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	96.66
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	96.03
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	90.83
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	88.86
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	88.0
d2akla2	38	Hypothetical protein PA0128, N-terminal domain {Ps	87.87
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	85.49
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	82.05
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	81.12
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	80.43

>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=99.79  E-value=6.6e-20  Score=122.30  Aligned_cols=88  Identities=22%  Similarity=0.498  Sum_probs=77.5

Q ss_pred             CcccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCC--cCcHHHHhhcCCHHHHHHH
Q 045388           41 PPSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKS--VLKFDACKSVLSKNVLELW  118 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~--~l~~~~~~~~l~~~~~~~~  118 (214)
                      ......|+||+++++.++++.++.|+|.||.+||..|+..+|.++.+.+|+||..+|..  .+...+|+.+++++++++|
T Consensus         2 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~~~~~~~~i~~ll~~~~~~ky   81 (94)
T d1wima_           2 SSGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQENEIECMVAAEIMQRY   81 (94)
T ss_dssp             CCSBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECHHHHHHHSCHHHHHHH
T ss_pred             CCCCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCCCCCcccCHHHHHHhCCHHHHHHH
Confidence            34578999999999988888778999999999999999999998887889999988864  5888999999999999999


Q ss_pred             HHHHHHHHhc
Q 045388          119 EKALSQELID  128 (214)
Q Consensus       119 ~~~~~~~~~~  128 (214)
                      +++.+++...
T Consensus        82 ~~~~l~~~~~   91 (94)
T d1wima_          82 KKLQFERSGP   91 (94)
T ss_dssp             HHHHHHSSCS
T ss_pred             HHHHHHhccc
Confidence            9998876543

>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=99.11  E-value=9.1e-12  Score=74.38  Aligned_cols=26  Identities=42%  Similarity=1.085  Sum_probs=23.8

Q ss_pred             hCCCccCCCCCccceecCCCCCeecC
Q 045388          189 KKQLRKCPNCKYHIERTGGCLHMTCL  214 (214)
Q Consensus       189 ~~~~k~CP~C~~~iek~~GCnhm~C~  214 (214)
                      ..++|+||+|+++|+|++|||||+|+
T Consensus         3 ~~ntK~CP~C~~~ieK~~GCnhM~C~   28 (60)
T d1wd2a_           3 AANTKECPKCHVTIEKDGGCNHMVCR   28 (60)
T ss_dssp             CCCCCCCTTTCCCCSSCCSCCSSSCC
T ss_pred             hhcCcCCCCCCCeEEECCCCCCeEeC
Confidence            35789999999999999999999994

>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=99.05  E-value=4.7e-12  Score=79.25  Aligned_cols=65  Identities=29%  Similarity=0.767  Sum_probs=52.1

Q ss_pred             HHHHHHHHHhcC-CCCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCC---CCChHHHHHHHHHH
Q 045388          118 WEKALSQELIDA-SQGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPW---HPGREELMMRELVK  188 (214)
Q Consensus       118 ~~~~~~~~~~~~-~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~---h~~~~~~~~~~~~~  188 (214)
                      |++++++++|.. ++.+|||  +|+++++.+.+.    +.++|+.|+..||+.|+.+|   |.|....++++|.+
T Consensus         3 Y~~~l~~~~l~~~~~~k~CP--~C~~~~~~~~~~----~~~~C~~C~~~fC~~C~~~w~~~H~~~tC~~~~~wk~   71 (73)
T d2ct7a1           3 FHKKLTEGVLMRDPKFLWCA--QCSFGFIYEREQ----LEATCPQCHQTFCVRCKRQWEEQHRGRSCEDFQNWKR   71 (73)
T ss_dssp             SSSCCCCSCCCSCCCEECCS--SSCCCEECCCSC----SCEECTTTCCEECSSSCSBCCTTTTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCCCC--CCCCEeEECCCC----CEEEcCCCCCeECcccCcchhcCCCCCCHHHHHHHHH
Confidence            344444555555 5778998  999999988764    78899999999999999999   99988888877743

>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=4e-10  Score=65.45  Aligned_cols=50  Identities=24%  Similarity=0.511  Sum_probs=38.0

Q ss_pred             ccccccccccccccc-cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcH
Q 045388           45 SSCEICRERRENDQM-FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF  103 (214)
Q Consensus        45 ~~C~iC~~~~~~~~~-~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~  103 (214)
                      .+|+||++++...+. +..+.|+|.||.+|+..|+..       ...+||.  |...++.
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~-------~~~~CP~--CR~~~~~   51 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTD-------ENGLCPA--CRKPYPE   51 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTT-------SCCBCTT--TCCBCSC
T ss_pred             CCCcCCChhhhCCCceEEecCCCCccchHHHHHHHhh-------cCCCCCc--cCCcCCC
Confidence            479999999876543 335689999999999999742       1347999  8887753

>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=98.80  E-value=2.2e-09  Score=71.46  Aligned_cols=69  Identities=28%  Similarity=0.462  Sum_probs=49.4

Q ss_pred             cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh-hcCCHHHHHHHHHHH
Q 045388           44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK-SVLSKNVLELWEKAL  122 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~-~~l~~~~~~~~~~~~  122 (214)
                      .++|+||++.+..+.   .++|||.||..|+..|+...    . ....||.  |+..+...+++ +....++.+++.+..
T Consensus        21 ~l~CpIC~~~~~~pv---~~~CgH~fC~~Ci~~~~~~~----~-~~~~CP~--Cr~~~~~~~l~~n~~l~~~ve~l~~~~   90 (103)
T d1jm7a_          21 ILECPICLELIKEPV---STKCDHIFCKFCMLKLLNQK----K-GPSQCPL--CKNDITKRSLQESTRFSQLVEELLKII   90 (103)
T ss_dssp             HTSCSSSCCCCSSCC---BCTTSCCCCSHHHHHHHHSS----S-SSCCCTT--TSCCCCTTTCBCCCSSSHHHHHHHHHH
T ss_pred             CcCCCccCchhCCeE---EcCCCCchhhHHHHHHHHHC----C-CCCcCcC--CCCcCChhhCCcCHHHHHHHHHHHHHH
Confidence            468999999886653   46899999999999997532    2 3468999  98888766653 233345666665443

>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=98.72  E-value=6.2e-09  Score=66.56  Aligned_cols=53  Identities=26%  Similarity=0.520  Sum_probs=41.4

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK  107 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~  107 (214)
                      +.++|+||++.+..+.   .+.|||.||+.|+..|+...       .-+||.  |+..+...++.
T Consensus        22 ~~l~C~IC~~~~~~pv---~~~CgH~FC~~Ci~~~~~~~-------~~~CP~--Cr~p~~~~~l~   74 (86)
T d1rmda2          22 KSISCQICEHILADPV---ETSCKHLFCRICILRCLKVM-------GSYCPS--CRYPCFPTDLE   74 (86)
T ss_dssp             HHTBCTTTCSBCSSEE---ECTTSCEEEHHHHHHHHHHT-------CSBCTT--TCCBCCGGGCB
T ss_pred             cCcCCccCCcchhcce---ecCCCChhhHHHHHHHHhhC-------CCcCcc--cCCCCChhhcc
Confidence            4578999999886653   57899999999999998631       236999  88888766543

>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=98.64  E-value=5e-09  Score=61.35  Aligned_cols=48  Identities=23%  Similarity=0.686  Sum_probs=37.1

Q ss_pred             cccccccccccccccccc-cCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388           44 RSSCEICRERRENDQMFK-IESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL  101 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~-~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l  101 (214)
                      ..+|+||++++...+.+. ...|+|.||.+|+..|+..        .-+||.  |...+
T Consensus         5 ~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~--------~~~CP~--CR~~i   53 (55)
T d1iyma_           5 GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGS--------HSTCPL--CRLTV   53 (55)
T ss_dssp             SCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTT--------CCSCSS--SCCCS
T ss_pred             CCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHh--------CCcCCC--CCCEe
Confidence            457999999998755443 4579999999999999752        236999  77654

>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=98.64  E-value=3.4e-09  Score=64.37  Aligned_cols=54  Identities=20%  Similarity=0.627  Sum_probs=38.9

Q ss_pred             cccccccccccccc--cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHH
Q 045388           44 RSSCEICRERREND--QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC  106 (214)
Q Consensus        44 ~~~C~iC~~~~~~~--~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~  106 (214)
                      ..+|+||++++..+  ..+....|+|.||.+|+..|+..    +.   -+||.  |...+...++
T Consensus         3 d~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~----~~---~~CP~--CR~~i~~~~~   58 (65)
T d1g25a_           3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVR----GA---GNCPE--CGTPLRKSNF   58 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHT----TS---SSCTT--TCCCCSSCCC
T ss_pred             CCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCc----Cc---CCCCC--CCcCcccccc
Confidence            47899999975332  22235689999999999999852    12   26999  9888765443

>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=98.58  E-value=2.3e-08  Score=62.96  Aligned_cols=47  Identities=30%  Similarity=0.734  Sum_probs=36.4

Q ss_pred             cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ...|+||++.+....   .+.|||.||.+|+..|+..    +   .-+||.  |+..+.
T Consensus        23 ~~~C~IC~~~~~~~~---~~~CgH~fC~~Ci~~wl~~----~---~~~CP~--Cr~~i~   69 (79)
T d1fbva4          23 FQLCKICAENDKDVK---IEPCGHLMCTSCLTSWQES----E---GQGCPF--CRCEIK   69 (79)
T ss_dssp             TTBCTTTSSSBCCEE---CSSSCCEECHHHHHHHHHT----T---CCSCTT--TCCCCC
T ss_pred             CCCCccCCCcCCCeE---EeCCCCeeeHHHHHHHHHH----C---cCcCCC--CCcCcc
Confidence            346999999876532   5789999999999999853    2   236999  887764

>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=98.56  E-value=2.5e-08  Score=67.38  Aligned_cols=54  Identities=22%  Similarity=0.544  Sum_probs=39.8

Q ss_pred             cccccccccccccc---------------cccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           44 RSSCEICRERREND---------------QMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        44 ~~~C~iC~~~~~~~---------------~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ...|+||++++...               ..+..+.|+|.||.+||..|+..+-..   ..++||.  |...+.
T Consensus        25 ~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~---~~~~CP~--CR~~~~   93 (114)
T d1v87a_          25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKD---GSLQCPS--CKTIYG   93 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCS---SCCBCTT--TCCBSS
T ss_pred             cccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcC---CCCcccc--ccchhc
Confidence            35799999987532               223357899999999999999765333   2478999  877663

>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=98.56  E-value=1.6e-08  Score=61.91  Aligned_cols=47  Identities=34%  Similarity=0.764  Sum_probs=36.9

Q ss_pred             cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ...|+||++.+....  ..+.|+|.||..|+..|+..        .-+||.  |+..+.
T Consensus         5 ~d~C~IC~~~~~~~~--~~~~C~H~Fc~~Ci~~w~~~--------~~~CP~--CR~~i~   51 (68)
T d1chca_           5 AERCPICLEDPSNYS--MALPCLHAFCYVCITRWIRQ--------NPTCPL--CKVPVE   51 (68)
T ss_dssp             CCCCSSCCSCCCSCE--EETTTTEEESTTHHHHHHHH--------SCSTTT--TCCCCC
T ss_pred             CCCCccCCcCccCCc--EEeCCCCcCcHHHHHHHHHh--------CCcCCC--CCcchH
Confidence            457999999986543  25799999999999999863        237999  887653

>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=98.56  E-value=1.4e-08  Score=63.88  Aligned_cols=66  Identities=24%  Similarity=0.408  Sum_probs=47.7

Q ss_pred             cccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHh-hcCCHHHHHHHH
Q 045388           42 PSRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACK-SVLSKNVLELWE  119 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~-~~l~~~~~~~~~  119 (214)
                      .+.+.|+||++.+..+.   .+.|||.||+.|+..|+..    +   .-.||.  |+..+...++. ++...+.++.|.
T Consensus         6 P~~l~CpIc~~~m~dPV---~~~cgh~fc~~ci~~~~~~----~---~~~cP~--~~~~l~~~~l~pN~~L~~~I~~~~   72 (78)
T d1t1ha_           6 PEYFRCPISLELMKDPV---IVSTGQTYERSSIQKWLDA----G---HKTCPK--SQETLLHAGLTPNYVLKSLIALWC   72 (78)
T ss_dssp             SSSSSCTTTSCCCSSEE---EETTTEEEEHHHHHHHHTT----T---CCBCTT--TCCBCSSCCCEECTTTHHHHHHHH
T ss_pred             CccCCCcCcCchhhCce---EccCCCcchHHHHHHHHHH----C---CCCCCc--ccccCCcccccchHHHHHHHHHHH
Confidence            35799999999987764   4689999999999999853    1   236898  77777655443 444556666653

>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=98.46  E-value=1.2e-08  Score=59.75  Aligned_cols=45  Identities=22%  Similarity=0.747  Sum_probs=34.9

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcH
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKF  103 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~  103 (214)
                      +..+|+||++.+..+.   .++|||.||..|+.+           ...+||.  |+..+..
T Consensus         5 ~~l~C~IC~~~~~~p~---~lpCgH~fC~~Ci~~-----------~~~~CP~--Cr~~~~~   49 (56)
T d1bora_           5 QFLRCQQCQAEAKCPK---LLPCLHTLCSGCLEA-----------SGMQCPI--CQAPWPL   49 (56)
T ss_dssp             CCSSCSSSCSSCBCCS---CSTTSCCSBTTTCSS-----------SSSSCSS--CCSSSSC
T ss_pred             CCCCCcccCcccCCCE---EecCCCHHhHHHHHc-----------CCCcCcC--CCCcccC
Confidence            4579999999987653   578999999999742           1458999  8876654

>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=98.45  E-value=2.9e-08  Score=62.73  Aligned_cols=51  Identities=16%  Similarity=0.044  Sum_probs=40.3

Q ss_pred             ccccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHH
Q 045388           43 SRSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDA  105 (214)
Q Consensus        43 ~~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~  105 (214)
                      +.+.|+||++-+..+.   .+.|||.||+.||..|+..   .    .-.||.  |+..+..++
T Consensus         6 ~~l~CpIc~~l~~dPv---~~~cGhtfc~~ci~~~l~~---~----~~~cP~--c~~~l~~~~   56 (80)
T d2c2la2           6 DYLCGKISFELMREPC---ITPSGITYDRKDIEEHLQR---V----GHFNPV--TRSPLTQEQ   56 (80)
T ss_dssp             STTBCTTTCSBCSSEE---ECSSCCEEETTHHHHHHHH---T----CSSCTT--TCCCCCGGG
T ss_pred             ccccCcCcCchhhhhc---ccCCcCeecHHHHHHHHhc---C----CccCCC--ccccccccc
Confidence            5689999999887763   4799999999999999853   1    236999  777776554

>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=98.42  E-value=3.3e-08  Score=58.00  Aligned_cols=51  Identities=12%  Similarity=0.105  Sum_probs=40.1

Q ss_pred             cccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHHhh
Q 045388           46 SCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDACKS  108 (214)
Q Consensus        46 ~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~~~  108 (214)
                      .|+||++.+..+.+  ...|||.||++|+..|+...        -+||.  |+..+..+++..
T Consensus         2 ~C~Ic~~~~~~Pv~--~~~cGh~fc~~cI~~~l~~~--------~~CP~--c~~~l~~~dLip   52 (56)
T d2baya1           2 LCAISGKVPRRPVL--SPKSRTIFEKSLLEQYVKDT--------GNDPI--TNEPLSIEEIVE   52 (56)
T ss_dssp             CCTTTCSCCSSEEE--ETTTTEEEEHHHHHHHHHHH--------SBCTT--TCCBCCGGGCEE
T ss_pred             CCccCCchHHhcCc--cCCCCCcccHHHHHHHHhhc--------cCCCc--cCCcCCHHhcee
Confidence            69999998876532  45799999999999999752        15999  888888776543

>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=98.40  E-value=1.4e-08  Score=66.63  Aligned_cols=48  Identities=23%  Similarity=0.611  Sum_probs=36.9

Q ss_pred             cccccccccccccccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHH
Q 045388           44 RSSCEICRERRENDQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDA  105 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~  105 (214)
                      .++|+||++.+..+..  ...|||.||..||..|+.          -.||.  |+..+...+
T Consensus        22 ~l~C~IC~~~~~~pv~--~~~CgH~fC~~Ci~~~~~----------~~CP~--Cr~~~~~~~   69 (97)
T d1jm7b_          22 LLRCSRCTNILREPVC--LGGCEHIFCSNCVSDCIG----------TGCPV--CYTPAWIQD   69 (97)
T ss_dssp             TTSCSSSCSCCSSCBC--CCSSSCCBCTTTGGGGTT----------TBCSS--SCCBCSCSS
T ss_pred             cCCCccCCchhhcCce--eCCCCCchhHHHHHHHHh----------ccccc--cCCcCchhh
Confidence            4689999999876532  358999999999998862          14999  887665443

>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=98.26  E-value=5.9e-07  Score=53.21  Aligned_cols=53  Identities=17%  Similarity=0.384  Sum_probs=39.0

Q ss_pred             cccccccccccccccccccc--cCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           42 PSRSSCEICRERRENDQMFK--IESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~--~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      .+...|.||++++....+..  ..+|+|.|+..||..|+..+-      ..+||.  |+..+.
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~------~~~CP~--Cr~~~~   58 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISR------NTACQI--CGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHT------CSBCTT--TCCBCC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCC------CCCCcc--cCCeee
Confidence            45677999999887654332  345679999999999996542      247999  887664

>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=97.79  E-value=6.8e-06  Score=52.36  Aligned_cols=49  Identities=24%  Similarity=0.492  Sum_probs=35.4

Q ss_pred             cccccccccccccccc---------------cccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCc
Q 045388           44 RSSCEICRERRENDQM---------------FKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLK  102 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~---------------~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~  102 (214)
                      ...|.||++++.....               +..+.|+|.|+.+||..|++.        .-+||.  |...+.
T Consensus        21 ~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~--------~~~CP~--CR~~~~   84 (88)
T d3dplr1          21 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKT--------RQVCPL--DNREWE   84 (88)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTT--------CSBCSS--SCSBCC
T ss_pred             CCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHH--------CCcCCC--CCCccc
Confidence            4468999887654221               224689999999999999853        236999  887664

>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=97.67  E-value=3.9e-06  Score=51.55  Aligned_cols=27  Identities=19%  Similarity=0.443  Sum_probs=24.6

Q ss_pred             HhCCCccCCCCCccceecCCCCCeecC
Q 045388          188 KKKQLRKCPNCKYHIERTGGCLHMTCL  214 (214)
Q Consensus       188 ~~~~~k~CP~C~~~iek~~GCnhm~C~  214 (214)
                      ++.+++.||+|+..|++++||+||+|+
T Consensus        14 ~~~~~k~CP~C~~~~~~~~~~~~~~C~   40 (73)
T d2ct7a1          14 RDPKFLWCAQCSFGFIYEREQLEATCP   40 (73)
T ss_dssp             SCCCEECCSSSCCCEECCCSCSCEECT
T ss_pred             HCCCCCCCCCCCCEeEECCCCCEEEcC
Confidence            456889999999999999999999995

>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=97.63  E-value=1.1e-05  Score=52.38  Aligned_cols=52  Identities=15%  Similarity=0.031  Sum_probs=37.8

Q ss_pred             cccccccccccccccccccccCCC-CccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcCcHHHH
Q 045388           42 PSRSSCEICRERRENDQMFKIESC-IHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVLKFDAC  106 (214)
Q Consensus        42 ~~~~~C~iC~~~~~~~~~~~~~~C-~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l~~~~~  106 (214)
                      .+.+.|+||++-+..+.   .+.| +|.||+.||..|+..    +.    .||.  |+..|..+++
T Consensus        20 P~~f~CPI~~~lm~dPV---~~~~~~~ty~r~~I~~~l~~----~~----~~P~--~~~~l~~~~L   72 (98)
T d1wgma_          20 CDEFLDPIMSTLMCDPV---VLPSSRVTVDRSTIARHLLS----DQ----TDPF--NRSPLTMDQI   72 (98)
T ss_dssp             CTTTBCTTTCSBCSSEE---ECTTTCCEEEHHHHHHHTTT----SC----BCTT--TCSBCCTTTS
T ss_pred             cHHhCCcCchhHHHHHH---hcccccchhhHHHHHHHHHh----cC----Cccc--ccccccchhh
Confidence            34799999999887764   3444 568999999999742    22    5888  7777765543

>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=96.89  E-value=0.00028  Score=41.04  Aligned_cols=39  Identities=26%  Similarity=0.733  Sum_probs=33.0

Q ss_pred             CCCcccCccCCCceeeecCCCCCCcCcccCC--CCChhhccccCCCC
Q 045388          130 SQGIYCPFKDCSAKLVYENDGEDVLSESECP--YCHRLFCAHCYVPW  174 (214)
Q Consensus       130 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~--~C~~~~C~~C~~~~  174 (214)
                      .+.+.||  +|...+....+-    +.++|.  .|+..||+.|..+|
T Consensus         4 ~ntK~CP--~C~~~ieK~~GC----nhM~C~~~~C~~~fCw~C~~~~   44 (60)
T d1wd2a_           4 ANTKECP--KCHVTIEKDGGC----NHMVCRNQNCKAEFCWVCLGPW   44 (60)
T ss_dssp             CCCCCCT--TTCCCCSSCCSC----CSSSCCSSGGGSCCSSSSCSCS
T ss_pred             hcCcCCC--CCCCeEEECCCC----CCeEeCCCCCCCeEECCCCCcc
Confidence            3467899  999999998774    888994  69999999999876

>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=96.66  E-value=0.0022  Score=37.69  Aligned_cols=54  Identities=30%  Similarity=0.636  Sum_probs=41.1

Q ss_pred             CcccccccccccccccccccccCC-CCccccHHHHHHHHHHHhhCCCcccccCCCC-CC
Q 045388           41 PPSRSSCEICRERRENDQMFKIES-CIHSFCSDCINKHVATKIQGGIITPVTCPGP-DC   97 (214)
Q Consensus        41 ~~~~~~C~iC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~-~C   97 (214)
                      +.....|.+|.+.+++..+++..+ =.|.||..|-+.+|+.+..++.   +.||.. .|
T Consensus         5 ~~~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~q~~~~e---vyCPSG~kC   60 (80)
T d2cs3a1           5 NSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKAQGATGE---VYCPSGEKC   60 (80)
T ss_dssp             SCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHHHHSSSC---CCCTTSSCC
T ss_pred             CCCceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHhcCCCCc---EECCCCCcc
Confidence            445689999999999888765222 2699999999999998887654   677773 44

>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=96.03  E-value=0.0034  Score=38.25  Aligned_cols=63  Identities=24%  Similarity=0.589  Sum_probs=48.5

Q ss_pred             CCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceecCCCCC
Q 045388          131 QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERTGGCLH  210 (214)
Q Consensus       131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~~GCnh  210 (214)
                      +...|.  -|+--+-.+..+   ...+.|..|+.-+|..|..             +.+....+.||.|+++..+..|+..
T Consensus        15 ~~q~Cq--iCGd~VG~~~~G---e~FVAC~eC~FPvCrpCyE-------------YErkeG~q~CpqCkt~Ykr~kgspr   76 (93)
T d1weoa_          15 DGQFCE--ICGDQIGLTVEG---DLFVACNECGFPACRPCYE-------------YERREGTQNCPQCKTRYKRLRGSPR   76 (93)
T ss_dssp             SSCBCS--SSCCBCCBCSSS---SBCCSCSSSCCCCCHHHHH-------------HHHHTSCSSCTTTCCCCCCCTTCCC
T ss_pred             ccchhh--hcccccccCCCC---CEEEEecccCCccchHHHH-------------HHHhccCccCcccCChhhhhcCCCC
Confidence            344677  777666665544   3788899999999998853             5566788999999999998888765


Q ss_pred             e
Q 045388          211 M  211 (214)
Q Consensus       211 m  211 (214)
                      +
T Consensus        77 v   77 (93)
T d1weoa_          77 V   77 (93)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=90.83  E-value=0.038  Score=31.18  Aligned_cols=37  Identities=27%  Similarity=0.678  Sum_probs=26.6

Q ss_pred             CCcccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCC
Q 045388          131 QGIYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHP  176 (214)
Q Consensus       131 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~  176 (214)
                      +.+.|-  +|...+.  +     .....|+.|+..||..|..-.|+
T Consensus        14 ~~~~C~--gC~~~l~--~-----~~~y~C~~C~~~FC~dCD~fiHe   50 (59)
T d1z60a1          14 GERFCY--GCQGELK--D-----QHVYVCAVCQNVFCVDCDVFVHD   50 (59)
T ss_dssp             SCCEET--TTTEECT--T-----SEEECCTTTTCCBCHHHHHTTTT
T ss_pred             CCCCcc--CCCCcCC--C-----CceEECcCCCCccccccchhhhh
Confidence            445677  7775442  1     24578999999999999877664

>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=88.86  E-value=0.095  Score=30.21  Aligned_cols=32  Identities=22%  Similarity=0.670  Sum_probs=23.3

Q ss_pred             CCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccceec
Q 045388          161 YCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIERT  205 (214)
Q Consensus       161 ~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek~  205 (214)
                      .||+.||..|...            |.. ...+.||.|+..|.++
T Consensus        25 ~C~H~fc~~Ci~~------------~~~-~~~~~CP~CR~~i~~~   56 (65)
T d1g25a_          25 VCGHTLCESCVDL------------LFV-RGAGNCPECGTPLRKS   56 (65)
T ss_dssp             TTCCCEEHHHHHH------------HHH-TTSSSCTTTCCCCSSC
T ss_pred             ccChHhhHHHHHH------------HhC-cCcCCCCCCCcCcccc
Confidence            5899999999643            332 2345799999988664

>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=88.00  E-value=0.11  Score=32.42  Aligned_cols=45  Identities=22%  Similarity=0.492  Sum_probs=30.7

Q ss_pred             cccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCcccee
Q 045388          133 IYCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIER  204 (214)
Q Consensus       133 ~~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~iek  204 (214)
                      ..||  -|...+..        + +....||+.||..|...|-.                ..||.|+..+..
T Consensus        23 l~C~--IC~~~~~~--------p-v~~~~CgH~fC~~Ci~~~~~----------------~~CP~Cr~~~~~   67 (97)
T d1jm7b_          23 LRCS--RCTNILRE--------P-VCLGGCEHIFCSNCVSDCIG----------------TGCPVCYTPAWI   67 (97)
T ss_dssp             TSCS--SSCSCCSS--------C-BCCCSSSCCBCTTTGGGGTT----------------TBCSSSCCBCSC
T ss_pred             CCCc--cCCchhhc--------C-ceeCCCCCchhHHHHHHHHh----------------ccccccCCcCch
Confidence            4588  77766632        1 23446999999999765531                249999987754

>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=87.87  E-value=0.083  Score=26.87  Aligned_cols=25  Identities=32%  Similarity=0.860  Sum_probs=18.8

Q ss_pred             ccCccCCCceeeecCCCCCCcCcccCCCCChh
Q 045388          134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRL  165 (214)
Q Consensus       134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~  165 (214)
                      .||  .|+.-+.+.++     ..+.||.|++.
T Consensus         5 ~CP--~C~seytYedg-----~l~vCPeC~hE   29 (38)
T d2akla2           5 PCP--QCNSEYTYEDG-----ALLVCPECAHE   29 (38)
T ss_dssp             CCT--TTCCCCCEECS-----SSEEETTTTEE
T ss_pred             cCC--CCCCcceEcCC-----CEEECCcccCc
Confidence            477  89988888776     56678877764

>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=85.49  E-value=0.2  Score=28.12  Aligned_cols=30  Identities=23%  Similarity=0.711  Sum_probs=25.6

Q ss_pred             cccccccccccccccccccCCCCccccHHH
Q 045388           44 RSSCEICRERRENDQMFKIESCIHSFCSDC   73 (214)
Q Consensus        44 ~~~C~iC~~~~~~~~~~~~~~C~H~fC~~C   73 (214)
                      ...|--|...+.....+....|++.||.+|
T Consensus        15 ~~~C~gC~~~l~~~~~y~C~~C~~~FC~dC   44 (59)
T d1z60a1          15 ERFCYGCQGELKDQHVYVCAVCQNVFCVDC   44 (59)
T ss_dssp             CCEETTTTEECTTSEEECCTTTTCCBCHHH
T ss_pred             CCCccCCCCcCCCCceEECcCCCCcccccc
Confidence            457999998888776677889999999999

>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=82.05  E-value=0.25  Score=31.06  Aligned_cols=47  Identities=32%  Similarity=0.782  Sum_probs=30.2

Q ss_pred             ccCccCCCceeeecCCCCCCcCcccCCCCChhhccccCCCCCCChHHHHHHHHHH-hCCCccCCCCCcccee
Q 045388          134 YCPFKDCSAKLVYENDGEDVLSESECPYCHRLFCAHCYVPWHPGREELMMRELVK-KKQLRKCPNCKYHIER  204 (214)
Q Consensus       134 ~Cp~~~C~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~-~~~~k~CP~C~~~iek  204 (214)
                      .||  =|...+..        + +.- .||+.||..|..            +|.. ..+...||.|+..+..
T Consensus        23 ~Cp--IC~~~~~~--------p-v~~-~CgH~fC~~Ci~------------~~~~~~~~~~~CP~Cr~~~~~   70 (103)
T d1jm7a_          23 ECP--ICLELIKE--------P-VST-KCDHIFCKFCML------------KLLNQKKGPSQCPLCKNDITK   70 (103)
T ss_dssp             SCS--SSCCCCSS--------C-CBC-TTSCCCCSHHHH------------HHHHSSSSSCCCTTTSCCCCT
T ss_pred             CCC--ccCchhCC--------e-EEc-CCCCchhhHHHH------------HHHHHCCCCCcCcCCCCcCCh
Confidence            488  77765531        1 122 489999999953            2333 2345689999988754

>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=81.12  E-value=0.61  Score=25.97  Aligned_cols=35  Identities=11%  Similarity=0.201  Sum_probs=24.2

Q ss_pred             ccCCCCChhhccccCCCCCCChHHHHHHHHHHhCCCccCCCCCccce
Q 045388          157 SECPYCHRLFCAHCYVPWHPGREELMMRELVKKKQLRKCPNCKYHIE  203 (214)
Q Consensus       157 ~~C~~C~~~~C~~C~~~~h~~~~~~~~~~~~~~~~~k~CP~C~~~ie  203 (214)
                      ..|..|+..|+..|..            .|+...+...||-|+..+.
T Consensus        24 c~c~~c~h~~H~~Cl~------------~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_          24 CGCTGELENVHRSCLS------------TWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CCCSSGGGSCCHHHHH------------HHHHHHTCSBCTTTCCBCC
T ss_pred             cccCCCCCEEcHHHHH------------HHHhhCCCCCCcccCCeee
Confidence            3566778888888854            3444334568999998764

>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=80.43  E-value=3.2  Score=24.74  Aligned_cols=55  Identities=25%  Similarity=0.561  Sum_probs=38.0

Q ss_pred             CCCCccccccccccccccc----ccccccCCCCccccHHHHHHHHHHHhhCCCcccccCCCCCCCCcC
Q 045388           38 PSSPPSRSSCEICRERREN----DQMFKIESCIHSFCSDCINKHVATKIQGGIITPVTCPGPDCKSVL  101 (214)
Q Consensus        38 ~~~~~~~~~C~iC~~~~~~----~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C~~~l  101 (214)
                      +........|.||-+++..    +.++..-.|+-.+|+.|+.--    +++|.   -.||.  |+..+
T Consensus        10 p~~~~~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYE----rkeG~---q~Cpq--Ckt~Y   68 (93)
T d1weoa_          10 PLKNLDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYE----RREGT---QNCPQ--CKTRY   68 (93)
T ss_dssp             CCSCCSSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHH----HHTSC---SSCTT--TCCCC
T ss_pred             ChhhcccchhhhcccccccCCCCCEEEEecccCCccchHHHHHH----HhccC---ccCcc--cCChh
Confidence            3344456789999999753    334446788999999997643    34555   47898  87655