Citrus Sinensis ID: 043865

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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---
Protein Sequence
KIECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSASGCLCKEKGDVYCHHYCAIISGLILIFTVLGVLGGVIYGIYCVIKRVLF
Secondary Structure (PSIPRED)
ccccccccccccccHHHHcccccHHHHHHHHHHHHHHHHcccccEEcccccccccccccccccccccccEEccccccccccccccccccccccHHHHccccccHHHHHHHHHHccccccccccccEEcccccccEEEcccccEEcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEEEcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccHHHHHHHccHHHHHHHHHHHHHHHcccccccEcccccccEEEEEcccccccccEEEEccccccEEEEcccccccccccHHHHHHcccccHHHHHHHHHHcccccccccccEEEEcccccEEEEEcccEEEHHccccHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
kiecpgvhcdqfldlftcklmipsnlfskWCDVLCEdyvlgfersycpnrncmaLVVNEgeinygtlkkarcpnckqwfCFQCKvawhagyrceesgnlrdwndIAFGKLVErmhgarrpacgscverkegcrvmycrcktsfcyecggnlksasgclckekgdvychHYCAIISGLILIFTVLGVLGGVIYGIYCVIKRVLF
Flexible Loop (DISEMBL)
kiecpgvhcDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERmhgarrpacgscverkegCRVMYCRCKTSFCYECGGNLKSASGCLCKEKGDVYCHHYCAIISGLILIFTVLGVLGGVIYGIYCVIKRVLF
Low Complexity Region (SEG)
KIECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSASGCLCKEKGDVYCHHYCAIISGLILIFTvlgvlggviygiycviKRVLF
Disordered region (IsUnstruct)
***CPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSASGCLCKEKGDVYCHHYCAIISGLILIFTVLGVLGGVIYGIYCVIKRVL*
Disordered Region (DISOPRED)
KIECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSASGCLCKEKGDVYCHHYCAIISGLILIFTVLGVLGGVIYGIYCVIKRVLF
Disordered Region (DISEMBL)
KIECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSASGCLCKEKGDVYCHHYCAIISGLILIFTVLGVLGGVIYGIYCVIKRVLF
Disordered Region (DISPRO)
KIECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSASGCLCKEKGDVYCHHYCAIISGLILIFTVLGVLGGVIYGIYCVIKRVLF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHHHiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
KIECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSASGCLCKEKGDVYCHHYCAIISGLILIFTVLGVLGGVIYGIYCVIKRVLF
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	203	2.2.26 [Sep-21-2011]
Q4KLT0	282	Probable E3 ubiquitin-pro	N/A	no	0.704	0.507	0.291	8e-10
P50876	292	Probable E3 ubiquitin-pro	yes	no	0.738	0.513	0.293	8e-09
Q8TC41	275	Probable E3 ubiquitin-pro	no	no	0.689	0.509	0.298	5e-08
D3YYI7	515	Probable E3 ubiquitin-pro	yes	no	0.665	0.262	0.313	8e-08
Q5RFV4	293	Probable E3 ubiquitin-pro	no	no	0.733	0.508	0.278	2e-07
Q7Z419	303	E3 ubiquitin-protein liga	no	no	0.778	0.521	0.295	2e-07
A5PK27	304	E3 ubiquitin-protein liga	no	no	0.778	0.519	0.295	2e-07
A4IIY1	292	Probable E3 ubiquitin-pro	no	no	0.911	0.633	0.271	2e-07
Q9NWF9	866	E3 ubiquitin-protein liga	no	no	0.384	0.090	0.359	2e-07
Q925F3	292	Probable E3 ubiquitin-pro	no	no	0.733	0.510	0.310	2e-07

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

 Score = 63.9 bits (154), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 49/168 (29%), Positives = 72/168 (42%), Gaps = 25/168 (14%)

Query: 1   KIECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFER-----SYCPNRNCMAL 55
           +I+CP   C++ LD  T    +P +      D++   Y L   R       CP       
Sbjct: 41  EIQCPITECNKHLDESTILYSLPHD------DIIKYKYFLELSRMDSSTKPCPQCKHFTT 94

Query: 56  VVNEGEINYGTLK----KARCPNCKQWFCFQCKVAWHAGYRCEESGN----LRDW-NDIA 106
              +  I   T      K +CP+C+  +CF+C   WH G  C E       LR W N+I 
Sbjct: 95  FKRKTHIPNPTKSENKLKIQCPSCQFIWCFRCHAPWHEGVNCREYKKGDKLLRHWANEIE 154

Query: 107 FGKLVERMHGARRPACGSCVERKEGCRVMYC-RCKTSFCYECGGNLKS 153
            G+     +  + P C   ++R EGC  M C +C T+FCY CG   + 
Sbjct: 155 HGQ----RNAQKCPRCKVHIQRTEGCDHMTCSQCNTNFCYRCGERYRQ 198

E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes in the form of a thioester and then directly transfers the ubiquitin to targeted substrates.
Xenopus laevis (taxid: 8355)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

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

 Score = 60.5 bits (145), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 47/160 (29%), Positives = 71/160 (44%), Gaps = 10/160 (6%)

Query: 2   IECPGVHCDQ--FLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFE--RSYCPNRNCMALVV 57
           I CP   C +   L     + M+ + +  ++  +  E  VL F+  R++CP   C A V 
Sbjct: 63  ISCPDAACPKQGHLQENEIECMVAAEIMQRYKKLQFEREVL-FDPCRTWCPASTCQA-VC 120

Query: 58  NEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGN---LRDWNDIAFGKLVERM 114
              ++   T +  +C  C+  FC  CK +WH G  C E+     L      AF    +  
Sbjct: 121 QLQDVGLQTPQPVQCKACRMEFCSTCKASWHPGQGCPETMPITFLPGETSAAFKMEEDDA 180

Query: 115 HGARRPACGSCVERKEGCRVMYCR-CKTSFCYECGGNLKS 153
              R P C   +ER EGC  M C+ CK +FC+ C  +L  
Sbjct: 181 PIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLDD 220

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|Q8TC41|RN217_HUMAN Probable E3 ubiquitin-protein ligase RNF217 OS=Homo sapiens GN=RNF217 PE=2 SV=3

 Score = 57.8 bits (138), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 51/171 (29%), Positives = 70/171 (40%), Gaps = 31/171 (18%)

Query: 1   KIECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFER-----SYCPNRNCMAL 55
           +I+CP   C +FL+  T    +  NL  +  D +   Y L   R       CP       
Sbjct: 9   EIKCPITECFEFLEETT----VVYNLTHE--DSIKYKYFLELGRIDSSTKPCPQCKHFTT 62

Query: 56  VVNEGEINYGTLK----KARCPNCKQWFCFQCKVAWHAGYRCEESGN----LRDWNDIAF 107
              +G I   +      K +CP C+  +CF+C   WH G  C+E       LR W     
Sbjct: 63  FKKKGHIPTPSRSESKYKIQCPTCQFVWCFKCHSPWHEGVNCKEYKKGDKLLRHWAS--- 119

Query: 108 GKLVERMHGARR----PACGSCVERKEGCRVMYC-RCKTSFCYECGGNLKS 153
               E  HG R     P C   ++R EGC  M C +C T+FCY CG   + 
Sbjct: 120 ----EIEHGQRNAQKCPKCKIHIQRTEGCDHMTCSQCNTNFCYRCGERYRQ 166

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.

Homo sapiens (taxid: 9606)

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 = 57.0 bits (136), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 52/166 (31%), Positives = 72/166 (43%), Gaps = 31/166 (18%)

Query: 1   KIECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFER-----SYCPNRNCMAL 55
           +I+CP   C +FL+  T    +  NL  +  D +   Y L   R       CP       
Sbjct: 274 EIKCPVTECFEFLEETT----VVYNLTHE--DSIKYKYFLELGRIDSSTKPCPQCKHFTT 327

Query: 56  VVNEGEINYGTLKKAR----CPNCKQWFCFQCKVAWHAGYRCEE--SGN--LRDWNDIAF 107
              +G I   +  ++R    CP C+  +CF+C   WH G  C+E   G+  LR W     
Sbjct: 328 FKKKGHIPTPSRSESRYKIQCPTCQLIWCFKCHSPWHEGVNCKEYKKGDKLLRHWAS--- 384

Query: 108 GKLVERMHGARR----PACGSCVERKEGCRVMYC-RCKTSFCYECG 148
               E  HG R     P C   ++R EGC  M C +C T+FCY CG
Sbjct: 385 ----EIEHGQRNAQKCPKCKIHIQRTEGCDHMTCSQCNTNFCYRCG 426

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

 Score = 56.2 bits (134), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 44/158 (27%), Positives = 72/158 (45%), Gaps = 9/158 (5%)

Query: 2   IECPGVHCDQ--FLDLFTCKLMIPSNLFSKWCDVLCE-DYVLGFERSYCPNRNCMALVVN 58
           I CP   C +   L     + M+ + +  ++  +  E + +L   R++CP+  C A V  
Sbjct: 63  ISCPDSACPKRGHLQENEIECMVATEIMQRYRKLQFEKEVLLDPSRTWCPSSTCQA-VCQ 121

Query: 59  EGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDW---NDIAFGKLVERMH 115
             E +    +  RC  C   FC  CK +WH    C+E+  +  +      +F K  +   
Sbjct: 122 LKESDTVLPQLVRCSVCTLEFCSACKASWHPDQDCQENVPITSFLPGESSSFFKADDDDA 181

Query: 116 GARR-PACGSCVERKEGCRVMYCR-CKTSFCYECGGNL 151
             +R P C   +ER EGC  M C+ CK +FC+ C  +L
Sbjct: 182 PIKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESL 219

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

Danio rerio (taxid: 7955)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score = 56.2 bits (134), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 52/176 (29%), Positives = 75/176 (42%), Gaps = 18/176 (10%)

Query: 1   KIECPGVHCDQFLDLFTCKL--MIPSNLFSKWCDVLCEDYV-LGFERSYCPNRNCMALVV 57
            I CP + C     L   ++  ++P + F  +  +  E  V L   R++CP  +C   V 
Sbjct: 72  PITCPDMVCLNHGTLQEAEIACLVPVDQFQLYQRLKFEREVHLDPYRTWCPVADCQT-VC 130

Query: 58  NEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGN--LRDWNDIAFGKLVERMH 115
                + G      CP+C   FC  CK AWHA   C +S    L   +   FG   E   
Sbjct: 131 PVASSDPGQPVLVECPSCHLKFCSCCKDAWHAEVSCRDSQPIVLPTEHRALFGTDAE-AP 189

Query: 116 GARRPACGSCVERKEGCRVMYCR-CKTSFCYECGGNLKSASGCLCKEKGDVYCHHY 170
             + P C   +ER EGC  M C+ CK +FC+ C  NL +          D++  HY
Sbjct: 190 IKQCPVCRVYIERNEGCAQMMCKNCKHTFCWYCLQNLDN----------DIFLRHY 235

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

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score = 55.8 bits (133), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 52/176 (29%), Positives = 76/176 (43%), Gaps = 18/176 (10%)

Query: 1   KIECPGVHCDQFLDLFTCKL--MIPSNLFSKWCDVLCEDYV-LGFERSYCPNRNCMALVV 57
            I CP + C     L   ++  ++P + F  +  +  E  V L   R++CP  +C   V 
Sbjct: 73  PITCPDMVCLNHGTLQEAEIACLVPVDQFQLYQRLKFEREVHLDPCRTWCPVADCQT-VC 131

Query: 58  NEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEES--GNLRDWNDIAFGKLVERMH 115
                + G      CP+C   FC  CK AWHA   C +S  G L   +   FG   +   
Sbjct: 132 PVATSDPGQPVLVECPSCHLKFCSCCKDAWHAEVSCRDSQPGILPTEHGTLFGTETD-AP 190

Query: 116 GARRPACGSCVERKEGCRVMYCR-CKTSFCYECGGNLKSASGCLCKEKGDVYCHHY 170
             + P C   +ER EGC  M C+ CK +FC+ C  NL +          D++  HY
Sbjct: 191 IKQCPVCRVYIERNEGCAQMMCKNCKHTFCWYCLQNLDN----------DIFLRHY 236

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

 Score = 55.8 bits (133), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 54/199 (27%), Positives = 88/199 (44%), Gaps = 14/199 (7%)

Query: 2   IECPGVHCDQ--FLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFE-RSYCPNRNCMALVVN 58
           I CP   C +   L     + M+ + +  K+  +  E  +L    R++CP+ +C A V  
Sbjct: 63  ISCPDASCPKRGHLQENEIECMVAAEIMQKYKKLQFEKEILLDPCRTWCPSSSCQA-VCK 121

Query: 59  EGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLR--DWNDIAFGKLVERMHG 116
             E      +  +C  C   FC  CK  WH G  C E+  +     +  +F K +E    
Sbjct: 122 LQEKGIQNPQLVQCSACDIEFCSACKANWHPGQGCPENMAITFLPGDSSSFFKSLEDDVP 181

Query: 117 ARR-PACGSCVERKEGCRVMYCR-CKTSFCYECGGNLKSASGCLCKEKG---DVYCHHYC 171
            +R P C   +ER EGC  M C+ CK +FC+ C  +L      +  +KG   +   H   
Sbjct: 182 IKRCPKCKVYIERDEGCAQMMCKNCKHAFCWYCLESLDDDFLLIHYDKGPCRNKLGHSRA 241

Query: 172 AII---SGLILIFTVLGVL 187
           ++I   + ++ IF   G+L
Sbjct: 242 SVIWHRTQVVGIFAGFGLL 260

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

Xenopus tropicalis (taxid: 8364)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9NWF9|RN216_HUMAN E3 ubiquitin-protein ligase RNF216 OS=Homo sapiens GN=RNF216 PE=1 SV=3

 Score = 55.8 bits (133), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 32/89 (35%), Positives = 45/89 (50%), Gaps = 11/89 (12%)

Query: 67  LKKARCPN--CKQWFCFQCKVAW--HAGYRCEESGNLRDWNDIAF-GKLVERMHGARRPA 121
           +K+  CPN  C++  C +C+  W  H G  CEE   L + +DI +   + E+M  AR   
Sbjct: 618 VKRFSCPNPHCRKETCRKCQGLWKEHNGLTCEE---LAEKDDIKYRTSIEEKMTAARIRK 674

Query: 122 CGSC---VERKEGCRVMYCRCKTSFCYEC 147
           C  C   + + EGC  M CRC    CY C
Sbjct: 675 CHKCGTGLIKSEGCNRMSCRCGAQMCYLC 703

Isoform 1 acts as an E3 ubiquitin ligase, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, and then transfers it to substrates promoting their degradation by the proteasome. Promotes degradation of TRAF3, TLR4 and TLR9. Contributes to the regulation of antiviral responses. Down-regulates activation of NF-kappa-B, IRF3 activation and IFNB production. Isoform 3/ZIN inhibits TNF and IL-1 mediated activation of NF-kappa-B. Promotes TNF and RIP mediated apoptosis.

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 = 55.8 bits (133), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 50/161 (31%), Positives = 72/161 (44%), Gaps = 12/161 (7%)

Query: 2   IECPGVHCDQ--FLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFE--RSYCPNRNCMALVV 57
           I CP   C +   L     + M+ + +  ++  +  E  VL F+  R++CP   C A V 
Sbjct: 63  ISCPDAACPKQGHLQENEIECMVAAEIMQRYKKLQFEREVL-FDPCRTWCPASTCQA-VC 120

Query: 58  NEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGN---LRDWNDIAFGKLVERM 114
              +I   T +  +C  C   FC  CK  WH G  C E+     L      AF K+ E  
Sbjct: 121 QLQDIGLQTPQLVQCKACDMEFCSACKARWHPGQGCPETMPITFLPGETSSAF-KMEEGD 179

Query: 115 HGARR-PACGSCVERKEGCRVMYCR-CKTSFCYECGGNLKS 153
              +R P C   +ER EGC  M C+ CK +FC+ C  +L  
Sbjct: 180 APIKRCPKCRVYIERDEGCAQMMCKNCKHAFCWYCLESLDD 220

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: -

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	203
224135813	228	predicted protein [Populus trichocarpa]	0.714	0.635	0.533	5e-36
224146525	241	predicted protein [Populus trichocarpa]	0.763	0.643	0.509	9e-36
255578926	255	zinc finger protein, putative [Ricinus c	0.724	0.576	0.493	5e-35
255578922	213	zinc finger protein, putative [Ricinus c	0.714	0.680	0.496	3e-33
359478253	212	PREDICTED: LOW QUALITY PROTEIN: probable	0.684	0.655	0.461	2e-29
224142755	307	predicted protein [Populus trichocarpa]	0.724	0.478	0.402	6e-25
356522436	292	PREDICTED: probable E3 ubiquitin-protein	0.758	0.527	0.360	5e-24
225444595	358	PREDICTED: probable E3 ubiquitin-protein	0.743	0.421	0.375	2e-23
297738503	329	unnamed protein product [Vitis vinifera]	0.743	0.458	0.375	3e-23
145338490	303	RING/U-box domain-containing protein [Ar	0.768	0.514	0.347	3e-23

>gi|224135813|ref|XP_002327310.1| predicted protein [Populus trichocarpa] gi|222835680|gb|EEE74115.1| predicted protein [Populus trichocarpa]

 Score =  156 bits (394), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 79/148 (53%), Positives = 98/148 (66%), Gaps = 3/148 (2%)

Query: 2   IECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGE 61
           IECPG++C Q LD  +C+ +I   +F KWCD LC+  VLG E  YCP R+C  LV+NE  
Sbjct: 72  IECPGLNCKQPLDPLSCRRIISKPIFEKWCDHLCDSTVLGSESCYCPYRDCSVLVLNECM 131

Query: 62  INYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPA 121
            N   LKK +CPNCK+ FCF CK+ WHAGYRC ES +LRD NDI  G+L+E     R   
Sbjct: 132 DN---LKKIKCPNCKKNFCFLCKIPWHAGYRCNESRHLRDRNDILVGELIEEKRWTRCYN 188

Query: 122 CGSCVERKEGCRVMYCRCKTSFCYECGG 149
           CG  VER  GCR + C+C   FC++CGG
Sbjct: 189 CGHSVERVSGCRDIKCKCGVQFCHQCGG 216

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224146525|ref|XP_002326038.1| predicted protein [Populus trichocarpa] gi|222862913|gb|EEF00420.1| predicted protein [Populus trichocarpa]

 Score =  155 bits (392), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 82/161 (50%), Positives = 100/161 (62%), Gaps = 6/161 (3%)

Query: 2   IECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGE 61
           IECPG++C Q LD  +C+ +I   +F KWCD LC+  VLG E  YCP R+C  LV+NE +
Sbjct: 72  IECPGLNCKQLLDPLSCRPIISKPIFEKWCDRLCDSMVLGSESCYCPYRDCSVLVLNECK 131

Query: 62  INYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPA 121
                LKK  CPNCK+ FCF CK+ WH GYRC ES +LRD NDI  G+L+E     R   
Sbjct: 132 ---DKLKKINCPNCKKNFCFLCKIPWHTGYRCSESRHLRDRNDILAGELIEEKKWTRCYN 188

Query: 122 CGSCVERKEGCRVMYCRCKTSFCYECGGNLKSASGCLCKEK 162
           C   VER  GCR + CRC   FC++CGG   S    LCK K
Sbjct: 189 CSHSVERVSGCRDIKCRCGFRFCHQCGGPFHSG---LCKHK 226

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255578926|ref|XP_002530316.1| zinc finger protein, putative [Ricinus communis] gi|223530172|gb|EEF32083.1| zinc finger protein, putative [Ricinus communis]

 Score =  152 bits (385), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 74/150 (49%), Positives = 96/150 (64%), Gaps = 3/150 (2%)

Query: 2   IECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGE 61
           I+CPG  C   LD  +C+ +I   +F KWCD+LC+  V G ER YCP R+C ALV+NE +
Sbjct: 72  IKCPGTSCKHPLDPLSCRSIISKPVFDKWCDLLCDSVVSGVERCYCPYRDCSALVLNECK 131

Query: 62  INYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPA 121
                LKK +CPNCK+  C+ CK+ WHAGY+C ESG LRD ND+  G+L+E     R   
Sbjct: 132 ---DKLKKIKCPNCKKNLCYVCKIPWHAGYQCNESGQLRDRNDVLIGELIEEKKWTRCYN 188

Query: 122 CGSCVERKEGCRVMYCRCKTSFCYECGGNL 151
           CG  VER  GCR + C+C   FC++CGG  
Sbjct: 189 CGHSVERVSGCRDVKCKCGVRFCHQCGGRF 218

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255578922|ref|XP_002530314.1| zinc finger protein, putative [Ricinus communis] gi|223530170|gb|EEF32081.1| zinc finger protein, putative [Ricinus communis]

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 73/147 (49%), Positives = 94/147 (63%), Gaps = 2/147 (1%)

Query: 2   IECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGE 61
           I+CP + CD+ L+  +C  +IP  +F KW D+LCE  VL +ER YCP  NC AL++NE  
Sbjct: 52  IKCPSLGCDRPLEPTSCMALIPKAIFDKWSDLLCEVRVLEWERCYCPYENCSALILNE-- 109

Query: 62  INYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPA 121
             Y  +KK  CPNCK+ FCF CK+ WH GY C ES  LRD ND+  G+L+E     R   
Sbjct: 110 CRYHKVKKVTCPNCKKNFCFNCKIPWHGGYWCRESRQLRDGNDVLAGELIENQRWTRCYN 169

Query: 122 CGSCVERKEGCRVMYCRCKTSFCYECG 148
           CG  VER +GC+ + CRC   FC+ECG
Sbjct: 170 CGHSVERVDGCKFISCRCGVEFCHECG 196

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359478253|ref|XP_003632093.1| PREDICTED: LOW QUALITY PROTEIN: probable E3 ubiquitin-protein ligase RNF144A-like [Vitis vinifera]

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 66/143 (46%), Positives = 93/143 (65%), Gaps = 4/143 (2%)

Query: 2   IECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVL-GFERSYCPNRNCMALVVNEG 60
           + CP + C   L+      ++P+ LF+KW D+LC+  VL GFER Y PN+ C  L+VNE 
Sbjct: 73  VACPALDCGHLLNPLHYLPILPATLFTKWSDLLCKKVVLLGFERCYYPNQTCSVLIVNEC 132

Query: 61  EINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRP 120
               G +++++CPNCK+ FCFQCK  WH+GYRC++   +RD ND+ FG+LVE    +R P
Sbjct: 133 G---GNVRRSKCPNCKKLFCFQCKSPWHSGYRCDKREEMRDVNDMLFGELVETKKWSRCP 189

Query: 121 ACGSCVERKEGCRVMYCRCKTSF 143
           +CG CVE  EGC  + C+   SF
Sbjct: 190 SCGHCVELVEGCPNVSCKFVFSF 212

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  119 bits (299), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 62/154 (40%), Positives = 90/154 (58%), Gaps = 7/154 (4%)

Query: 1   KIECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEG 60
           KI CP   C   L+   C+ ++P N+F +W + LCE  +LG ++ YCP ++C A+++++G
Sbjct: 141 KICCPVPDCKGALEPEDCRSVLPENVFDRWGNALCEAVILGSQKFYCPFKDCSAMLIDDG 200

Query: 61  EINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNL----RDWNDIAFGKLVERMHG 116
           E     ++++ CPNC + FC QCKV WH+   CEE   L    R+ +DI    L +  + 
Sbjct: 201 E---EVVRESECPNCWRMFCAQCKVPWHSQISCEEYKMLHKDERERDDILLMNLAKNKNW 257

Query: 117 ARRPACGSCVERKEGCRVMYCRCKTSFCYECGGN 150
            R P C   VE+ EGCR M CRC T FCY CG  
Sbjct: 258 RRCPKCRIFVEKIEGCRYMKCRCGTQFCYSCGST 291

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 58/161 (36%), Positives = 90/161 (55%), Gaps = 7/161 (4%)

Query: 2   IECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGE 61
           ++CP   C   ++   C+  IP  +F +W D LCE+ V G ++ YCP ++C A+++N+ E
Sbjct: 132 VKCPHPKCKGVIEPQYCRSFIPKEVFDRWEDALCENLVPGSQKFYCPFKDCSAMLINDAE 191

Query: 62  INYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDW----NDIAFGKLVERMHGA 117
                +  + CP+C + FC QCKV+WHAG  C+E  NL+++     D+   +L +  +  
Sbjct: 192 ---EIVTVSECPHCNRLFCAQCKVSWHAGVECKEFQNLKEYEREREDLMVMELAKNKNWK 248

Query: 118 RRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSASGCL 158
           R P C   VER +GC  + CRC   FCY CG    S   C+
Sbjct: 249 RCPKCSFYVERIDGCTHISCRCGNEFCYACGSKWGSHHACV 289

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 60/160 (37%), Positives = 92/160 (57%), Gaps = 9/160 (5%)

Query: 1   KIECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVV-NE 59
           +I CP  +C   L+   C+ ++PS++F +W + LCE  +LG ++ YCP ++C AL++ +E
Sbjct: 166 RISCPAPNCTGVLEPQQCRPILPSHVFDRWGNALCEALILGSQKFYCPYKDCSALLIRDE 225

Query: 60  GEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNL----RDWNDIAFGKLVERMH 115
           GE+    +K++ CPNC++ FC QC+V WH+G  C E   L    R   DI    L +  +
Sbjct: 226 GEV----IKESECPNCRRLFCAQCEVPWHSGIDCGEFQKLNKDERGREDILMMNLAKTNN 281

Query: 116 GARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSAS 155
             R P C   VE+  GC  + CRC  +FCY CG    + S
Sbjct: 282 WKRCPKCKFYVEKSFGCMYIRCRCGFAFCYNCGAPSSTIS 321

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 60/160 (37%), Positives = 92/160 (57%), Gaps = 9/160 (5%)

Query: 1   KIECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVV-NE 59
           +I CP  +C   L+   C+ ++PS++F +W + LCE  +LG ++ YCP ++C AL++ +E
Sbjct: 166 RISCPAPNCTGVLEPQQCRPILPSHVFDRWGNALCEALILGSQKFYCPYKDCSALLIRDE 225

Query: 60  GEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNL----RDWNDIAFGKLVERMH 115
           GE+    +K++ CPNC++ FC QC+V WH+G  C E   L    R   DI    L +  +
Sbjct: 226 GEV----IKESECPNCRRLFCAQCEVPWHSGIDCGEFQKLNKDERGREDILMMNLAKTNN 281

Query: 116 GARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSAS 155
             R P C   VE+  GC  + CRC  +FCY CG    + S
Sbjct: 282 WKRCPKCKFYVEKSFGCMYIRCRCGFAFCYNCGAPSSTIS 321

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145338490|ref|NP_188042.2| RING/U-box domain-containing protein [Arabidopsis thaliana] gi|91806425|gb|ABE65940.1| zinc finger protein-like protein [Arabidopsis thaliana] gi|332641973|gb|AEE75494.1| RING/U-box domain-containing protein [Arabidopsis thaliana]

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 57/164 (34%), Positives = 93/164 (56%), Gaps = 8/164 (4%)

Query: 1   KIECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEG 60
           +I+CP V C + ++ +TC+ +IP ++F +W  +LCE  +  +++ YCP ++C A++VN  
Sbjct: 137 RIKCPDVECTRLIEPYTCRDLIPKDVFDRWEKILCESLISSWDKFYCPFKDCSAMMVN-N 195

Query: 61  EINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEE---SGNLR----DWNDIAFGKLVER 113
           E     + +  C +C + FC QCKV WHAG  C+E    GN +    D +D    ++ + 
Sbjct: 196 ENGDANVTQTECRSCHRLFCVQCKVTWHAGIGCDEFQRFGNTKKKSSDEDDALLIQMAKN 255

Query: 114 MHGARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSASGC 157
               R P+C   V++ EGC+ + CRC   FCY CG    S+  C
Sbjct: 256 KQWRRCPSCKFYVDKVEGCQHIKCRCGYQFCYGCGSVWSSSHAC 299

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	203
TAIR|locus:2091030	303	AT3G14250 [Arabidopsis thalian	0.768	0.514	0.347	5.6e-29
TAIR|locus:2084116	320	AT3G53690 [Arabidopsis thalian	0.709	0.45	0.355	6.6e-26
TAIR|locus:2085612	348	AT3G45540 [Arabidopsis thalian	0.748	0.436	0.320	1e-18
TAIR|locus:1006230127	384	AT2G26135 [Arabidopsis thalian	0.743	0.393	0.308	1.5e-17
TAIR|locus:2057401	398	AT2G26130 [Arabidopsis thalian	0.876	0.447	0.275	3.9e-17
TAIR|locus:2133935	532	AT4G19670 [Arabidopsis thalian	0.763	0.291	0.291	1.4e-15
TAIR|locus:2143995	655	AT5G60250 [Arabidopsis thalian	0.763	0.236	0.331	1.6e-15
TAIR|locus:2151689	444	AT5G37560 [Arabidopsis thalian	0.684	0.313	0.296	1.9e-15
TAIR|locus:2085622	222	AT3G45470 [Arabidopsis thalian	0.798	0.729	0.279	4.2e-15
TAIR|locus:2050100	468	AT2G21420 [Arabidopsis thalian	0.788	0.341	0.299	7.6e-15

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

 Score = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 57/164 (34%), Positives = 93/164 (56%)

Query:     1 KIECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEG 60
             +I+CP V C + ++ +TC+ +IP ++F +W  +LCE  +  +++ YCP ++C A++VN  
Sbjct:   137 RIKCPDVECTRLIEPYTCRDLIPKDVFDRWEKILCESLISSWDKFYCPFKDCSAMMVNN- 195

Query:    61 EINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEES---GNLR----DWNDIAFGKLVER 113
             E     + +  C +C + FC QCKV WHAG  C+E    GN +    D +D    ++ + 
Sbjct:   196 ENGDANVTQTECRSCHRLFCVQCKVTWHAGIGCDEFQRFGNTKKKSSDEDDALLIQMAKN 255

Query:   114 MHGARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSASGC 157
                 R P+C   V++ EGC+ + CRC   FCY CG    S+  C
Sbjct:   256 KQWRRCPSCKFYVDKVEGCQHIKCRCGYQFCYGCGSVWSSSHAC 299

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 293 (108.2 bits), Expect = 6.6e-26, P = 6.6e-26
 Identities = 54/152 (35%), Positives = 82/152 (53%)

Query:     2 IECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALV-VNEG 60
             IECP   C   L+   C+ ++P  +F +W D LCE  V+  ++ YCP ++C ALV + E 
Sbjct:   157 IECPVSGCSGRLEPDQCRQILPKEVFDRWGDALCEAVVMRSKKFYCPYKDCSALVFLEES 216

Query:    61 EINYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEE----SGNLRDWNDIAFGKLVERMHG 116
             E+    +K + CP+C +  C +C   WH    CEE    + N R  +DI    + ++   
Sbjct:   217 EVK---MKDSECPHCHRMVCVECGTQWHPEMTCEEFQKLAANERGRDDILLATMAKQKKW 273

Query:   117 ARRPACGSCVERKEGCRVMYCRCKTSFCYECG 148
              R P+C   +E+ +GC  M CRC  +FCY CG
Sbjct:   274 KRCPSCKFYIEKSQGCLYMKCRCGLAFCYNCG 305

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2085612 AT3G45540 [Arabidopsis thaliana (taxid:3702)]

 Score = 226 (84.6 bits), Expect = 1.0e-18, P = 1.0e-18
 Identities = 52/162 (32%), Positives = 74/162 (45%)

Query:     2 IECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGE 61
             + CP   C   L    C  ++   +   W   + ED +    R YCPN  C AL+ +E E
Sbjct:   142 MRCPHYRCKTTLKFGGCINLLTPKIREMWQQRIKEDLIPVTGRIYCPNSRCSALM-SETE 200

Query:    62 INYGTLK-KAR--CPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGAR 118
             ++  T + + R  C  C Q FC +CKV+WH+   C +   L  +     GK+    +  R
Sbjct:   201 LSISTKEDEVRRCCFKCGQIFCIKCKVSWHSNLSCNDYKKLNPYPTENDGKIKALANQKR 260

Query:   119 RPACGSC---VERKEGCRVMYCRCKTSFCYECGGNLKSASGC 157
                CG C   +E  +GC  + CRC   FCY CG     A GC
Sbjct:   261 WRQCGKCQHMIELSKGCVQVKCRCGHKFCYRCG---VQAGGC 299

GO:0008270 "zinc ion binding" evidence=IEA

GO:0048446 "petal morphogenesis" evidence=RCA

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

 Score = 218 (81.8 bits), Expect = 1.5e-17, P = 1.5e-17
 Identities = 49/159 (30%), Positives = 71/159 (44%)

Query:     2 IECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGE 61
             I CP   C   L   +C  ++   +   W   + ED +   +R YCPN  C AL+ +  E
Sbjct:   195 ITCPSYRCKSKLTYGSCVNILTPKVKEMWIQRMGEDSIPVTDRVYCPNPTCSALM-SVTE 253

Query:    62 INYGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNL---RDWNDIAFGKLVERMHGAR 118
             ++  T  K  C  C + FC +CKV WH    C+    L   R  ND    +L  +    +
Sbjct:   254 LDQLTGSKRCCVKCGESFCIKCKVPWHDNLSCKRYKKLHSNRTTNDKQLNELANQESWRQ 313

Query:   119 RPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSASGC 157
                C   +E  +GC  + CRC   FCY CG +    +GC
Sbjct:   314 CSKCKHMIELTQGCVRVICRCGHEFCYGCGAD----AGC 348

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:2057401 AT2G26130 [Arabidopsis thaliana (taxid:3702)]

 Score = 215 (80.7 bits), Expect = 3.9e-17, P = 3.9e-17
 Identities = 51/185 (27%), Positives = 81/185 (43%)

Query:     2 IECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGE 61
             I CP   C+  L    C  ++   L   W     ++ +   +R YCPN  C  L+ +E E
Sbjct:   201 ITCPHYRCNSLLTSVRCGNLLTPKLNKMWEQKTKDELIPVMDRVYCPNPRCSTLM-SETE 259

Query:    62 INYGTLKKARC-PNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRP 120
             ++   +   RC   C + FC +CKV+WH    C+E   L        G+L +  +     
Sbjct:   260 LSGLNIGVRRCCVKCGEPFCVKCKVSWHNNLSCDEYKTLHPNPTENDGRLRDLANEKSWR 319

Query:   121 ACGSC---VERKEGCRVMYCRCKTSFCYECGGNLKSASGCLCKEKGDVY--CHHYCAIIS 175
              C  C   +E   GC  + CRC  +FCY+CG +       L ++  D+   C   C  + 
Sbjct:   320 QCSKCKHMIELSSGCISVVCRCGHTFCYQCGADAGDCFHGLGRDDLDLTQCCGSCCCFVF 379

Query:   176 GLILI 180
              L++I
Sbjct:   380 FLVII 384

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 204 (76.9 bits), Expect = 1.4e-15, P = 1.4e-15
 Identities = 51/175 (29%), Positives = 72/175 (41%)

Query:     2 IECPGVHCDQFLDLFTCKLMIPSNLFSKWCDV-LCEDYVLGFERSYCPNRNCMALV---- 56
             I CP V C  +L    CK  +P   F  + +  +C        + YCP  NC  L+    
Sbjct:   248 IRCPQVQCKHYLSAAECKSFLPVTTFKSFEEANVCSK---NNGKIYCPYPNCSFLLDPQE 304

Query:    57 -VNEGEINYGTLKKAR------CPNCKQWFCFQCKVAWHAGYRCEESGNL----RDWNDI 105
              ++ G  +  +  ++       CP C+++ C  C V WHA   CEE   L    R  +DI
Sbjct:   305 CLSSGRASSSSSTQSENSCCVECPVCERFVCVDCGVPWHASMSCEEFQILPVDERYPDDI 364

Query:   106 AFGKLVERMHGARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSASG-CLC 159
                +L       R   C   +E  +GC  M CRC   FCY CG   +     C C
Sbjct:   365 TLHRLARYKRWRRCQQCRIMIELAQGCNHMTCRCGHEFCYSCGAEYREGQQTCTC 419

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 205 (77.2 bits), Expect = 1.6e-15, P = 1.6e-15
 Identities = 56/169 (33%), Positives = 72/169 (42%)

Query:     3 ECPGVHCDQFLDLFTC-KLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALV----V 57
             +CP   C   L +  C KL+ P  L   W   L E+ +   ER YCP   C AL+    +
Sbjct:   343 KCPHDGCKSELVIDACGKLLTPK-LSKLWQQRLQENAIPVTERVYCPYPRCSALMSKTKI 401

Query:    58 NEGEINYGTL-KKA---RCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVER 113
             +E   +  +L  K+   RC  C+  FC  CKV WH    C E   L         KL   
Sbjct:   402 SESAKSLLSLYPKSGVRRCVECRGLFCVDCKVPWHGNLSCTEYKKLHPEPPADDVKLKSL 461

Query:   114 MHGARRPACGSC---VERKEGCRVMYCRCKTSFCYECGGNLKSASG-CL 158
              +      CG C   +E  +GC  + CRC   FCY CGG      G CL
Sbjct:   462 ANNKMWRQCGKCQHMIELSQGCNHITCRCGHEFCYNCGGGWNKIMGTCL 510

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 201 (75.8 bits), Expect = 1.9e-15, P = 1.9e-15
 Identities = 43/145 (29%), Positives = 67/145 (46%)

Query:     9 CDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEINY-GTL 67
             C   L L +C +++   L   W   + ED +   E+ YCP R+C ++++++ E++     
Sbjct:   229 CKSELTLESCSMVLTPKLIEMWKRKMEEDLIPDAEKIYCPYRSC-SMLMSKTELSREAEQ 287

Query:    68 KKAR-CPNCKQWFCFQCKVAWHAGYRCEESGNL---RDWNDIAFGKLVERMHGARRPACG 123
                R C  C + FC  CKV WH+   C +   +   R  ND+    L       +   C 
Sbjct:   288 SNVRACIKCSELFCIDCKVPWHSDLSCADYKRIHSERLVNDMMLKVLANDQMWRQCSECK 347

Query:   124 SCVERKEGCRVMYCRCKTSFCYECG 148
               +E  EGC  + CRC   FCY CG
Sbjct:   348 HMIELTEGCNHITCRCGYEFCYRCG 372

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 191 (72.3 bits), Expect = 4.2e-15, P = 4.2e-15
 Identities = 48/172 (27%), Positives = 70/172 (40%)

Query:     4 CPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEIN 63
             C    C   L L  C  ++   +   W  ++ E+ +   +R YCP  NC  L+ ++ EI+
Sbjct:    49 CLDYECKLKLSLENCFKVLKPKVIELWKHMMKEESIPLAKRIYCPYINCSTLM-SKTEIS 107

Query:    64 YGTLKKAR-CPNCKQWFCFQCKVAWHAGYRCEESGNLRD---WNDIAFGKLVERMHGARR 119
                    R C  C    C  CKV WH+   C E   L      +D+    L       + 
Sbjct:   108 RSNKSNDRACIKCSGLVCIDCKVPWHSDLSCAEYKKLHPDPVLDDLTLKLLANDQKWRQC 167

Query:   120 PACGSCVERKEGCRVMYCRCKTSFCYECG-----GNLKSASGCLCKEKGDVY 166
               C   +E  +GC  M CRC   FCY+CG     G +   +GC    +G  Y
Sbjct:   168 VKCRHLIELNQGCNHMTCRCGYQFCYKCGVEWKKGQVTCPTGCPRTGQGYFY 219

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 196 (74.1 bits), Expect = 7.6e-15, P = 7.6e-15
 Identities = 50/167 (29%), Positives = 66/167 (39%)

Query:     4 CPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEIN 63
             C    C+  L   +C  ++  NL   W   + ED V   ++ YCP R C  L+       
Sbjct:   230 CLHFPCNSELTFESCSKVLTPNLIEFWKRKIEEDLVPAADKIYCPYRRCSMLMSKTALSR 289

Query:    64 YGTLKKAR-CPNCKQWFCFQCKVAWHAGYRCEESGNLRD--WNDIAFGKLVERMHGARRP 120
                    R C  C + FC  CKV  HAG  C +   L      D+    L  +    +  
Sbjct:   290 ETDQSNVRACIKCCRLFCIDCKVPSHAGLSCVDYKKLNPDPLYDVKLKSLANKKKWRQCV 349

Query:   121 ACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSASGCL---CKEKGD 164
              C + VE  EGC  + CRC   FCY CG       GCL   C +  D
Sbjct:   350 QCSNLVELFEGCNHITCRCGFEFCYVCGKEWNQR-GCLSPGCDDDDD 395

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

Your Input: eugene3.00410007 hypothetical protein (228 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	203
pfam01485	63	pfam01485, IBR, IBR domain	6e-05
smart00647	64	smart00647, IBR, In Between Ring fingers	2e-04

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

 Score = 39.1 bits (91), Expect = 6e-05
 Identities = 15/51 (29%), Positives = 20/51 (39%), Gaps = 4/51 (7%)

Query: 43 ERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRC 93
             +CP  +C  ++        G  +   C  C   FCF CK  WH G  C
Sbjct: 17 NLKWCPTPDCGNIIEKTD----GGSQNVTCSKCGTEFCFSCKEPWHEGLTC 63

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

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

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 4/66 (6%)

Query: 29 KWCDVLCEDYVL-GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAW 87
          K+  +L E YV    +  +CP  +C A ++   E       +  CP C   FCF+CKV W
Sbjct: 2  KYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEG---CNRVTCPKCGFSFCFRCKVPW 58

Query: 88 HAGYRC 93
          H+   C
Sbjct: 59 HSPVSC 64

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	203
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	99.97
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	99.97
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	99.9
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	99.89
smart00647	64	IBR In Between Ring fingers. the domains occurs be	99.48
PF01485	64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	99.46
smart00647	64	IBR In Between Ring fingers. the domains occurs be	98.68
PF01485	64	IBR: IBR domain; InterPro: IPR002867 Zinc finger (	98.47
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.76
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	95.17
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	94.24
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	93.32
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	92.82
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	92.48
smart00661	52	RPOL9 RNA polymerase subunit 9.	92.2
PF13248	26	zf-ribbon_3: zinc-ribbon domain	91.98
PF09889	59	DUF2116: Uncharacterized protein containing a Zn-r	91.76
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	91.51
PRK00432	50	30S ribosomal protein S27ae; Validated	91.19
PHA00626	59	hypothetical protein	90.85
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	90.65
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	90.44
PLN03086	567	PRLI-interacting factor K; Provisional	89.75
COG1998	51	RPS31 Ribosomal protein S27AE [Translation, riboso	88.71
PF09297	32	zf-NADH-PPase: NADH pyrophosphatase zinc ribbon do	88.43
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	86.36
KOG2906	105	consensus RNA polymerase III subunit C11 [Transcri	85.22
PF02150	35	RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; I	84.8
smart00661	52	RPOL9 RNA polymerase subunit 9.	84.55
PHA03049	68	IMV membrane protein; Provisional	83.81
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	82.77
PF01599	47	Ribosomal_S27: Ribosomal protein S27a; InterPro: I	82.21
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	81.84
KOG0006	446	consensus E3 ubiquitin-protein ligase (Parkin prot	81.76
PF05961	68	Chordopox_A13L: Chordopoxvirus A13L protein; Inter	81.56
PF09788	256	Tmemb_55A: Transmembrane protein 55A; InterPro: IP	80.76
PF03119	28	DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc f	80.24

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

Probab=99.97  E-value=4.4e-32  Score=234.19  Aligned_cols=154  Identities=34%  Similarity=0.720  Sum_probs=133.5

Q ss_pred             ccCCcccCCCcCCHHHHhhcCCHHHHHHHHHHHHHhhccCCCceeCCCCCCCceeeecCccccCCCCceeCCCccccccc
Q 043865            2 IECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCF   81 (203)
Q Consensus         2 I~CP~~~C~~~l~~~~i~~~l~~e~~~~y~~~~~~~~i~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~   81 (203)
                      |+||..+|+..++.++...+|++++.++|++++.+.+++..+.+|||+|+|...+......+........|+.|+..||.
T Consensus       191 ~~C~~~~C~~~l~~~~c~~llt~kl~e~~e~~~~e~~i~~~~~~ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv  270 (384)
T KOG1812|consen  191 IRCPHDGCESRLTLESCRKLLTPKLREMWEQRLKEEVIPSLDRVYCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCV  270 (384)
T ss_pred             ccCCCCCCCccCCHHHHhhhcCHHHHHHHHHHHHHHhhhhhhcccCCCCCchHhhhhhhhccchhhcccccccCCCceee
Confidence            78999999999999999999999999999999999999855555999999999887655422234667789999999999


Q ss_pred             cCCcCCCCCCccccccccccc--hhHHHHHHHHhccCCCCCCCCceeEecCCcceeEecccccccccccccCcCCCC
Q 043865           82 QCKVAWHAGYRCEESGNLRDW--NDIAFGKLVERMHGARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSASG  156 (203)
Q Consensus        82 ~C~~~~H~~~~C~~~~~~~~~--~d~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~~~~~  156 (203)
                      +|+.+||++.+|++++++..+  .|...++++. ++|++||+|+..||+++|||||+|+||++|||.|+.+|..+++
T Consensus       271 ~C~~~wh~~~sC~eykk~~~~~~~d~~~~~~la-~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~~~~~  346 (384)
T KOG1812|consen  271 KCKVPWHANLSCEEYKKLNPEEYVDDITLKYLA-KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWKTHNG  346 (384)
T ss_pred             cCCCcCCCCCCHHHHHHhCCcccccHHHHHHHH-HhcCcCcccceeeeecCCcceEEeeccccchhhcCcchhhCCc
Confidence            999999999999999998743  3334444443 8999999999999999999999999999999999999987654

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

Probab=99.97  E-value=1.4e-31  Score=225.22  Aligned_cols=167  Identities=25%  Similarity=0.498  Sum_probs=142.4

Q ss_pred             CccCCcccCCCcCCHHHHhhcCCHHHHHHHHHHHHHhhcc-CCCceeCCCCCCCceeeecCccccCCCCceeCCCccccc
Q 043865            1 KIECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVL-GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWF   79 (203)
Q Consensus         1 ~I~CP~~~C~~~l~~~~i~~~l~~e~~~~y~~~~~~~~i~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~   79 (203)
                      .++||+++|++...+..++++|+.|+++||++.+.+.++. ..+.+|||++.|..+...++.     ...+.|.+|+..|
T Consensus       229 ~l~Cp~~~C~~~a~~g~vKelvg~EL~arYe~l~lqk~l~~msdv~yCPr~~Cq~p~~~d~~-----~~l~~CskCnFaF  303 (445)
T KOG1814|consen  229 CLKCPDPKCGSVAPPGQVKELVGDELFARYEKLMLQKTLELMSDVVYCPRACCQLPVKQDPG-----RALAICSKCNFAF  303 (445)
T ss_pred             eecCCCCCCcccCCchHHHHHHHHHHHHHHHHHHHHHHHHhhcccccCChhhccCccccCch-----hhhhhhccCccHH
Confidence            4799999999999999999999999999999999999996 899999999999999855554     8899999999999


Q ss_pred             cccCCcCCCCCCccccccc--------cccc---------------------hhHHHHHHHHhccCCCCCCCCceeEecC
Q 043865           80 CFQCKVAWHAGYRCEESGN--------LRDW---------------------NDIAFGKLVERMHGARRPACGSCVERKE  130 (203)
Q Consensus        80 C~~C~~~~H~~~~C~~~~~--------~~~~---------------------~d~~~~~~~~~~~~k~CP~C~~~iek~~  130 (203)
                      |+.|+..||++..|.--..        +.+.                     +|.+..+|. ..+.|+||+|.+.|||++
T Consensus       304 CtlCk~t~HG~s~Ck~~~~~~~~l~~~~~~~d~a~k~ele~Ryg~rvve~~vn~~lsekwl-~~N~krCP~C~v~IEr~e  382 (445)
T KOG1814|consen  304 CTLCKLTWHGVSPCKVKAEKLIELYLEYLEADEARKRELEKRYGKRVVEELVNDFLSEKWL-ESNSKRCPKCKVVIERSE  382 (445)
T ss_pred             HHHHHHhhcCCCcccCchHHHHHHHHHHhhcCHHHHHHHHHHhhHHHHHHHHHHHHHHHHH-HhcCCCCCcccceeecCC
Confidence            9999999999888974321        1110                     111111222 346799999999999999


Q ss_pred             CcceeEe-cccccccccccccCcCCCCCCCCcCCcccchhhHHH
Q 043865          131 GCRVMYC-RCKTSFCYECGGNLKSASGCLCKEKGDVYCHHYCAI  173 (203)
Q Consensus       131 GCnhm~C-~C~~~FC~~C~~~~~~~~~C~~~~~~~~~~~~~~~~  173 (203)
                      |||+|+| .|++.|||.|+....+.+++.|+..+.+.|..+.+.
T Consensus       383 GCnKM~C~~c~~~fc~~c~~~l~~~nPYkHF~e~~s~c~~~~~~  426 (445)
T KOG1814|consen  383 GCNKMHCTKCGTYFCWICAELLYPENPYKHFSEPGSECYGQFFG  426 (445)
T ss_pred             CccceeeccccccceeehhhhcCCCChhhhhcCCcCccccchhh
Confidence            9999999 899999999999999988999999999999887655

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

Probab=99.90  E-value=2e-24  Score=176.88  Aligned_cols=144  Identities=25%  Similarity=0.562  Sum_probs=116.5

Q ss_pred             ccCCcccCCC-cCCHHHHhhcCCHHHHHHHHHHHHHhhccCCCceeCCCCCCCceeeecCccccCCCCceeCCC-ccccc
Q 043865            2 IECPGVHCDQ-FLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEINYGTLKKARCPN-CKQWF   79 (203)
Q Consensus         2 I~CP~~~C~~-~l~~~~i~~~l~~e~~~~y~~~~~~~~i~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~-C~~~~   79 (203)
                      +-||. +|.. .|..-+..++|+.+.|.+|+++.+|..+...+.+-||+|+|+..+.++++     ..+++|+. |++.|
T Consensus       273 lpc~a-gc~~s~i~e~HHF~ilg~e~Y~rYQr~atEe~vlq~gGVlCP~pgCG~gll~EPD-----~rkvtC~~gCgf~F  346 (446)
T KOG0006|consen  273 LPCVA-GCPNSLIKELHHFRILGEEQYNRYQRYATEECVLQMGGVLCPRPGCGAGLLPEPD-----QRKVTCEGGCGFAF  346 (446)
T ss_pred             ccccC-CCchHHHHhhhhheecchhHHHHHHHhhhhhheeecCCEecCCCCCCcccccCCC-----CCcccCCCCchhHh
Confidence            45776 7875 55555667899999999999999999998778999999999999999887     88999997 99999


Q ss_pred             cccCCcCCCCCCcccccc--------ccccch--------hHHHHHHHHhccCCCCCCCCceeEecCCcceeEe-c--cc
Q 043865           80 CFQCKVAWHAGYRCEESG--------NLRDWN--------DIAFGKLVERMHGARRPACGSCVERKEGCRVMYC-R--CK  140 (203)
Q Consensus        80 C~~C~~~~H~~~~C~~~~--------~~~~~~--------d~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm~C-~--C~  140 (203)
                      |.+|+..+|.|. |.+.-        .+.-++        |+..++.+ +..+|+||+|.++.||++||.||.| +  ||
T Consensus       347 CR~C~e~yh~ge-C~~~~~as~t~tc~y~vde~~a~~arwd~as~~TI-k~tTkpCPkChvptErnGGCmHm~Ct~~~Cg  424 (446)
T KOG0006|consen  347 CRECKEAYHEGE-CSAVFEASGTTTCAYRVDERAAEQARWDAASKETI-KKTTKPCPKCHVPTERNGGCMHMKCTQPQCG  424 (446)
T ss_pred             HHHHHhhhcccc-ceeeeccccccceeeecChhhhhhhhhhhhhhhhh-hhccCCCCCccCccccCCceEEeecCCCCCC
Confidence            999999999984 55211        111111        22222222 3567999999999999999999999 4  99


Q ss_pred             ccccccccccCcC
Q 043865          141 TSFCYECGGNLKS  153 (203)
Q Consensus       141 ~~FC~~C~~~~~~  153 (203)
                      .+|||.|+.+|+.
T Consensus       425 ~eWCw~C~tEW~r  437 (446)
T KOG0006|consen  425 LEWCWNCGTEWNR  437 (446)
T ss_pred             ceeEeccCChhhh
Confidence            9999999999996

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

Probab=99.89  E-value=6e-24  Score=187.61  Aligned_cols=158  Identities=23%  Similarity=0.468  Sum_probs=131.7

Q ss_pred             ccCCcccCCCcCCHHHHhhcCCH-HHHHHHHHHHHHhhcc-CCCceeCCCCCCCceeeecCccccCCCCceeCCCccccc
Q 043865            2 IECPGVHCDQFLDLFTCKLMIPS-NLFSKWCDVLCEDYVL-GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWF   79 (203)
Q Consensus         2 I~CP~~~C~~~l~~~~i~~~l~~-e~~~~y~~~~~~~~i~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~   79 (203)
                      |+||..+|.+.++.+++..++++ +..++|.+.+.++++. .....|||+|+|+..+....    .....+.|. |++.|
T Consensus       114 i~cp~~~C~a~v~~~~i~~~~s~~~~~~ky~~~i~~syve~~~~lkwCP~~~C~~av~~~~----~~~~~v~C~-~g~~F  188 (444)
T KOG1815|consen  114 IKCPAHGCPALVGEDTVEKLVSDKEDKEKYQRYILRSYVEDNVPLKWCPAPGCGLAVKFGS----LESVEVDCG-CGHEF  188 (444)
T ss_pred             ccCCCCCccccCCCceeeeecCCHHHHHHHHHHHHHHHHhcCCccccCCCCCCCceeeccC----CCccceeCC-CCchh
Confidence            78999999999999999999998 5999999999999997 55689999999999887632    136789995 67799


Q ss_pred             cccCCcCCCCCCccccccccccch--hHHHHHHHHhccCCCCCCCCceeEecCCcceeEe-c--ccccccccccccCcCC
Q 043865           80 CFQCKVAWHAGYRCEESGNLRDWN--DIAFGKLVERMHGARRPACGSCVERKEGCRVMYC-R--CKTSFCYECGGNLKSA  154 (203)
Q Consensus        80 C~~C~~~~H~~~~C~~~~~~~~~~--d~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm~C-~--C~~~FC~~C~~~~~~~  154 (203)
                      |+.|+.+||++.+|.....|....  +....+|+ ..++++||+|..+|||++|||||+| .  |+++|||.|++.|..|
T Consensus       189 C~~C~~~~H~p~~C~~~~~wl~k~~~~se~~~wi-~~ntk~CP~c~~~iek~~gc~~~~~~~~~c~~~FCw~Cl~~~~~h  267 (444)
T KOG1815|consen  189 CFACGEESHSPVSCPGAKKWLKKCRDDSETINWI-LANTKECPKCKVPIEKDGGCNHMTCKSASCKHEFCWVCLASLSDH  267 (444)
T ss_pred             HhhccccccCCCcccchHHHHHhhhhhhhhhhhh-hccCccCCCcccchhccCCccccccccCCcCCeeceeeecccccc
Confidence            999999999999999988876442  22223355 4677899999999999999999999 4  9999999999999998


Q ss_pred             C-----CCCCCcCCcc
Q 043865          155 S-----GCLCKEKGDV  165 (203)
Q Consensus       155 ~-----~C~~~~~~~~  165 (203)
                      +     .|..+..+..
T Consensus       268 ~~~~~~~c~~~~~~~~  283 (444)
T KOG1815|consen  268 GSSTGYSCNRYVDGKS  283 (444)
T ss_pred             cccceeeeeeeechhh
Confidence            4     4555555443

>smart00647 IBR In Between Ring fingers

Probab=99.48  E-value=6.4e-14  Score=91.30  Aligned_cols=63  Identities=35%  Similarity=0.847  Sum_probs=55.8

Q ss_pred             HHHHHHHHHhhcc-CCCceeCCCCCCCceeeecCccccCCCCceeCCCccccccccCCcCCCCCCcc
Q 043865           28 SKWCDVLCEDYVL-GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRC   93 (203)
Q Consensus        28 ~~y~~~~~~~~i~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C   93 (203)
                      ++|++++.+.+++ +++++|||+|+|+.++..++.   .....+.|+.|+..||+.|+.+||++.+|
T Consensus         1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~---~~~~~v~C~~C~~~fC~~C~~~~H~~~~C   64 (64)
T smart00647        1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEE---EGCNRVTCPKCGFSFCFRCKVPWHSPVSC   64 (64)
T ss_pred             ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCC---CCCCeeECCCCCCeECCCCCCcCCCCCCC
Confidence            4799999999997 689999999999999988642   24788999999999999999999999987

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=99.46  E-value=1.3e-14  Score=94.56  Aligned_cols=63  Identities=29%  Similarity=0.769  Sum_probs=42.4

Q ss_pred             HHHHHHHHHhhcc-CCCceeCCCCCCCceeeecCccccCCCCceeCCCccccccccCCcCCCCCCcc
Q 043865           28 SKWCDVLCEDYVL-GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYRC   93 (203)
Q Consensus        28 ~~y~~~~~~~~i~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C   93 (203)
                      |||++++++.++. +++++|||+|+|+.++..++.   .....++|+.|++.||+.|+.+||+|.+|
T Consensus         1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~---~~~~~~~C~~C~~~fC~~C~~~~H~~~~C   64 (64)
T PF01485_consen    1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDG---CNSPIVTCPSCGTEFCFKCGEPWHEGVTC   64 (64)
T ss_dssp             HCHHHCCCHS---S---CC--TTSST---ECS-SS---TTS--CCTTSCCSEECSSSTSESCTTS-H
T ss_pred             ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCC---CCCCeeECCCCCCcCccccCcccCCCCCC
Confidence            5788899999886 778899999999999998876   11224999999999999999999999887

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.

>smart00647 IBR In Between Ring fingers

Probab=98.68  E-value=3.7e-08  Score=63.80  Aligned_cols=50  Identities=28%  Similarity=0.636  Sum_probs=41.6

Q ss_pred             HHHHHHHHh-ccCCCCC--CCCceeEecC--CcceeEe-cccccccccccccCcCC
Q 043865          105 IAFGKLVER-MHGARRP--ACGSCVERKE--GCRVMYC-RCKTSFCYECGGNLKSA  154 (203)
Q Consensus       105 ~~~~~~~~~-~~~k~CP--~C~~~iek~~--GCnhm~C-~C~~~FC~~C~~~~~~~  154 (203)
                      ..++.+++. .+++.||  +|+..|+..+  |..+|+| .|++.|||.|+.+|...
T Consensus         6 ~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~   61 (64)
T smart00647        6 LLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSP   61 (64)
T ss_pred             HHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCC
Confidence            344555544 5788999  9999999975  9999999 89999999999999754

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=98.47  E-value=4.2e-08  Score=63.48  Aligned_cols=41  Identities=29%  Similarity=0.819  Sum_probs=29.9

Q ss_pred             ccCCCCCC--CCceeEecCCcce--eEe-cccccccccccccCcCC
Q 043865          114 MHGARRPA--CGSCVERKEGCRV--MYC-RCKTSFCYECGGNLKSA  154 (203)
Q Consensus       114 ~~~k~CP~--C~~~iek~~GCnh--m~C-~C~~~FC~~C~~~~~~~  154 (203)
                      ...+.||+  |+..+++.+|.++  |+| .|+++|||.|+.+|...
T Consensus        16 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~   61 (64)
T PF01485_consen   16 PNIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEG   61 (64)
T ss_dssp             --CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTT
T ss_pred             CCccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCC
Confidence            45689988  9999999999999  999 59999999999999653

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.

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

Probab=95.76  E-value=0.0023  Score=55.42  Aligned_cols=46  Identities=26%  Similarity=0.545  Sum_probs=41.0

Q ss_pred             cCCCCCC--CCceeEecCCcceeEe-cccccccccccccCcCCCCCCCC
Q 043865          115 HGARRPA--CGSCVERKEGCRVMYC-RCKTSFCYECGGNLKSASGCLCK  160 (203)
Q Consensus       115 ~~k~CP~--C~~~iek~~GCnhm~C-~C~~~FC~~C~~~~~~~~~C~~~  160 (203)
                      .+.-||+  |+.++-.+.|..-..| .|...||.+|...|....+|.-.
T Consensus       272 dv~yCPr~~Cq~p~~~d~~~~l~~CskCnFaFCtlCk~t~HG~s~Ck~~  320 (445)
T KOG1814|consen  272 DVVYCPRACCQLPVKQDPGRALAICSKCNFAFCTLCKLTWHGVSPCKVK  320 (445)
T ss_pred             ccccCChhhccCccccCchhhhhhhccCccHHHHHHHHhhcCCCcccCc
Confidence            5689998  9999977899999999 89999999999999987767665

>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=95.17  E-value=0.0087  Score=31.64  Aligned_cols=23  Identities=30%  Similarity=0.816  Sum_probs=15.0

Q ss_pred             CCCCCCCceeEecCCcceeEe-cccccc
Q 043865          117 ARRPACGSCVERKEGCRVMYC-RCKTSF  143 (203)
Q Consensus       117 k~CP~C~~~iek~~GCnhm~C-~C~~~F  143 (203)
                      |.||.|+..|..+    -..| .|||.|
T Consensus         1 K~CP~C~~~V~~~----~~~Cp~CG~~F   24 (26)
T PF10571_consen    1 KTCPECGAEVPES----AKFCPHCGYDF   24 (26)
T ss_pred             CcCCCCcCCchhh----cCcCCCCCCCC
Confidence            5788888888432    3556 466665

Several members are annotated as putative helicases.

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

Probab=94.24  E-value=0.031  Score=48.91  Aligned_cols=43  Identities=21%  Similarity=0.624  Sum_probs=36.0

Q ss_pred             CCceeCCCCCCCceeeecCccccCCCCceeCCCccccccccCCcCCCCCCc
Q 043865           42 FERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAWHAGYR   92 (203)
Q Consensus        42 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H~~~~   92 (203)
                      ..++.||  .|+..+.....     ...++|. |++.||+.|..+|+.+..
T Consensus       304 ~~wr~Cp--kC~~~ie~~~G-----Cnhm~Cr-C~~~fcy~C~~~~~~~~~  346 (384)
T KOG1812|consen  304 KRWRQCP--KCKFMIELSEG-----CNHMTCR-CGHQFCYMCGGDWKTHNG  346 (384)
T ss_pred             HhcCcCc--ccceeeeecCC-----cceEEee-ccccchhhcCcchhhCCc
Confidence            5688999  69988866554     8999998 999999999999966554

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=93.32  E-value=0.087  Score=30.18  Aligned_cols=33  Identities=30%  Similarity=0.681  Sum_probs=24.0

Q ss_pred             ceeCCCCCCCceeeecCc-cccCCCCceeCCCccccc
Q 043865           44 RSYCPNRNCMALVVNEGE-INYGTLKKARCPNCKQWF   79 (203)
Q Consensus        44 ~~~Cp~~~C~~~~~~~~~-~~~~~~~~~~C~~C~~~~   79 (203)
                      .+.||  +|+..+..++. ++ .+...++|+.|++.|
T Consensus         2 ~i~CP--~C~~~f~v~~~~l~-~~~~~vrC~~C~~~f   35 (37)
T PF13719_consen    2 IITCP--NCQTRFRVPDDKLP-AGGRKVRCPKCGHVF   35 (37)
T ss_pred             EEECC--CCCceEEcCHHHcc-cCCcEEECCCCCcEe
Confidence            46788  59988876554 33 346699999999875

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=92.82  E-value=0.12  Score=29.44  Aligned_cols=33  Identities=36%  Similarity=0.655  Sum_probs=23.8

Q ss_pred             ceeCCCCCCCceeeecCc-cccCCCCceeCCCccccc
Q 043865           44 RSYCPNRNCMALVVNEGE-INYGTLKKARCPNCKQWF   79 (203)
Q Consensus        44 ~~~Cp~~~C~~~~~~~~~-~~~~~~~~~~C~~C~~~~   79 (203)
                      .+.||  +|+..+..++. ++ .....++|+.|++.|
T Consensus         2 ~i~Cp--~C~~~y~i~d~~ip-~~g~~v~C~~C~~~f   35 (36)
T PF13717_consen    2 IITCP--NCQAKYEIDDEKIP-PKGRKVRCSKCGHVF   35 (36)
T ss_pred             EEECC--CCCCEEeCCHHHCC-CCCcEEECCCCCCEe
Confidence            46788  59988766554 44 346689999999875

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

Probab=92.48  E-value=0.097  Score=46.72  Aligned_cols=45  Identities=27%  Similarity=0.584  Sum_probs=37.5

Q ss_pred             CCCCC--CCCceeEe-cCCcceeEecccccccccccccCcCCCCCCCC
Q 043865          116 GARRP--ACGSCVER-KEGCRVMYCRCKTSFCYECGGNLKSASGCLCK  160 (203)
Q Consensus       116 ~k~CP--~C~~~iek-~~GCnhm~C~C~~~FC~~C~~~~~~~~~C~~~  160 (203)
                      .+-||  .|+..+.. .+....+.|.|++.|||.|+.+|.....|+..
T Consensus       158 lkwCP~~~C~~av~~~~~~~~~v~C~~g~~FC~~C~~~~H~p~~C~~~  205 (444)
T KOG1815|consen  158 LKWCPAPGCGLAVKFGSLESVEVDCGCGHEFCFACGEESHSPVSCPGA  205 (444)
T ss_pred             cccCCCCCCCceeeccCCCccceeCCCCchhHhhccccccCCCcccch
Confidence            45565  79999988 78899999999999999999999986655543

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=92.20  E-value=0.11  Score=31.81  Aligned_cols=27  Identities=33%  Similarity=0.624  Sum_probs=20.7

Q ss_pred             CCCCCCCceeEecCC--cceeEe-cccccc
Q 043865          117 ARRPACGSCVERKEG--CRVMYC-RCKTSF  143 (203)
Q Consensus       117 k~CP~C~~~iek~~G--Cnhm~C-~C~~~F  143 (203)
                      +.||.|+.++...++  -++..| .||+++
T Consensus         1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~   30 (52)
T smart00661        1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEE   30 (52)
T ss_pred             CCCCCCCCccccccCCCCCEEECCcCCCeE
Confidence            469999998877644  468899 699764

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=91.98  E-value=0.075  Score=27.93  Aligned_cols=23  Identities=30%  Similarity=0.858  Sum_probs=14.5

Q ss_pred             CCCCCCCceeEecCCcceeEeccccccccccccc
Q 043865          117 ARRPACGSCVERKEGCRVMYCRCKTSFCYECGGN  150 (203)
Q Consensus       117 k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~  150 (203)
                      +.||+|+..++..           ..||-.||++
T Consensus         3 ~~Cp~Cg~~~~~~-----------~~fC~~CG~~   25 (26)
T PF13248_consen    3 MFCPNCGAEIDPD-----------AKFCPNCGAK   25 (26)
T ss_pred             CCCcccCCcCCcc-----------cccChhhCCC
Confidence            5688888866442           4566666654

>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown

Probab=91.76  E-value=0.21  Score=31.75  Aligned_cols=26  Identities=27%  Similarity=0.722  Sum_probs=19.1

Q ss_pred             CCCCCCCceeEecCCcceeEecccccccc-cccccCcC
Q 043865          117 ARRPACGSCVERKEGCRVMYCRCKTSFCY-ECGGNLKS  153 (203)
Q Consensus       117 k~CP~C~~~iek~~GCnhm~C~C~~~FC~-~C~~~~~~  153 (203)
                      |.||.||.+|.-           ...||. .|++.|..
T Consensus         4 kHC~~CG~~Ip~-----------~~~fCS~~C~~~~~k   30 (59)
T PF09889_consen    4 KHCPVCGKPIPP-----------DESFCSPKCREEYRK   30 (59)
T ss_pred             CcCCcCCCcCCc-----------chhhhCHHHHHHHHH
Confidence            678888888874           357774 77777774

They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=91.51  E-value=0.084  Score=26.98  Aligned_cols=11  Identities=36%  Similarity=0.785  Sum_probs=7.2

Q ss_pred             CCCCCCceeEe
Q 043865          118 RRPACGSCVER  128 (203)
Q Consensus       118 ~CP~C~~~iek  128 (203)
                      .||+|+..|+.
T Consensus         1 ~Cp~CG~~~~~   11 (23)
T PF13240_consen    1 YCPNCGAEIED   11 (23)
T ss_pred             CCcccCCCCCC
Confidence            37777777754

>PRK00432 30S ribosomal protein S27ae; Validated

Probab=91.19  E-value=0.14  Score=31.49  Aligned_cols=27  Identities=22%  Similarity=0.449  Sum_probs=20.0

Q ss_pred             cCCCCCCCCc-eeEecCCcceeEe-cccccc
Q 043865          115 HGARRPACGS-CVERKEGCRVMYC-RCKTSF  143 (203)
Q Consensus       115 ~~k~CP~C~~-~iek~~GCnhm~C-~C~~~F  143 (203)
                      ..+.||+|+. ......  +.++| +||+.+
T Consensus        19 ~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~   47 (50)
T PRK00432         19 KNKFCPRCGSGFMAEHL--DRWHCGKCGYTE   47 (50)
T ss_pred             ccCcCcCCCcchheccC--CcEECCCcCCEE
Confidence            3468999998 444434  79999 799865

>PHA00626 hypothetical protein

Probab=90.85  E-value=0.19  Score=31.43  Aligned_cols=26  Identities=27%  Similarity=0.586  Sum_probs=19.4

Q ss_pred             CCCCCCc-eeEecCCcce----eEe-cccccc
Q 043865          118 RRPACGS-CVERKEGCRV----MYC-RCKTSF  143 (203)
Q Consensus       118 ~CP~C~~-~iek~~GCnh----m~C-~C~~~F  143 (203)
                      .||+|+. .|.|.+-|+.    ..| .||+.|
T Consensus         2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f   33 (59)
T PHA00626          2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND   33 (59)
T ss_pred             CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence            5999999 5778766544    678 688776

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=90.65  E-value=0.29  Score=27.90  Aligned_cols=32  Identities=25%  Similarity=0.545  Sum_probs=21.4

Q ss_pred             eeCCCCCCCceeeecCc-cccCCCCceeCCCccccc
Q 043865           45 SYCPNRNCMALVVNEGE-INYGTLKKARCPNCKQWF   79 (203)
Q Consensus        45 ~~Cp~~~C~~~~~~~~~-~~~~~~~~~~C~~C~~~~   79 (203)
                      +.||  +|+..+..++. +. +....+.||.|++.|
T Consensus         3 ~~CP--~C~~~~~v~~~~~~-~~~~~v~C~~C~~~~   35 (38)
T TIGR02098         3 IQCP--NCKTSFRVVDSQLG-ANGGKVRCGKCGHVW   35 (38)
T ss_pred             EECC--CCCCEEEeCHHHcC-CCCCEEECCCCCCEE
Confidence            5688  59987765543 22 223479999998764

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.

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

Probab=90.44  E-value=0.24  Score=29.65  Aligned_cols=29  Identities=24%  Similarity=0.400  Sum_probs=20.1

Q ss_pred             CCCCCCCceeEecCCcceeEe-cccccccc
Q 043865          117 ARRPACGSCVERKEGCRVMYC-RCKTSFCY  145 (203)
Q Consensus       117 k~CP~C~~~iek~~GCnhm~C-~C~~~FC~  145 (203)
                      -+||+|+..++..++=..++| .||..+=+
T Consensus         4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~   33 (46)
T PRK00398          4 YKCARCGREVELDEYGTGVRCPYCGYRILF   33 (46)
T ss_pred             EECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence            358888888877755557788 58776543

>PLN03086 PRLI-interacting factor K; Provisional

Probab=89.75  E-value=0.65  Score=42.62  Aligned_cols=56  Identities=23%  Similarity=0.565  Sum_probs=33.7

Q ss_pred             ccCCcccCCCcCCHHHHhhcCCHHHHHHHHHHHHHhhccCCCceeCCCCCCCceeeecCccccCCCCceeCCCccccc
Q 043865            2 IECPGVHCDQFLDLFTCKLMIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWF   79 (203)
Q Consensus         2 I~CP~~~C~~~l~~~~i~~~l~~e~~~~y~~~~~~~~i~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~   79 (203)
                      +.||.  |+..+....+...+.              +- .-+.+-||+.+|+..+.....     .....|+.|+..|
T Consensus       408 V~C~N--C~~~i~l~~l~lHe~--------------~C-~r~~V~Cp~~~Cg~v~~r~el-----~~H~~C~~Cgk~f  463 (567)
T PLN03086        408 VECRN--CKHYIPSRSIALHEA--------------YC-SRHNVVCPHDGCGIVLRVEEA-----KNHVHCEKCGQAF  463 (567)
T ss_pred             EECCC--CCCccchhHHHHHHh--------------hC-CCcceeCCcccccceeecccc-----ccCccCCCCCCcc
Confidence            45774  777776655543221              00 124567887678888765544     4556788887765

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

Probab=88.71  E-value=0.28  Score=29.87  Aligned_cols=27  Identities=22%  Similarity=0.391  Sum_probs=21.1

Q ss_pred             cCCCCCCCCceeEecCCcceeEe-cccc
Q 043865          115 HGARRPACGSCVERKEGCRVMYC-RCKT  141 (203)
Q Consensus       115 ~~k~CP~C~~~iek~~GCnhm~C-~C~~  141 (203)
                      .-+.||+|+.-+...+-=+...| +||+
T Consensus        18 k~~~CPrCG~gvfmA~H~dR~~CGkCgy   45 (51)
T COG1998          18 KNRFCPRCGPGVFMADHKDRWACGKCGY   45 (51)
T ss_pred             ccccCCCCCCcchhhhcCceeEeccccc
Confidence            34789999977766666668899 8986

>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=88.43  E-value=0.57  Score=25.72  Aligned_cols=27  Identities=19%  Similarity=0.336  Sum_probs=17.2

Q ss_pred             CCCCCCCCceeEecCCcceeEe-ccccc
Q 043865          116 GARRPACGSCVERKEGCRVMYC-RCKTS  142 (203)
Q Consensus       116 ~k~CP~C~~~iek~~GCnhm~C-~C~~~  142 (203)
                      .+-||+|+.+.+...+=-.|.| .|+.+
T Consensus         3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~   30 (32)
T PF09297_consen    3 HRFCGRCGAPTKPAPGGWARRCPSCGHE   30 (32)
T ss_dssp             TSB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred             CcccCcCCccccCCCCcCEeECCCCcCE
Confidence            4779999999999888778888 68865

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

>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=86.36  E-value=0.27  Score=30.31  Aligned_cols=25  Identities=40%  Similarity=0.990  Sum_probs=16.0

Q ss_pred             CCceeCCCccccccccCCcCCCCCC
Q 043865           67 LKKARCPNCKQWFCFQCKVAWHAGY   91 (203)
Q Consensus        67 ~~~~~C~~C~~~~C~~C~~~~H~~~   91 (203)
                      ....+||.|++.||..|-.-.|+.+
T Consensus        19 ~~~y~C~~C~~~FC~dCD~fiHE~L   43 (51)
T PF07975_consen   19 SSRYRCPKCKNHFCIDCDVFIHETL   43 (51)
T ss_dssp             -EEE--TTTT--B-HHHHHTTTTTS
T ss_pred             CCeEECCCCCCccccCcChhhhccc
Confidence            5679999999999999988778754

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.

>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]

Probab=85.22  E-value=0.71  Score=32.29  Aligned_cols=29  Identities=28%  Similarity=0.637  Sum_probs=22.2

Q ss_pred             CCCCCCceeEec--CCcceeEe-ccccccccc
Q 043865          118 RRPACGSCVERK--EGCRVMYC-RCKTSFCYE  146 (203)
Q Consensus       118 ~CP~C~~~iek~--~GCnhm~C-~C~~~FC~~  146 (203)
                      .||.|+.+..-.  +.||...| .|.|.|=-.
T Consensus         3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~   34 (105)
T KOG2906|consen    3 FCPTCGNMLIVESGESCNRFSCRTCPYVFPIS   34 (105)
T ss_pred             ccCCCCCEEEEecCCeEeeEEcCCCCceeeEe
Confidence            599999865544  44999999 699987543

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

Probab=84.80  E-value=0.66  Score=26.19  Aligned_cols=28  Identities=25%  Similarity=0.673  Sum_probs=18.0

Q ss_pred             eeCCCCCCCceeeecCccccCCCCceeCCCcccc
Q 043865           45 SYCPNRNCMALVVNEGEINYGTLKKARCPNCKQW   78 (203)
Q Consensus        45 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~   78 (203)
                      ++||  .|++.+.+...   . .....|+.|++.
T Consensus         2 ~FCp--~C~nlL~p~~~---~-~~~~~C~~C~Y~   29 (35)
T PF02150_consen    2 RFCP--ECGNLLYPKED---K-EKRVACRTCGYE   29 (35)
T ss_dssp             -BET--TTTSBEEEEEE---T-TTTEEESSSS-E
T ss_pred             eeCC--CCCccceEcCC---C-ccCcCCCCCCCc
Confidence            5788  69999987665   1 222278888764

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 ....

>smart00661 RPOL9 RNA polymerase subunit 9

Probab=84.55  E-value=0.84  Score=27.70  Aligned_cols=28  Identities=18%  Similarity=0.628  Sum_probs=19.2

Q ss_pred             eCCCCCCCceeeecCccccCCCCceeCCCcccc
Q 043865           46 YCPNRNCMALVVNEGEINYGTLKKARCPNCKQW   78 (203)
Q Consensus        46 ~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~   78 (203)
                      +||  .|+..+.....   +......|+.|++.
T Consensus         2 FCp--~Cg~~l~~~~~---~~~~~~vC~~Cg~~   29 (52)
T smart00661        2 FCP--KCGNMLIPKEG---KEKRRFVCRKCGYE   29 (52)
T ss_pred             CCC--CCCCccccccC---CCCCEEECCcCCCe
Confidence            687  69998876543   12247889988864

>PHA03049 IMV membrane protein; Provisional

Probab=83.81  E-value=1.6  Score=28.18  Aligned_cols=22  Identities=32%  Similarity=0.788  Sum_probs=16.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhh
Q 043865          175 SGLILIFTVLGVLGGVIYGIYC  196 (203)
Q Consensus       175 ~~~~~~f~~l~~~~~~~~~~~~  196 (203)
                      .-++|+-+-..++|+++|++|=
T Consensus         3 ~d~~l~iICVaIi~lIvYgiYn   24 (68)
T PHA03049          3 GDIILVIICVVIIGLIVYGIYN   24 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHh
Confidence            3356666677888899999994

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

Probab=82.77  E-value=1.9  Score=25.61  Aligned_cols=29  Identities=24%  Similarity=0.393  Sum_probs=21.3

Q ss_pred             eeCCCCCCCceeeecCccccCCCCceeCCCcccccc
Q 043865           45 SYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFC   80 (203)
Q Consensus        45 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C   80 (203)
                      ..||  +|+..+..++.     ...+.||.||..+=
T Consensus         4 y~C~--~CG~~~~~~~~-----~~~~~Cp~CG~~~~   32 (46)
T PRK00398          4 YKCA--RCGREVELDEY-----GTGVRCPYCGYRIL   32 (46)
T ss_pred             EECC--CCCCEEEECCC-----CCceECCCCCCeEE
Confidence            4677  69998877665     33789999987643

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

Probab=82.21  E-value=1.1  Score=27.05  Aligned_cols=30  Identities=27%  Similarity=0.484  Sum_probs=20.2

Q ss_pred             CceeCCCCCCCceeeecCccccCCCCceeCCCccc
Q 043865           43 ERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQ   77 (203)
Q Consensus        43 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~   77 (203)
                      ....||++.|+..+.....     .....|.+|+.
T Consensus        17 ~rk~CP~~~CG~GvFMA~H-----~dR~~CGKCg~   46 (47)
T PF01599_consen   17 LRKECPSPRCGAGVFMAEH-----KDRHYCGKCGY   46 (47)
T ss_dssp             SSEE-TSTTTTSSSEEEE------SSEEEETTTSS
T ss_pred             hhhcCCCcccCCceEeeec-----CCCccCCCccc
Confidence            3689999999986554444     45778877764

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

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

Probab=81.84  E-value=1.1  Score=28.47  Aligned_cols=33  Identities=24%  Similarity=0.598  Sum_probs=21.6

Q ss_pred             eeCCCCCCCceeeecCccccCCCCceeCCCccccccccCC
Q 043865           45 SYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCK   84 (203)
Q Consensus        45 ~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~   84 (203)
                      -.|.  +|+..+.+...     ...+.||.|+...=.+|.
T Consensus        10 ~~Ct--SCg~~i~p~e~-----~v~F~CPnCGe~~I~Rc~   42 (61)
T COG2888          10 PVCT--SCGREIAPGET-----AVKFPCPNCGEVEIYRCA   42 (61)
T ss_pred             ceec--cCCCEeccCCc-----eeEeeCCCCCceeeehhh
Confidence            3455  47777644443     678999999976654444

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

Probab=81.76  E-value=1.3  Score=37.60  Aligned_cols=40  Identities=23%  Similarity=0.757  Sum_probs=31.1

Q ss_pred             CceeCCCCCCCceeeecCccccCCCCceeCCC--ccccccccCCcCCCC
Q 043865           43 ERSYCPNRNCMALVVNEGEINYGTLKKARCPN--CKQWFCFQCKVAWHA   89 (203)
Q Consensus        43 ~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~H~   89 (203)
                      ....||  .|......++.     .-.+.|+.  |+..+|++|+.+|..
T Consensus       396 tTkpCP--kChvptErnGG-----CmHm~Ct~~~Cg~eWCw~C~tEW~r  437 (446)
T KOG0006|consen  396 TTKPCP--KCHVPTERNGG-----CMHMKCTQPQCGLEWCWNCGTEWNR  437 (446)
T ss_pred             ccCCCC--CccCccccCCc-----eEEeecCCCCCCceeEeccCChhhh
Confidence            445566  68877666554     77889976  999999999999965

>PF05961 Chordopox_A13L: Chordopoxvirus A13L protein; InterPro: IPR009236 This family consists of A13L proteins from the Chordopoxviruses

Probab=81.56  E-value=2.2  Score=27.66  Aligned_cols=24  Identities=33%  Similarity=0.715  Sum_probs=17.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhh
Q 043865          175 SGLILIFTVLGVLGGVIYGIYCVI  198 (203)
Q Consensus       175 ~~~~~~f~~l~~~~~~~~~~~~~~  198 (203)
                      .-++|+-+=..++|+++|++|==.
T Consensus         3 ~d~iLi~ICVaii~lIlY~iYnr~   26 (68)
T PF05961_consen    3 GDFILIIICVAIIGLILYGIYNRK   26 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcc
Confidence            335666677788889999999533

A13L or p8 is one of the three most abundant membrane proteins of the intracellular mature Vaccinia virus [].

>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=80.76  E-value=11  Score=31.13  Aligned_cols=45  Identities=18%  Similarity=0.431  Sum_probs=28.7

Q ss_pred             CCCCC--CCceeEec--------------CCcceeEe-cccccccccccccCcCCCCCCCCcC
Q 043865          117 ARRPA--CGSCVERK--------------EGCRVMYC-RCKTSFCYECGGNLKSASGCLCKEK  162 (203)
Q Consensus       117 k~CP~--C~~~iek~--------------~GCnhm~C-~C~~~FC~~C~~~~~~~~~C~~~~~  162 (203)
                      --||+  |+..|...              .|--.++| .|...|=|.=... +....|+|=.+
T Consensus       124 IaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~-~tlARCPHCrK  185 (256)
T PF09788_consen  124 IACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLTS-NTLARCPHCRK  185 (256)
T ss_pred             ccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcEeccCCCC-CccccCCCCce
Confidence            35875  99988754              24455899 8999999984331 12234665443

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

Probab=80.24  E-value=1.9  Score=23.02  Aligned_cols=20  Identities=40%  Similarity=0.718  Sum_probs=13.7

Q ss_pred             CCCCCCceeEecCCcceeEe
Q 043865          118 RRPACGSCVERKEGCRVMYC  137 (203)
Q Consensus       118 ~CP~C~~~iek~~GCnhm~C  137 (203)
                      .||.|+..+.+.+|=-..+|
T Consensus         1 ~CP~C~s~l~~~~~ev~~~C   20 (28)
T PF03119_consen    1 TCPVCGSKLVREEGEVDIRC   20 (28)
T ss_dssp             B-TTT--BEEE-CCTTCEEE
T ss_pred             CcCCCCCEeEcCCCCEeEEC
Confidence            59999999999998777777

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

---

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	203
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	1e-05

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

 Score = 41.5 bits (97), Expect = 1e-05
 Identities = 21/77 (27%), Positives = 29/77 (37%), Gaps = 8/77 (10%)

Query: 31  CDVLCEDYVLGFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAW--- 87
                 + VL  +  +     C    + E E       +A CP C Q FC +CK  W   
Sbjct: 10  FHKKLTEGVLMRDPKFLWCAQCSFGFIYEREQ-----LEATCPQCHQTFCVRCKRQWEEQ 64

Query: 88  HAGYRCEESGNLRDWND 104
           H G  CE+  N +  N 
Sbjct: 65  HRGRSCEDFQNWKRMNS 81

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	203
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	99.67
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	99.58
2jmo_A	80	Parkin; IBR, E3 ligase, zinc binding domain, RBR;	99.49
2jmo_A	80	Parkin; IBR, E3 ligase, zinc binding domain, RBR;	97.78
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	97.7
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	97.7
1wd2_A	60	Ariadne-1 protein homolog; ring, IBR, triad, zinc	96.77
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	94.71
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	89.98
2k4x_A	55	30S ribosomal protein S27AE; metal-binding, ribonu	89.44
3j20_Y	50	30S ribosomal protein S27AE; archaea, archaeal, KI	87.8
1vq8_Z	83	50S ribosomal protein L37AE; ribosome 50S, protein	86.79
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	85.85
2jrp_A	81	Putative cytoplasmic protein; two-zinc binding pro	85.76
1pft_A	50	TFIIB, PFTFIIBN; N-terminal domain, transcription	85.26
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	83.16
1z60_A	59	TFIIH basal transcription factor complex P44 subun	81.82
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	80.54

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

Probab=99.67  E-value=5.4e-18  Score=108.23  Aligned_cols=42  Identities=31%  Similarity=0.817  Sum_probs=39.2

Q ss_pred             ccCCCCCCCCceeEecCCcceeEe-c--ccccccccccccCcCCC
Q 043865          114 MHGARRPACGSCVERKEGCRVMYC-R--CKTSFCYECGGNLKSAS  155 (203)
Q Consensus       114 ~~~k~CP~C~~~iek~~GCnhm~C-~--C~~~FC~~C~~~~~~~~  155 (203)
                      .++|+||+|+++|||++|||||+| +  |+++|||.|+++|+.++
T Consensus         4 ~~~k~CP~C~~~Iek~~GCnhmtC~~~~C~~~FCw~C~~~~~~~~   48 (60)
T 1wd2_A            4 ANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHG   48 (60)
T ss_dssp             CCCCCCTTTCCCCSSCCSCCSSSCCSSGGGSCCSSSSCSCSGGGG
T ss_pred             ccceECcCCCCeeEeCCCCCcEEECCCCcCCEEeeCcCCCcccCC
Confidence            578999999999999999999999 4  99999999999999764

>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=99.58  E-value=1.3e-17  Score=114.45  Aligned_cols=76  Identities=29%  Similarity=0.576  Sum_probs=66.4

Q ss_pred             CHHHHHHHHHHHHHhhcc-CCCceeCCCCCCCceeeecCccccCCCCceeCCCccccccccCCcCC---CCCCccccccc
Q 043865           23 PSNLFSKWCDVLCEDYVL-GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAW---HAGYRCEESGN   98 (203)
Q Consensus        23 ~~e~~~~y~~~~~~~~i~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~---H~~~~C~~~~~   98 (203)
                      +++++++|++++.+.+|. +++++|||  +|+++++.++.     ...++||.|++.||+.|+.+|   |.|.+|++++.
T Consensus         3 s~~~~e~y~~~l~e~~v~~~~~~~wCP--~C~~~~~~~~~-----~~~v~C~~C~~~FC~~C~~~w~~~H~~~sC~~~~~   75 (86)
T 2ct7_A            3 SGSSGALFHKKLTEGVLMRDPKFLWCA--QCSFGFIYERE-----QLEATCPQCHQTFCVRCKRQWEEQHRGRSCEDFQN   75 (86)
T ss_dssp             CCCCCCSSSSCCCCSCCCSCCCEECCS--SSCCCEECCCS-----CSCEECTTTCCEECSSSCSBCCTTTTTSCHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEeECc--CCCchheecCC-----CCceEeCCCCCccccccCCchhhcCCCCChHHHHH
Confidence            456788999999999996 88899999  99999987654     567999999999999999999   99999999998


Q ss_pred             cccchhH
Q 043865           99 LRDWNDI  105 (203)
Q Consensus        99 ~~~~~d~  105 (203)
                      |..++|.
T Consensus        76 w~~~n~~   82 (86)
T 2ct7_A           76 WKRMNSG   82 (86)
T ss_dssp             HHHHHTC
T ss_pred             HHHhCcc
Confidence            8766554

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

Probab=99.49  E-value=4.9e-16  Score=105.12  Aligned_cols=70  Identities=26%  Similarity=0.562  Sum_probs=62.6

Q ss_pred             cCCHHHHHHHHHHHHHhhccCCCceeCCCCCCCceeeecCccccCCCCceeCC-----CccccccccCCcCCCCCCcccc
Q 043865           21 MIPSNLFSKWCDVLCEDYVLGFERSYCPNRNCMALVVNEGEINYGTLKKARCP-----NCKQWFCFQCKVAWHAGYRCEE   95 (203)
Q Consensus        21 ~l~~e~~~~y~~~~~~~~i~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~-----~C~~~~C~~C~~~~H~~~~C~~   95 (203)
                      +|++++++||++++.+.++...+.+|||+|+|++++..++.     ...++|+     .|++.||+.|+.+||+ .+|++
T Consensus         2 ~l~~~~~~rY~~~~~e~~v~~~~~~~CP~p~C~~~v~~~~~-----~~~v~C~~~~~~~C~~~FC~~C~~~wH~-~~C~~   75 (80)
T 2jmo_A            2 HMGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPD-----QRKVTCEGGNGLGCGFAFCRECKEAYHE-GECSA   75 (80)
T ss_dssp             CCCCCCCCSCCCSSSCCSSCCCSSCCCCSSSCCCCCCCCSC-----TTSBCTTSSSTTCCSCCEETTTTEECCS-SCSSS
T ss_pred             CCCHHHHHHHHHHHHHHHhhhCCcEECCCCCCCcccEECCC-----CCcCCCCCCCCCCCCCeeccccCccccC-Ccccc
Confidence            68889999999999999997556999999999999987654     5679998     9999999999999999 99986


Q ss_pred             c
Q 043865           96 S   96 (203)
Q Consensus        96 ~   96 (203)
                      .
T Consensus        76 ~   76 (80)
T 2jmo_A           76 V   76 (80)
T ss_dssp             C
T ss_pred             c
Confidence            4

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

Probab=97.78  E-value=2.3e-06  Score=57.24  Aligned_cols=45  Identities=29%  Similarity=0.654  Sum_probs=39.8

Q ss_pred             ccCCCCCC--CCceeEecCCcceeEe------cccccccccccccCcCCCCCCC
Q 043865          114 MHGARRPA--CGSCVERKEGCRVMYC------RCKTSFCYECGGNLKSASGCLC  159 (203)
Q Consensus       114 ~~~k~CP~--C~~~iek~~GCnhm~C------~C~~~FC~~C~~~~~~~~~C~~  159 (203)
                      ...+-||.  |+..|...++...++|      .|++.||+.|+..|.. ..|.-
T Consensus        23 ~~~~~CP~p~C~~~v~~~~~~~~v~C~~~~~~~C~~~FC~~C~~~wH~-~~C~~   75 (80)
T 2jmo_A           23 MGGVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGCGFAFCRECKEAYHE-GECSA   75 (80)
T ss_dssp             CSSCCCCSSSCCCCCCCCSCTTSBCTTSSSTTCCSCCEETTTTEECCS-SCSSS
T ss_pred             CCcEECCCCCCCcccEECCCCCcCCCCCCCCCCCCCeeccccCccccC-Ccccc
Confidence            45788997  9999999999999999      6999999999999988 66754

>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=97.70  E-value=3.4e-05  Score=52.78  Aligned_cols=40  Identities=18%  Similarity=0.370  Sum_probs=37.4

Q ss_pred             ccCCcccCCCc--CCHHHHhhcCCHHHHHHHHHHHHHhhccC
Q 043865            2 IECPGVHCDQF--LDLFTCKLMIPSNLFSKWCDVLCEDYVLG   41 (203)
Q Consensus         2 I~CP~~~C~~~--l~~~~i~~~l~~e~~~~y~~~~~~~~i~~   41 (203)
                      |+||.++|...  +++++++.+|+++++++|++++.+.++++
T Consensus        51 i~CP~~~C~~~~~~~~~~i~~ll~~~~~~ky~~~~~~~~v~~   92 (94)
T 1wim_A           51 ISCPDAACPKQGHLQENEIECMVAAEIMQRYKKLQFERSGPS   92 (94)
T ss_dssp             EECSCTTCSSCCEECHHHHHHHSCHHHHHHHHHHHHHSSCSS
T ss_pred             ccCccccCCCCCccCHHHHHHHCCHHHHHHHHHHHHHhhhcc
Confidence            78999999999  99999999999999999999999988863

>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=97.70  E-value=1.8e-05  Score=53.59  Aligned_cols=38  Identities=16%  Similarity=0.320  Sum_probs=33.7

Q ss_pred             ccCCCCCCCCceeEecCCcceeEe-cccccccccccccC
Q 043865          114 MHGARRPACGSCVERKEGCRVMYC-RCKTSFCYECGGNL  151 (203)
Q Consensus       114 ~~~k~CP~C~~~iek~~GCnhm~C-~C~~~FC~~C~~~~  151 (203)
                      .+.+-||+|+..+....+-..++| .|++.||+.|+.+|
T Consensus        23 ~~~~wCP~C~~~~~~~~~~~~v~C~~C~~~FC~~C~~~w   61 (86)
T 2ct7_A           23 PKFLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKRQW   61 (86)
T ss_dssp             CCEECCSSSCCCEECCCSCSCEECTTTCCEECSSSCSBC
T ss_pred             CCEeECcCCCchheecCCCCceEeCCCCCccccccCCch
Confidence            344569999999988888888999 69999999999999

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

Probab=96.77  E-value=0.0013  Score=41.16  Aligned_cols=40  Identities=30%  Similarity=0.821  Sum_probs=33.9

Q ss_pred             CCceeCCCCCCCceeeecCccccCCCCceeCCC--ccccccccCCcCCC
Q 043865           42 FERSYCPNRNCMALVVNEGEINYGTLKKARCPN--CKQWFCFQCKVAWH   88 (203)
Q Consensus        42 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~--C~~~~C~~C~~~~H   88 (203)
                      .+.+.||  .|+..+..++.     .+.++|..  |+..||+.|..+|-
T Consensus         4 ~~~k~CP--~C~~~Iek~~G-----CnhmtC~~~~C~~~FCw~C~~~~~   45 (60)
T 1wd2_A            4 ANTKECP--KCHVTIEKDGG-----CNHMVCRNQNCKAEFCWVCLGPWE   45 (60)
T ss_dssp             CCCCCCT--TTCCCCSSCCS-----CCSSSCCSSGGGSCCSSSSCSCSG
T ss_pred             ccceECc--CCCCeeEeCCC-----CCcEEECCCCcCCEEeeCcCCCcc
Confidence            4567788  69999887665     88999988  99999999999983

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

Probab=94.71  E-value=0.0014  Score=46.87  Aligned_cols=80  Identities=16%  Similarity=0.334  Sum_probs=49.7

Q ss_pred             CCCccccccccCCcCC-CCCCccccccccccchhHHHHHHHHhccCCCCCCCCceeEecC--CcceeEeccccccccccc
Q 043865           72 CPNCKQWFCFQCKVAW-HAGYRCEESGNLRDWNDIAFGKLVERMHGARRPACGSCVERKE--GCRVMYCRCKTSFCYECG  148 (203)
Q Consensus        72 C~~C~~~~C~~C~~~~-H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~iek~~--GCnhm~C~C~~~FC~~C~  148 (203)
                      -..||+.||..|-..| ....+|..-+......+  +..+........||-|...++...  +=..+...||+.||+.|.
T Consensus        29 ~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~--l~~l~i~~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci  106 (133)
T 4ap4_A           29 STECGHVFCSQCLRDSLKNANTCPTCRKKINHKR--YHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCL  106 (133)
T ss_dssp             EETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTC--EEECBCSSSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHH
T ss_pred             ecCCCChhhHHHHHHHHHhCCCCCCCCCcCcccc--ccccccCCCCCCCCCCCCccccccccCcceEeCCCCChhhHHHH
Confidence            3468999999999988 33446664433211111  000111234567999988876542  223355589999999999


Q ss_pred             ccCcC
Q 043865          149 GNLKS  153 (203)
Q Consensus       149 ~~~~~  153 (203)
                      .+|..
T Consensus       107 ~~~~~  111 (133)
T 4ap4_A          107 RDSLK  111 (133)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            88864

>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=89.98  E-value=0.21  Score=37.25  Aligned_cols=68  Identities=16%  Similarity=0.353  Sum_probs=36.2

Q ss_pred             CceeCCCCCCCceeeecCccc---cCCCCceeCCCccccccccCCcCCCCCCccccccccccchhHHHHHHHHhccCCCC
Q 043865           43 ERSYCPNRNCMALVVNEGEIN---YGTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARR  119 (203)
Q Consensus        43 ~~~~Cp~~~C~~~~~~~~~~~---~~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~C  119 (203)
                      -.++||+.+|+..+......+   .=....+.||.|+..+ .+....+|....|..                   ....|
T Consensus        81 l~v~C~n~GC~~~~~~~~l~~H~~~C~~~~v~C~~C~~~~-~r~~l~~H~~~~C~~-------------------r~~~C  140 (170)
T 3hcs_A           81 LMVKCPNEGCLHKMELRHLEDHQAHCEFALMDCPQCQRPF-QKFHINIHILKDCPR-------------------RQVSC  140 (170)
T ss_dssp             SEEECCSTTCCCEEEGGGHHHHHTTCTTSEEECTTTCCEE-EGGGHHHHHHHTCTT-------------------CEEEC
T ss_pred             cccCCCCCCCCceecHhHHHHHHhcCCceeeECCCCChHH-HHHHHHHHhhhhCCC-------------------CCeEC
Confidence            468999999998876554310   0013345666555544 233333443333432                   22457


Q ss_pred             CCCCceeEecC
Q 043865          120 PACGSCVERKE  130 (203)
Q Consensus       120 P~C~~~iek~~  130 (203)
                      |.|+..+.+.+
T Consensus       141 ~~C~~~~~~~~  151 (170)
T 3hcs_A          141 DNCAASMAFED  151 (170)
T ss_dssp             TTTCCEEEGGG
T ss_pred             CCCCCccCHHH
Confidence            77777666543

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

Probab=89.44  E-value=0.13  Score=31.35  Aligned_cols=28  Identities=29%  Similarity=0.401  Sum_probs=20.8

Q ss_pred             CCCCCCCCceeEecCCcceeEe-cccccc
Q 043865          116 GARRPACGSCVERKEGCRVMYC-RCKTSF  143 (203)
Q Consensus       116 ~k~CP~C~~~iek~~GCnhm~C-~C~~~F  143 (203)
                      .+.||+|+..+.-...-+.++| +|++.+
T Consensus        18 ~~fCPkCG~~~~ma~~~dr~~C~kCgyt~   46 (55)
T 2k4x_A           18 HRFCPRCGPGVFLAEHADRYSCGRCGYTE   46 (55)
T ss_dssp             SCCCTTTTTTCCCEECSSEEECTTTCCCE
T ss_pred             cccCcCCCCceeEeccCCEEECCCCCCEE
Confidence            4789999985543344579999 799874

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

Probab=87.80  E-value=0.18  Score=30.04  Aligned_cols=29  Identities=21%  Similarity=0.349  Sum_probs=19.7

Q ss_pred             cCCCCCCCCceeEecCCcceeEe-cccccc
Q 043865          115 HGARRPACGSCVERKEGCRVMYC-RCKTSF  143 (203)
Q Consensus       115 ~~k~CP~C~~~iek~~GCnhm~C-~C~~~F  143 (203)
                      ..+.||+|+..+.-...=+.+.| +||+.+
T Consensus        18 ~~k~CP~CG~~~fm~~~~~R~~C~kCG~t~   47 (50)
T 3j20_Y           18 KNKFCPRCGPGVFMADHGDRWACGKCGYTE   47 (50)
T ss_dssp             SSEECSSSCSSCEEEECSSEEECSSSCCEE
T ss_pred             ecccCCCCCCceEEecCCCeEECCCCCCEE
Confidence            45789999984433333378999 798643

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

Probab=86.79  E-value=0.5  Score=31.24  Aligned_cols=31  Identities=23%  Similarity=0.530  Sum_probs=26.1

Q ss_pred             ccCCCCCCCCceeEecCCcceeEe-ccccccc
Q 043865          114 MHGARRPACGSCVERKEGCRVMYC-RCKTSFC  144 (203)
Q Consensus       114 ~~~k~CP~C~~~iek~~GCnhm~C-~C~~~FC  144 (203)
                      ...-.||.|+....+..+-..+.| .|++.|-
T Consensus        25 ~~~y~Cp~CG~~~v~r~atGiW~C~~Cg~~~a   56 (83)
T 1vq8_Z           25 NEDHACPNCGEDRVDRQGTGIWQCSYCDYKFT   56 (83)
T ss_dssp             HSCEECSSSCCEEEEEEETTEEEETTTCCEEE
T ss_pred             cccCcCCCCCCcceeccCCCeEECCCCCCEec
Confidence            345689999999999988889999 6998774

>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=85.85  E-value=0.14  Score=34.76  Aligned_cols=32  Identities=19%  Similarity=0.459  Sum_probs=26.7

Q ss_pred             CCCCCCCceeEecCCcceeEe-cccccccccccccCcC
Q 043865          117 ARRPACGSCVERKEGCRVMYC-RCKTSFCYECGGNLKS  153 (203)
Q Consensus       117 k~CP~C~~~iek~~GCnhm~C-~C~~~FC~~C~~~~~~  153 (203)
                      -.||-|...+.     +-+++ .|||.||+.|...|-.
T Consensus        23 ~~C~IC~~~~~-----~p~~~~~CgH~FC~~Ci~~~~~   55 (100)
T 3lrq_A           23 FRCFICMEKLR-----DARLCPHCSKLCCFSCIRRWLT   55 (100)
T ss_dssp             TBCTTTCSBCS-----SEEECTTTCCEEEHHHHHHHHH
T ss_pred             CCCccCCcccc-----CccccCCCCChhhHHHHHHHHH
Confidence            57999998885     46787 7999999999988853

>2jrp_A Putative cytoplasmic protein; two-zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium LT2}

Probab=85.76  E-value=0.54  Score=30.90  Aligned_cols=35  Identities=26%  Similarity=0.686  Sum_probs=20.4

Q ss_pred             CCCCCCCceeEecCCcceeEe-cccc-----cccccccccCcC
Q 043865          117 ARRPACGSCVERKEGCRVMYC-RCKT-----SFCYECGGNLKS  153 (203)
Q Consensus       117 k~CP~C~~~iek~~GCnhm~C-~C~~-----~FC~~C~~~~~~  153 (203)
                      ..||.|+..++.+++  +..| .|+.     -||-.|++++..
T Consensus         3 ~~CP~C~~~l~~~~~--~~~C~~C~~~~~~~afCPeCgq~Le~   43 (81)
T 2jrp_A            3 ITCPVCHHALERNGD--TAHCETCAKDFSLQALCPDCRQPLQV   43 (81)
T ss_dssp             CCCSSSCSCCEECSS--EEECTTTCCEEEEEEECSSSCSCCCE
T ss_pred             CCCCCCCCccccCCC--ceECccccccCCCcccCcchhhHHHH
Confidence            356666666666655  4446 4652     256666666543

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

Probab=85.26  E-value=0.86  Score=26.74  Aligned_cols=29  Identities=21%  Similarity=0.351  Sum_probs=22.2

Q ss_pred             cCCCCCCCCc-eeEecCCcceeEe-cccccc
Q 043865          115 HGARRPACGS-CVERKEGCRVMYC-RCKTSF  143 (203)
Q Consensus       115 ~~k~CP~C~~-~iek~~GCnhm~C-~C~~~F  143 (203)
                      ....||.|+. .+..+..=..+.| .||..+
T Consensus         4 ~~~~CP~C~~~~l~~d~~~gelvC~~CG~v~   34 (50)
T 1pft_A            4 KQKVCPACESAELIYDPERGEIVCAKCGYVI   34 (50)
T ss_dssp             SCCSCTTTSCCCEEEETTTTEEEESSSCCBC
T ss_pred             ccEeCcCCCCcceEEcCCCCeEECcccCCcc
Confidence            3467999998 7777766678999 688754

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

Probab=83.16  E-value=0.21  Score=30.55  Aligned_cols=33  Identities=18%  Similarity=0.505  Sum_probs=26.0

Q ss_pred             CCCCCCCCceeEecCCcceeEecccccccccccccCcC
Q 043865          116 GARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKS  153 (203)
Q Consensus       116 ~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~~  153 (203)
                      ...||-|...+.     +-++-.||+.||+.|...|..
T Consensus        20 ~~~C~IC~~~~~-----~p~~~~CgH~fC~~Ci~~~~~   52 (63)
T 2ysj_A           20 EVICPICLDILQ-----KPVTIDCGHNFCLKCITQIGE   52 (63)
T ss_dssp             CCBCTTTCSBCS-----SCEECTTSSEECHHHHHHHHH
T ss_pred             CCCCCcCCchhC-----CeEEeCCCCcchHHHHHHHHH
Confidence            357999987765     244558999999999998874

>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=81.82  E-value=0.48  Score=29.24  Aligned_cols=23  Identities=30%  Similarity=0.738  Sum_probs=19.5

Q ss_pred             ceeCCCccccccccCCcCCCCCC
Q 043865           69 KARCPNCKQWFCFQCKVAWHAGY   91 (203)
Q Consensus        69 ~~~C~~C~~~~C~~C~~~~H~~~   91 (203)
                      ..+|+.|++.||..|-.-.|+.+
T Consensus        30 ~y~C~~C~~~FC~dCD~fiHe~L   52 (59)
T 1z60_A           30 VYVCAVCQNVFCVDCDVFVHDSL   52 (59)
T ss_dssp             EECCTTTTCCBCHHHHHTTTTTS
T ss_pred             cEECCccCcCcccchhHHHHhhc
Confidence            36899999999999988888754

>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=80.54  E-value=1.2  Score=29.78  Aligned_cols=45  Identities=22%  Similarity=0.316  Sum_probs=32.2

Q ss_pred             CCCCceeCCCccccccccCCcCCCCCCccccccccccchhHHHHHHHHhccCCCCCCCCceeEecCCcc
Q 043865           65 GTLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPACGSCVERKEGCR  133 (203)
Q Consensus        65 ~~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~iek~~GCn  133 (203)
                      ++...+-|..|++..|..          |-+|.              ..++.+.||+|+....+..|.-
T Consensus        31 ~Ge~FVAC~eC~FPvCrp----------CyEYE--------------rkeG~q~CpqCktrYkr~kgsp   75 (93)
T 1weo_A           31 EGDLFVACNECGFPACRP----------CYEYE--------------RREGTQNCPQCKTRYKRLRGSP   75 (93)
T ss_dssp             SSSBCCSCSSSCCCCCHH----------HHHHH--------------HHTSCSSCTTTCCCCCCCTTCC
T ss_pred             CCCEEEeeeccCChhhHH----------HHHHH--------------HhccCccccccCCccccccCCC
Confidence            346788888888888853          44442              2467789999999988766553

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	203
d1wd2a_	60	Ariadne-1 protein homolog {Human (Homo sapiens) [T	99.69
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	99.44
d2ct7a1	73	Ring finger protein 31 {Human (Homo sapiens) [TaxI	99.21
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	97.41
d1wd2a_	60	Ariadne-1 protein homolog {Human (Homo sapiens) [T	96.98
d2k4xa1	55	Ribosomal protein S27ae {Thermoplasma acidophilum	91.85
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	90.58
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	87.46
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	86.25
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	85.52
d1wfha_	64	Zinc finger A20 and AN1 domains containing protein	84.21
d2jnea1	71	Hypothetical protein YfgJ {Escherichia coli [TaxId	82.94
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	82.07
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	81.94

>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=99.69  E-value=1.8e-18  Score=108.83  Aligned_cols=42  Identities=33%  Similarity=0.852  Sum_probs=39.1

Q ss_pred             ccCCCCCCCCceeEecCCcceeEec---ccccccccccccCcCCC
Q 043865          114 MHGARRPACGSCVERKEGCRVMYCR---CKTSFCYECGGNLKSAS  155 (203)
Q Consensus       114 ~~~k~CP~C~~~iek~~GCnhm~C~---C~~~FC~~C~~~~~~~~  155 (203)
                      +++|+||+|+++|||++|||||+|+   |+++|||+|+++|..++
T Consensus         4 ~ntK~CP~C~~~ieK~~GCnhM~C~~~~C~~~fCw~C~~~~~~~~   48 (60)
T d1wd2a_           4 ANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHG   48 (60)
T ss_dssp             CCCCCCTTTCCCCSSCCSCCSSSCCSSGGGSCCSSSSCSCSGGGG
T ss_pred             hcCcCCCCCCCeEEECCCCCCeEeCCCCCCCeEECCCCCccccCC
Confidence            5689999999999999999999994   99999999999998754

>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=99.44  E-value=2.1e-15  Score=98.69  Aligned_cols=65  Identities=32%  Similarity=0.704  Sum_probs=56.9

Q ss_pred             HHHHHHHHhhcc-CCCceeCCCCCCCceeeecCccccCCCCceeCCCccccccccCCcCC---CCCCccccccccc
Q 043865           29 KWCDVLCEDYVL-GFERSYCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAW---HAGYRCEESGNLR  100 (203)
Q Consensus        29 ~y~~~~~~~~i~-~~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~---H~~~~C~~~~~~~  100 (203)
                      +|++++.+.++. +++++|||  +|+++++.++.     .+.++|+.|++.||+.|+.+|   |+|.+|+++++|+
T Consensus         2 ~Y~~~l~~~~l~~~~~~k~CP--~C~~~~~~~~~-----~~~~~C~~C~~~fC~~C~~~w~~~H~~~tC~~~~~wk   70 (73)
T d2ct7a1           2 LFHKKLTEGVLMRDPKFLWCA--QCSFGFIYERE-----QLEATCPQCHQTFCVRCKRQWEEQHRGRSCEDFQNWK   70 (73)
T ss_dssp             SSSSCCCCSCCCSCCCEECCS--SSCCCEECCCS-----CSCEECTTTCCEECSSSCSBCCTTTTTSCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHCCCCCCCC--CCCCEeEECCC-----CCEEEcCCCCCeECcccCcchhcCCCCCCHHHHHHHH
Confidence            356667777886 88999997  79999988776     788999999999999999999   9999999998764

>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=99.21  E-value=1.3e-12  Score=85.06  Aligned_cols=41  Identities=15%  Similarity=0.306  Sum_probs=38.5

Q ss_pred             hccCCCCCCCCceeEecCCcceeEe-cccccccccccccCcC
Q 043865          113 RMHGARRPACGSCVERKEGCRVMYC-RCKTSFCYECGGNLKS  153 (203)
Q Consensus       113 ~~~~k~CP~C~~~iek~~GCnhm~C-~C~~~FC~~C~~~~~~  153 (203)
                      +.+++.||+|+..|++++||++|+| .|+++|||.|+++|..
T Consensus        15 ~~~~k~CP~C~~~~~~~~~~~~~~C~~C~~~fC~~C~~~w~~   56 (73)
T d2ct7a1          15 DPKFLWCAQCSFGFIYEREQLEATCPQCHQTFCVRCKRQWEE   56 (73)
T ss_dssp             CCCEECCSSSCCCEECCCSCSCEECTTTCCEECSSSCSBCCT
T ss_pred             CCCCCCCCCCCCEeEECCCCCEEEcCCCCCeECcccCcchhc
Confidence            4678999999999999999999999 8999999999999964

>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=97.41  E-value=6.2e-05  Score=49.83  Aligned_cols=40  Identities=18%  Similarity=0.385  Sum_probs=35.3

Q ss_pred             CccCCcccCCC--cCCHHHHhhcCCHHHHHHHHHHHHHhhcc
Q 043865            1 KIECPGVHCDQ--FLDLFTCKLMIPSNLFSKWCDVLCEDYVL   40 (203)
Q Consensus         1 ~I~CP~~~C~~--~l~~~~i~~~l~~e~~~~y~~~~~~~~i~   40 (203)
                      .|+||..+|+.  .+++++|+.+|++++++||++++++.+.+
T Consensus        50 ~i~CP~~~C~~~~~~~~~~i~~ll~~~~~~ky~~~~l~~~~~   91 (94)
T d1wima_          50 AISCPDAACPKQGHLQENEIECMVAAEIMQRYKKLQFERSGP   91 (94)
T ss_dssp             CEECSCTTCSSCCEECHHHHHHHSCHHHHHHHHHHHHHSSCS
T ss_pred             ccCCcCCCCCCCcccCHHHHHHhCCHHHHHHHHHHHHHhccc
Confidence            37899988965  68999999999999999999999998764

>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=96.98  E-value=0.0003  Score=42.68  Aligned_cols=39  Identities=31%  Similarity=0.839  Sum_probs=32.8

Q ss_pred             CCceeCCCCCCCceeeecCccccCCCCceeCC--CccccccccCCcCC
Q 043865           42 FERSYCPNRNCMALVVNEGEINYGTLKKARCP--NCKQWFCFQCKVAW   87 (203)
Q Consensus        42 ~~~~~Cp~~~C~~~~~~~~~~~~~~~~~~~C~--~C~~~~C~~C~~~~   87 (203)
                      .+.+.||  .|+..+...+.     .+.++|.  .|++.||+.|..+|
T Consensus         4 ~ntK~CP--~C~~~ieK~~G-----CnhM~C~~~~C~~~fCw~C~~~~   44 (60)
T d1wd2a_           4 ANTKECP--KCHVTIEKDGG-----CNHMVCRNQNCKAEFCWVCLGPW   44 (60)
T ss_dssp             CCCCCCT--TTCCCCSSCCS-----CCSSSCCSSGGGSCCSSSSCSCS
T ss_pred             hcCcCCC--CCCCeEEECCC-----CCCeEeCCCCCCCeEECCCCCcc
Confidence            3467787  69999988765     8999995  59999999999988

>d2k4xa1 g.41.8.8 (A:1-55) Ribosomal protein S27ae {Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Rubredoxin-like
superfamily: Zn-binding ribosomal proteins
family: Ribosomal protein S27a
domain: Ribosomal protein S27ae
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=91.85  E-value=0.027  Score=32.65  Aligned_cols=27  Identities=30%  Similarity=0.464  Sum_probs=22.7

Q ss_pred             CCCCCCCCceeEecCCcceeEe-ccccc
Q 043865          116 GARRPACGSCVERKEGCRVMYC-RCKTS  142 (203)
Q Consensus       116 ~k~CP~C~~~iek~~GCnhm~C-~C~~~  142 (203)
                      -+.||+|+.-|...+-=|..+| +|++-
T Consensus        18 ~k~CP~CG~GvFmA~H~dR~~CGKCgyT   45 (55)
T d2k4xa1          18 HRFCPRCGPGVFLAEHADRYSCGRCGYT   45 (55)
T ss_dssp             SCCCTTTTTTCCCEECSSEEECTTTCCC
T ss_pred             cCcCcCCCCcEEeeecCCCccccCCccc
Confidence            3789999988887777799999 89864

>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=90.58  E-value=0.045  Score=34.68  Aligned_cols=46  Identities=22%  Similarity=0.307  Sum_probs=35.2

Q ss_pred             CCCceeCCCccccccccCCcCCCCCCccccccccccchhHHHHHHHHhccCCCCCCCCceeEecCCccee
Q 043865           66 TLKKARCPNCKQWFCFQCKVAWHAGYRCEESGNLRDWNDIAFGKLVERMHGARRPACGSCVERKEGCRVM  135 (203)
Q Consensus        66 ~~~~~~C~~C~~~~C~~C~~~~H~~~~C~~~~~~~~~~d~~~~~~~~~~~~k~CP~C~~~iek~~GCnhm  135 (203)
                      +...+.|..|+.-.|.          +|-+|..              +++.+-||+|++...+..|+-.|
T Consensus        32 Ge~FVAC~eC~FPvCr----------pCyEYEr--------------keG~q~CpqCkt~Ykr~kgsprv   77 (93)
T d1weoa_          32 GDLFVACNECGFPACR----------PCYEYER--------------REGTQNCPQCKTRYKRLRGSPRV   77 (93)
T ss_dssp             SSBCCSCSSSCCCCCH----------HHHHHHH--------------HTSCSSCTTTCCCCCCCTTCCCC
T ss_pred             CCEEEEecccCCccch----------HHHHHHH--------------hccCccCcccCChhhhhcCCCCC
Confidence            5778889999998885          4555532              46779999999999988887654

>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=87.46  E-value=0.052  Score=32.58  Aligned_cols=36  Identities=22%  Similarity=0.436  Sum_probs=26.6

Q ss_pred             CCCCCCCceeEecCCcceeEecccccccccccccCc
Q 043865          117 ARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLK  152 (203)
Q Consensus       117 k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~  152 (203)
                      ..||-|...+.....-.-+.-.|||.||..|...|-
T Consensus         4 ~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~   39 (65)
T d1g25a_           4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLF   39 (65)
T ss_dssp             TCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHH
T ss_pred             CCCCcCCceeecCCceEEEeCccChHhhHHHHHHHh
Confidence            468988876655544455555799999999998884

>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=86.25  E-value=0.16  Score=29.34  Aligned_cols=20  Identities=25%  Similarity=0.557  Sum_probs=15.9

Q ss_pred             ceeCCCccccccccCCcCCC
Q 043865           69 KARCPNCKQWFCFQCKVAWH   88 (203)
Q Consensus        69 ~~~C~~C~~~~C~~C~~~~H   88 (203)
                      ..+.+.|++.|+..|-..|-
T Consensus        21 ~~~l~~C~H~Fh~~Ci~~Wl   40 (55)
T d1iyma_          21 ARFLPRCGHGFHAECVDMWL   40 (55)
T ss_dssp             CEECSSSCCEECTTHHHHTT
T ss_pred             EEEeCCCCCcccHHHHHHHH
Confidence            45677799999999888774

>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=85.52  E-value=0.11  Score=31.32  Aligned_cols=33  Identities=24%  Similarity=0.479  Sum_probs=25.7

Q ss_pred             CCCCCCCCceeEecCCcceeEe-cccccccccccccCcC
Q 043865          116 GARRPACGSCVERKEGCRVMYC-RCKTSFCYECGGNLKS  153 (203)
Q Consensus       116 ~k~CP~C~~~iek~~GCnhm~C-~C~~~FC~~C~~~~~~  153 (203)
                      ...||=|...+.     +..+. .||+.||+.|...|-.
T Consensus         5 ~d~C~IC~~~~~-----~~~~~~~C~H~Fc~~Ci~~w~~   38 (68)
T d1chca_           5 AERCPICLEDPS-----NYSMALPCLHAFCYVCITRWIR   38 (68)
T ss_dssp             CCCCSSCCSCCC-----SCEEETTTTEEESTTHHHHHHH
T ss_pred             CCCCccCCcCcc-----CCcEEeCCCCcCcHHHHHHHHH
Confidence            457999987764     34567 7999999999988864

>d1wfha_ g.80.1.1 (A:) Zinc finger A20 and AN1 domains containing protein At2g36320 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: AN1-like Zinc finger
superfamily: AN1-like Zinc finger
family: AN1-like Zinc finger
domain: Zinc finger A20 and AN1 domains containing protein At2g36320
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=84.21  E-value=0.2  Score=29.88  Aligned_cols=43  Identities=28%  Similarity=0.470  Sum_probs=30.3

Q ss_pred             cCCCCCCCCceeEecCCcceeEecccccccccccccCcCCCCCCCCcCC
Q 043865          115 HGARRPACGSCVERKEGCRVMYCRCKTSFCYECGGNLKSASGCLCKEKG  163 (203)
Q Consensus       115 ~~k~CP~C~~~iek~~GCnhm~C~C~~~FC~~C~~~~~~~~~C~~~~~~  163 (203)
                      ...+|..|+..+...+    ++|+|+..||-.-..+-.  +.|...++.
T Consensus        14 k~~RC~~C~KKl~l~~----~~CrCg~~FC~~HR~pe~--H~CtfDyK~   56 (64)
T d1wfha_          14 RPNRCTVCRKRVGLTG----FMCRCGTTFCGSHRYPEV--HGCTFDFKS   56 (64)
T ss_dssp             SCCCCTTTCCCCCTTC----EECSSSCEECTTTCSTTT--TTCCCCCSC
T ss_pred             CCCcChhhCCCcccee----eeccCCCEehhhcCCCcC--cCCCCcchh
Confidence            3468999998887653    899999999987654432  345554443

>d2jnea1 g.41.18.1 (A:1-71) Hypothetical protein YfgJ {Escherichia coli [TaxId: 562]}

class: Small proteins
fold: Rubredoxin-like
superfamily: YfgJ-like
family: YfgJ-like
domain: Hypothetical protein YfgJ
species: Escherichia coli [TaxId: 562]

Probab=82.94  E-value=0.39  Score=29.05  Aligned_cols=35  Identities=23%  Similarity=0.657  Sum_probs=29.2

Q ss_pred             CCCCCCCceeEecCCcceeEe-ccccc-----ccccccccCcC
Q 043865          117 ARRPACGSCVERKEGCRVMYC-RCKTS-----FCYECGGNLKS  153 (203)
Q Consensus       117 k~CP~C~~~iek~~GCnhm~C-~C~~~-----FC~~C~~~~~~  153 (203)
                      ..||.|+..++..+|  +..| .|...     ||-.|.+++..
T Consensus         3 ~~CP~C~~eL~~~~~--~~~C~~C~~~~~~~a~CPdC~~~Le~   43 (71)
T d2jnea1           3 LHCPQCQHVLDQDNG--HARCRSCGEFIEMKALCPDCHQPLQV   43 (71)
T ss_dssp             CBCSSSCSBEEEETT--EEEETTTCCEEEEEEECTTTCSBCEE
T ss_pred             CcCCCccCcccccCC--CEehhhhhhhheeEEeCCccccHHHH
Confidence            479999999999887  9999 78855     68899888764

>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=82.07  E-value=0.33  Score=31.09  Aligned_cols=31  Identities=19%  Similarity=0.551  Sum_probs=21.5

Q ss_pred             eCCCCCCCceeeecCccccCCCCceeCCCccccccccCCcCCC
Q 043865           46 YCPNRNCMALVVNEGEINYGTLKKARCPNCKQWFCFQCKVAWH   88 (203)
Q Consensus        46 ~Cp~~~C~~~~~~~~~~~~~~~~~~~C~~C~~~~C~~C~~~~H   88 (203)
                      .||-  |...+.  +        .+..+.|++.||..|-..|-
T Consensus        24 ~C~I--C~~~~~--~--------pv~~~~CgH~fC~~Ci~~~~   54 (97)
T d1jm7b_          24 RCSR--CTNILR--E--------PVCLGGCEHIFCSNCVSDCI   54 (97)
T ss_dssp             SCSS--SCSCCS--S--------CBCCCSSSCCBCTTTGGGGT
T ss_pred             CCcc--CCchhh--c--------CceeCCCCCchhHHHHHHHH
Confidence            5774  776652  1        13455699999999987774

>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=81.94  E-value=0.24  Score=29.03  Aligned_cols=24  Identities=29%  Similarity=0.715  Sum_probs=20.1

Q ss_pred             CceeCCCccccccccCCcCCCCCC
Q 043865           68 KKARCPNCKQWFCFQCKVAWHAGY   91 (203)
Q Consensus        68 ~~~~C~~C~~~~C~~C~~~~H~~~   91 (203)
                      ...+|+.|++.||..|-.-.|+.+
T Consensus        29 ~~y~C~~C~~~FC~dCD~fiHe~l   52 (59)
T d1z60a1          29 HVYVCAVCQNVFCVDCDVFVHDSL   52 (59)
T ss_dssp             EEECCTTTTCCBCHHHHHTTTTTS
T ss_pred             ceEECcCCCCccccccchhhhhhh
Confidence            457899999999999988778654