Citrus Sinensis ID: 018299

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------36
Protein Sequence
MSLSPPRIRINGANDANGDGNGNGANRNYPLYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEIEISRPRLVVDFTAFDPSPEARLLEALSLILDPPIRRFDHGLFDDQEEPTQARRRSWFRRRNVNIDQEPGIGRSNVHRRPRRNRSFDGNTNEETDALPRPRTWIILRHAEPPNPLEPILRPGQNPLPPGVNPRDYFLGQGMQQLIEEITQNDRPGPPPVPEAAIQAIPTVKIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSASSSHDVDSDDEHGDGARRRCLRLRQLAFLWPFRSRYNRRINPEGDNIAPSQAENSGWRHCGIL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccEEEccccccEEEcccccccccccccccccEEEEcccccccccccccccccHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccHHHHHccccEEEccccccccccccccccccccccEEEEcccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccEEEcccccccccccccHcccccccEEEEEccEEEEEcccccccccccccccccEEEccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccccccccccccHHHHHHHHHHHccccccccccHHHHHccccEEEEHHHccccccccccHHHccccHHHcccccccccccccEcHHHHHccccccEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mslsppriringandangdgngnganrnyplywcyqchravrisstnpseiacprcsghfvseieisrprlvvdftafdpspEARLLEALSLildppirrfdhglfddqeeptqARRRSWFRrrnvnidqepgigrsnvhrrprrnrsfdgntneetdalprprtwiilrhaeppnplepilrpgqnplppgvnprdyflGQGMQQLIEEItqndrpgpppvpeaaiqaiptvkimeshlandttcpvckeefkvgGEARELACKHIyhsecivpwlrlhnscpvcrhevpvssassshdvdsddehgdgARRRCLRLRQLAFLwpfrsrynrrinpegdniapsqaensgwrhcgil
Flexible Loop (DISEMBL)
mslsppriringandangdgngnGANRNYPLYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEIEISRPRLVVDFTAFDPSPEARLLEALSLILDPPIRRFdhglfddqeeptqarrrswfrrrnvnidqepgigrsnvhrrprrnrsfdgntneetdalprprtWIILRHAEPPNPLEPILRPGQNPLPPGVNPRDYFLGQGMQQLIEEITQNDRPGPPPVPEAAIQAIPTVKIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVpvssassshdvdsddehgdgARRRCLRLRQLaflwpfrsryNRRINPegdniapsqaensgwrhcgil
Low Complexity Region (SEG)
MSLSPPRIRIngandangdgngnganRNYPLYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEIEISRPRLVVDFTAFDPSPEARLLEALSLILDPPIRRFDHGLFDDQEEPTQArrrswfrrrNVNIDQEPGIGrsnvhrrprrnrsFDGNTNEETDALPRPRTWIILRHAEPPNPLEPILRPGQNPLPPGVNPRDYFLGQGMQQLIEEITQNDRPGPPPVPEAAIQAIPTVKIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPvssassshdvdsddehgdgarrrclrlrqlAFLWPFRSRYNRRINPEGDNIAPSQAENSGWRHCGIL
Disordered region (IsUnstruct)
**************************RNYPLYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEIEISRPRLVVDFTAFDPSPEARLLEALSLILDPPIRRFDHGLF**********************************************************TWIILR***************************YFLG*************************IQAIPTVKIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEV**********************RRCLRLRQLAFLWPFRSRYNR*************************
Disordered Region (DISOPRED)
*******************************YWCYQCHRAVRISSTNPSEIACPRCSGHFVS*****************************LILDP***********************************************************************************************GVNPRDYFLGQGMQQLI******************IQAIPTVKIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRH********************************************************************IL
Disordered Region (DISEMBL)
MSLSPPRIRINGANDANGDGNGNGANRNYPLYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEIEISRPRLVVDFTAFDPSPEARLLEALSLILDPPIRRFDHGLFDDQEEPTQARRRSWFRRRNVNIDQEPGIGRSNVHRRPRRNRSFDGNTNEETDALPRPRTWIILRHAEPPNPLEPILRPGQNPLPPGVNPRDYFLGQGMQQLIEEITQNDRPGPPPVPEAAIQAIPTVKIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHE********************GARRRCLRLRQLAFLWPFRSRYNRRINPEGDNIAPSQAENSGWRHCGIL
Disordered Region (DISPRO)
****************************YPLYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEIEI****************EARLLEALSLILDPPIRRFDHGLF*****************************************************LPRPRTWIILRHAEPPNPLEPILRPGQNPLPPGVNPRDYFLGQGMQQLIEEITQNDRPGPPPVPEAAIQAIPTVKIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEV********************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSLSPPRIRINGANDANGDGNGNGANRNYPLYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEIEISRPRLVVDFTAFDPSPEARLLEALSLILDPPIRRFDHGLFDDQEEPTQARRRSWFRRRNVNIDQEPGIGRSNVHRRPRRNRSFDGNTNEETDALPRPRTWIILRHAEPPNPLEPILRPGQNPLPPGVNPRDYFLGQGMQQLIEEITQNDRPGPPPVPEAAIQAIPTVKIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSASSSHDVDSDDEHGDGARRRCLRLRQLAFLWPFRSRYNRRINPEGDNIAPSQAENSGWRHCGIL
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	358	2.2.26 [Sep-21-2011]
P0CH30	338	E3 ubiquitin-protein liga	N/A	no	0.821	0.869	0.316	2e-33
Q8LPN7	328	E3 ubiquitin-protein liga	no	no	0.692	0.756	0.313	1e-28
Q6DIP3	311	RING finger protein 126 O	no	no	0.662	0.762	0.293	4e-22
Q91YL2	313	RING finger protein 126 O	yes	no	0.667	0.763	0.305	2e-21
Q9BV68	326	RING finger protein 126 O	yes	no	0.667	0.733	0.307	4e-21
Q6IRP0	312	RING finger protein 126-B	N/A	no	0.270	0.310	0.444	5e-21
Q7T0Q3	312	RING finger protein 126-A	N/A	no	0.270	0.310	0.444	5e-21
Q0II22	313	RING finger protein 126 O	yes	no	0.270	0.309	0.444	4e-20
Q9Y4L5	304	E3 ubiquitin-protein liga	no	no	0.270	0.319	0.434	1e-19
Q9D0C1	305	E3 ubiquitin-protein liga	no	no	0.270	0.318	0.424	2e-19

>sp|P0CH30|RING1_GOSHI E3 ubiquitin-protein ligase RING1 OS=Gossypium hirsutum GN=RING1 PE=2 SV=1

 Score =  143 bits (361), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 106/335 (31%), Positives = 162/335 (48%), Gaps = 41/335 (12%)

Query: 19  DGN---GNGANR----NYPLYWCYQCHRAVRISSTNPS-EIACPRCSGHFVSEIEISRPR 70
           DGN   G GAN     N P ++CYQC+R V ++ + PS +  CP C+  F+ E +   P 
Sbjct: 4   DGNVTGGGGANTVGVTNKP-FFCYQCNRTVNVTISPPSSDPTCPICNEGFLEEYDNPNPN 62

Query: 71  LVVDFTAFDPSPEARLLEALSLILDPPIRRFDHGLFDDQEEPTQARRRSWFRRRNVNIDQ 130
               F   +P+P +     L L L  P       LF      T     +     N ++  
Sbjct: 63  QGSGF--LNPNPNSIPFHDLFLTLSDPFASLLPLLFPSSSS-TTTSSSASIDPNNPSLSG 119

Query: 131 EPGIGRSNVHRRPRRNRSFDGNTNEETDALPRPRTWIILRHAEPPNPLEPILRPGQNPLP 190
               GR +         +FD  T  +        +   +      NP +   R     LP
Sbjct: 120 PTRSGRGDPF-------AFDPFTFIQNHLNDLRSSGAQIEFVIQNNPSDQGFR-----LP 167

Query: 191 PGVNPRDYFLGQGMQQLIEEITQND--RPGPPPVPEAAIQAIPTVKIMESHLAND-TTCP 247
              N  DYF+G G++QLI+++ +ND  R G PP  ++AI+A+P V I +S+L ++   C 
Sbjct: 168 --ANIGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPLVNITKSNLNSEFNQCA 225

Query: 248 VCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVS------------SA 295
           VC ++F+ G EA+++ CKH+YH +C++PWL LHNSCPVCRHE+P                
Sbjct: 226 VCMDDFEEGTEAKQMPCKHLYHKDCLLPWLELHNSCPVCRHELPTDDPDYERRVRGAQGT 285

Query: 296 SSSHDVDSDDEHGDGARRRCLRLRQLAFLWPFRSR 330
           S  +D D+  +  DG  R   R  +++  WPF++R
Sbjct: 286 SGGNDGDNSGQRSDGDNRTVERSFRISLPWPFQAR 320

E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Promotes polyubiquitination of target proteins.
Gossypium hirsutum (taxid: 3635)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp|Q8LPN7|RNG1L_ARATH E3 ubiquitin-protein ligase RING1-like OS=Arabidopsis thaliana GN=At3g19950 PE=2 SV=1

 Score =  127 bits (319), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 92/293 (31%), Positives = 147/293 (50%), Gaps = 45/293 (15%)

Query: 13  ANDANGDGNGNGANRNYPLYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEIEISRPRLV 72
           ++  N  G+   A     +++CYQC++ V IS ++ ++  CP C+  F+ E E   P   
Sbjct: 2   SSGVNSTGSAAAAPEVDKMFFCYQCNQTVTISISSSADPFCPICNQGFLEEYEDPNPNQS 61

Query: 73  VDFT-----AFDP--SPEARLLEAL--SLILDPPIRRFDHGLFDDQEEPTQARRRSWFRR 123
           ++F      +F P   P + LL  +  S    P    F   LF    +P QAR      +
Sbjct: 62  LNFNPNSSDSFFPMADPFSTLLPLIFGSSAAAPSGMDF-MSLFGPSMQP-QARST----Q 115

Query: 124 RNVNIDQEPGIGRSNVHRRPRRNRSFDGNTNEETDALPRPRTWIILRH-AEPPNPLEPIL 182
           +N   D          H +  R+      T+ E         ++I  H ++P N +    
Sbjct: 116 QNPQSDAFDPFTFLQNHLQTLRS----SGTHFE---------FVIENHPSDPGNRM---- 158

Query: 183 RPGQNPLPPGVNPRDYFLGQGMQQLIEEITQND--RPGPPPVPEAAIQAIPTVKIMESHL 240
                   PG N  DYF G G++QLI+++ +ND  R G PP  ++AI A+PTVK+ +  L
Sbjct: 159 --------PG-NFGDYFFGPGLEQLIQQLAENDPNRYGTPPASKSAIDALPTVKVTKDML 209

Query: 241 ANDTT-CPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV 292
            ++   C VC +EF+ G + +++ CKH++H +C++PWL LHNSCPVCR E+P 
Sbjct: 210 KSEMNQCAVCMDEFEDGSDVKQMPCKHVFHQDCLLPWLELHNSCPVCRFELPT 262

E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Promotes polyubiquitination of target proteins.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q6DIP3|RN126_XENTR RING finger protein 126 OS=Xenopus tropicalis GN=rnf126 PE=2 SV=1

 Score =  105 bits (263), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/283 (29%), Positives = 121/283 (42%), Gaps = 46/283 (16%)

Query: 32  YWCYQCHRAVRISSTNPSEIACPRCSGHFVSEIEISRPRLVVDFTAFDPS---PEARLLE 88
           Y+C+ C     I    P E  CPRC   F+ E+  +R                P    LE
Sbjct: 11  YFCHSC--TAEIIPRLP-EYTCPRCDSGFIEELPETRNSENNSSNNSGTDQNRPSFENLE 67

Query: 89  ALSLILDPPIRRFDHGLFDDQEEPTQARRRSWFRRRNVNIDQEPGIGRSNVHRRPRRNRS 148
           +    L     +   G+F                  N  +D  P  G S     PR   S
Sbjct: 68  SAQFTLPSGYGQVTFGIF------------------NEGLDF-PIFGTSGPVEEPRDGES 108

Query: 149 FDGNTNEETDALPRPRTWIILRHAEPPN----PLEPILRPGQNPL------------PPG 192
              + + +     +PR  +  R A   N     LE I++   N +            P G
Sbjct: 109 RREHQSRQRYGARQPRARLSTRRAAGRNEGVPTLEGIIQQLVNGIIAPTAMSNLGVGPWG 168

Query: 193 V---NPRDYFLG-QGMQQLIEEI-TQNDRPGPPPVPEAAIQAIPTVKIMESHLANDTTCP 247
           V   NP DY  G  G+  +I ++  Q +  GPPP     IQA+PT++I E H+ +   CP
Sbjct: 169 VLHSNPMDYAWGANGLDTIITQLLNQFENTGPPPADTEKIQALPTIQITEEHVGSGLECP 228

Query: 248 VCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEV 290
           VCKE++ VG   R+L C H++H++CI+PWL  H++CPVCR  +
Sbjct: 229 VCKEDYTVGESVRQLPCNHLFHNDCIIPWLEQHDTCPVCRKSL 271

Xenopus tropicalis (taxid: 8364)

>sp|Q91YL2|RN126_MOUSE RING finger protein 126 OS=Mus musculus GN=Rnf126 PE=1 SV=1

 Score =  103 bits (256), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 87/285 (30%), Positives = 128/285 (44%), Gaps = 46/285 (16%)

Query: 32  YWCYQCHRAVRISSTNPSEIACPRCSGHFVSEI-EISRPRLVVDFTAFDPSPEARL---- 86
           Y+C+ C  +V I    P  I CPRC   F+ E+ E +R        +  P+ + R     
Sbjct: 11  YFCHCC--SVEIVPRLPDYI-CPRCESGFIEELPEETRNTENGSAPSTAPTDQNRQPFEN 67

Query: 87  LEALSLILDPPIRRFDHGLFDDQEEPTQARRRSWFRRRNVNIDQEPGIGRSNVHRRPRRN 146
           ++     L     +F  G+FDD  E                I   P   +++  R P   
Sbjct: 68  VDQHLFTLPQGYSQFAFGIFDDSFE----------------IPTFPPGAQADDGRDPESR 111

Query: 147 RSFDGNTNEETDALPRPRTWIILRHA----EPPNPLEPILRPGQNPL------------P 190
           R  +  +     A  +PR  +  R A    E    LE I++   N +            P
Sbjct: 112 REREHQSRHRYGAR-QPRARLTARRATGRHEGVPTLEGIIQQLVNGIISPAAVPSLGLGP 170

Query: 191 PGV---NPRDYFLG-QGMQQLIEEI-TQNDRPGPPPVPEAAIQAIPTVKIMESHLANDTT 245
            GV   NP DY  G  G+  +I ++  Q +  GPPP  +  IQA+PTV + E H+ +   
Sbjct: 171 WGVLHSNPMDYAWGANGLDTIITQLLNQFENTGPPPADKEKIQALPTVPVTEEHVGSGLE 230

Query: 246 CPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEV 290
           CPVCKE++ +G   R+L C H++H  CIVPWL  H+SCPVCR  +
Sbjct: 231 CPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSL 275

Mus musculus (taxid: 10090)

>sp|Q9BV68|RN126_HUMAN RING finger protein 126 OS=Homo sapiens GN=RNF126 PE=1 SV=1

 Score =  102 bits (255), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 87/283 (30%), Positives = 129/283 (45%), Gaps = 44/283 (15%)

Query: 32  YWCYQCHRAVRISSTNPSEIACPRCSGHFVSEI-EISRPRLVVDFTAFDPSPEAR----L 86
           Y+C+ C  +V I    P  I CPRC   F+ E+ E +R        +  P+ ++R     
Sbjct: 11  YFCHCC--SVEIVPRLPDYI-CPRCESGFIEELPEETRSTENGSAPSTAPTDQSRPPLEH 67

Query: 87  LEALSLILDPPIRRFDHGLFDDQEEPTQARRRSWFRRRNVNIDQEPGIGRSNVHRRPRRN 146
           ++     L     +F  G+FDD  E                I   P   +++  R P   
Sbjct: 68  VDQHLFTLPQGYGQFAFGIFDDSFE----------------IPTFPPGAQADDGRDPESR 111

Query: 147 RSFDGNTNEETDALPRPRTWIILRHA----EPPNPLEPILRPGQNPL----------PPG 192
           R  D  +     A  +PR  +  R A    E    LE I++   N +          P G
Sbjct: 112 RERDHPSRHRYGAR-QPRARLTTRRATGRHEGVPTLEGIIQQLVNGIITPATIPSLGPWG 170

Query: 193 V---NPRDYFLG-QGMQQLIEEI-TQNDRPGPPPVPEAAIQAIPTVKIMESHLANDTTCP 247
           V   NP DY  G  G+  +I ++  Q +  GPPP  +  IQA+PTV + E H+ +   CP
Sbjct: 171 VLHSNPMDYAWGANGLDAIITQLLNQFENTGPPPADKEKIQALPTVPVTEEHVGSGLECP 230

Query: 248 VCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEV 290
           VCK+++ +G   R+L C H++H  CIVPWL  H+SCPVCR  +
Sbjct: 231 VCKDDYALGERVRQLPCNHLFHDGCIVPWLEQHDSCPVCRKSL 273

Homo sapiens (taxid: 9606)

>sp|Q6IRP0|R126B_XENLA RING finger protein 126-B OS=Xenopus laevis GN=rnf126-b PE=2 SV=1

 Score =  102 bits (254), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 44/99 (44%), Positives = 64/99 (64%), Gaps = 2/99 (2%)

Query: 194 NPRDYFLG-QGMQQLIEEI-TQNDRPGPPPVPEAAIQAIPTVKIMESHLANDTTCPVCKE 251
           NP DY  G  G+  +I ++  Q +  GPPP     IQA+PT++I E H+     CPVCKE
Sbjct: 174 NPMDYAWGANGLDTIITQLLNQFENTGPPPADTDKIQALPTIQITEEHVGFGLECPVCKE 233

Query: 252 EFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEV 290
           ++ VG   R+L C H++H++CI+PWL  H++CPVCR  +
Sbjct: 234 DYTVGESVRQLPCNHLFHNDCIIPWLEQHDTCPVCRKSL 272

Xenopus laevis (taxid: 8355)

>sp|Q7T0Q3|R126A_XENLA RING finger protein 126-A OS=Xenopus laevis GN=rnf126-a PE=2 SV=1

 Score =  102 bits (254), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 44/99 (44%), Positives = 65/99 (65%), Gaps = 2/99 (2%)

Query: 194 NPRDYFLG-QGMQQLIEEI-TQNDRPGPPPVPEAAIQAIPTVKIMESHLANDTTCPVCKE 251
           NP DY  G  G+  +I ++  Q +  GPPP     IQA+PT++I E H+ +   CPVCKE
Sbjct: 174 NPMDYAWGANGLDTIITQLLNQFENTGPPPADNEKIQALPTIQITEEHVGSGLECPVCKE 233

Query: 252 EFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEV 290
           ++ VG   R+L C H++H++CI+PWL  H++CPVCR  +
Sbjct: 234 DYTVGECVRQLPCNHLFHNDCIIPWLEQHDTCPVCRKSL 272

Xenopus laevis (taxid: 8355)

>sp|Q0II22|RN126_BOVIN RING finger protein 126 OS=Bos taurus GN=RNF126 PE=2 SV=1

 Score = 99.4 bits (246), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 44/99 (44%), Positives = 63/99 (63%), Gaps = 2/99 (2%)

Query: 194 NPRDYFLG-QGMQQLIEEI-TQNDRPGPPPVPEAAIQAIPTVKIMESHLANDTTCPVCKE 251
           NP DY  G  G+  +I ++  Q +  GPPP  +  IQA+PTV + E H+ +   CPVCK+
Sbjct: 178 NPMDYAWGANGLDAIITQLLNQFENTGPPPADKEKIQALPTVPVTEEHVGSGLECPVCKD 237

Query: 252 EFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEV 290
           ++ +G   R+L C H++H  CIVPWL  H+SCPVCR  +
Sbjct: 238 DYGLGEHVRQLPCNHLFHDGCIVPWLEQHDSCPVCRKSL 276

Bos taurus (taxid: 9913)

>sp|Q9Y4L5|RN115_HUMAN E3 ubiquitin-protein ligase RNF115 OS=Homo sapiens GN=RNF115 PE=1 SV=2

 Score = 97.4 bits (241), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 43/99 (43%), Positives = 62/99 (62%), Gaps = 2/99 (2%)

Query: 194 NPRDYFLGQ-GMQQLIEEIT-QNDRPGPPPVPEAAIQAIPTVKIMESHLANDTTCPVCKE 251
           NP DY  GQ G+  ++ ++  Q +  GPPP  +  I ++PTV + +  +     CPVCKE
Sbjct: 174 NPGDYAWGQTGLDAIVTQLLGQLENTGPPPADKEKITSLPTVTVTQEQVDMGLECPVCKE 233

Query: 252 EFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEV 290
           ++ V  E R+L C H +HS CIVPWL LH++CPVCR  +
Sbjct: 234 DYTVEEEVRQLPCNHFFHSSCIVPWLELHDTCPVCRKSL 272

Acts as an E2-dependent E3 ubiquitin-protein ligase. May be involved in endocytic trafficking.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9D0C1|RN115_MOUSE E3 ubiquitin-protein ligase RNF115 OS=Mus musculus GN=Rnf115 PE=1 SV=1

 Score = 97.4 bits (241), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 42/99 (42%), Positives = 62/99 (62%), Gaps = 2/99 (2%)

Query: 194 NPRDYFLGQ-GMQQLIEEIT-QNDRPGPPPVPEAAIQAIPTVKIMESHLANDTTCPVCKE 251
           NP DY  GQ G+  ++ ++  Q +  GPPP  +  I ++PTV + +  +     CPVCKE
Sbjct: 175 NPGDYAWGQTGLDAIVTQLLGQLENTGPPPADKEKITSLPTVTVTQEQVNTGLECPVCKE 234

Query: 252 EFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEV 290
           ++ V  + R+L C H +HS CIVPWL LH++CPVCR  +
Sbjct: 235 DYTVEEKVRQLPCNHFFHSSCIVPWLELHDTCPVCRKSL 273

Acts as an E2-dependent E3 ubiquitin-protein ligase. May be involved in endocytic trafficking.

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	358
255545450	382	zinc finger protein, putative [Ricinus c	0.930	0.871	0.554	2e-96
224066851	338	predicted protein [Populus trichocarpa]	0.916	0.970	0.576	3e-96
147783582	409	hypothetical protein VITISV_014950 [Viti	0.891	0.779	0.506	4e-84
225459511	333	PREDICTED: E3 ubiquitin-protein ligase R	0.896	0.963	0.504	4e-84
357461573	328	RING finger protein [Medicago truncatula	0.860	0.939	0.505	1e-82
302141841	303	unnamed protein product [Vitis vinifera]	0.843	0.996	0.468	3e-72
356507662	309	PREDICTED: E3 ubiquitin-protein ligase R	0.762	0.883	0.512	5e-70
15219060	327	RING/U-box domain-containing protein [Ar	0.863	0.944	0.476	1e-64
297846702	326	zinc finger family protein [Arabidopsis	0.865	0.950	0.476	1e-64
449449881	321	PREDICTED: E3 ubiquitin-protein ligase R	0.857	0.956	0.454	4e-64

>gi|255545450|ref|XP_002513785.1| zinc finger protein, putative [Ricinus communis] gi|223546871|gb|EEF48368.1| zinc finger protein, putative [Ricinus communis]

 Score =  358 bits (920), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 203/366 (55%), Positives = 241/366 (65%), Gaps = 33/366 (9%)

Query: 1   MSLSPPRIRINGANDANGDGNGNGANRNYPLYWCYQCHRAVRISSTNPSEIACPRCSGHF 60
           MSLSPPR RI            +   R +  YWCYQCHR VRI++++PSEI CPRCS  F
Sbjct: 1   MSLSPPRTRIR---------TYDATTRTFQPYWCYQCHRMVRIAASDPSEIICPRCSSQF 51

Query: 61  VSEIEISRPRLVVDFTAFDPSPEARLLEALSLILDPPIRRFDHGLFD-DQEEPTQARR-R 118
           + E+E++R RLVVDF AFDPSPEARLLEALSL LDPPIRR      D   +EP    R R
Sbjct: 52  LCELEMNRQRLVVDFAAFDPSPEARLLEALSLTLDPPIRRRRRRTLDFGLDEPEWGTRGR 111

Query: 119 SWFRRRNVNIDQEPGIGRSNVHRRPRRNRSFDGNTN--EETDALPRPRTWIILRHAEPPN 176
           SWF R N           + +H R RRNRS DG  N  EE    P PRTWI+LR  +P +
Sbjct: 112 SWFGRPNPE---------AEIHPRRRRNRSLDGRDNWEEEPGIQPSPRTWIVLRPFDPFS 162

Query: 177 PLEPILRPGQNPLPPGVNPRDYFLGQGMQQLIEEITQNDRPGPPPVPEAAIQAIPTVKIM 236
           P++P  R G N +PP  NPRDYFLG G+  LIE++TQ+DRPGPPP PE+ + AIP+VKI 
Sbjct: 163 PIQPNSRTG-NLIPPRANPRDYFLGPGLNDLIEQLTQDDRPGPPPAPESTVGAIPSVKIN 221

Query: 237 ESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV---- 292
            SHL ND+ CPVCKEEFKVGGEAREL CKHIYH++CIVPWLRLHNSCPVCR  +PV    
Sbjct: 222 ASHLVNDSDCPVCKEEFKVGGEARELPCKHIYHTDCIVPWLRLHNSCPVCRQALPVLPEN 281

Query: 293 ---SSASSSHDVDSDDEHGDGARRRCLRL-RQLAFLWPFRSRYNRRINPEG-DNIAPSQA 347
                 S++ +     E G+G   RCLR  RQLA LWPFR RY  RI P G D++  SQ 
Sbjct: 282 ITLPENSTTQNDQECQEDGEGTNGRCLRWRRQLANLWPFRPRYG-RIAPHGEDHVGTSQG 340

Query: 348 ENSGWR 353
             + W+
Sbjct: 341 GKALWK 346

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224066851|ref|XP_002302246.1| predicted protein [Populus trichocarpa] gi|222843972|gb|EEE81519.1| predicted protein [Populus trichocarpa]

 Score =  358 bits (918), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 204/354 (57%), Positives = 240/354 (67%), Gaps = 26/354 (7%)

Query: 1   MSLSPPRIRINGANDANGDGNGNGANRNYPLYWCYQCHRAVRISSTNPSEIACPRCSGHF 60
           MSLSPPR R NG               N+  YWCYQCH+ VRI++T+PSEI CPRCSG F
Sbjct: 1   MSLSPPRTRTNGTTG------------NFQPYWCYQCHQMVRIATTDPSEIICPRCSGQF 48

Query: 61  VSEIEISRPRLVVDFTAFDPSPEARLLEALSLILDPPIRRFDHGLFDDQEEPTQARRRSW 120
           + EI I+RP LVVDFTAFDPSPEARLLEALSL+LDPPIRRF++ L + + EP    RRSW
Sbjct: 49  LCEIGINRPILVVDFTAFDPSPEARLLEALSLMLDPPIRRFNYSLDEPEPEPP---RRSW 105

Query: 121 FRRRNVNIDQEPGIGRSNVHRRPRRNR--SFDGN--TNEETDALPRPRTWIILRHAEPPN 176
            R  ++ +D        +   RPRR+R  S DG      E     RPRTWI  R   P N
Sbjct: 106 RRNLSLELDGRDNWDSLDPEIRPRRSRDWSLDGRGILEHEPGIQSRPRTWIQYR---PRN 162

Query: 177 PL-EPI--LRPGQNPLPPGVNPRDYFLGQGMQQLIEEITQNDRPGPPPVPEAAIQAIPTV 233
           PL EPI  L   +NP+ P V+PRD+F+G G+ +LIE++TQNDR GPPP PE AI  IPTV
Sbjct: 163 PLGEPIEPLSQSENPVRPLVDPRDFFVGSGLNELIEQLTQNDRQGPPPAPEIAIDTIPTV 222

Query: 234 KIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVS 293
           KI  SHL ND+ CPVC EEFKVGGEAREL CKHIYHSECIVPWLRLHNSCPVCR E+PV+
Sbjct: 223 KIEASHLVNDSHCPVCMEEFKVGGEARELPCKHIYHSECIVPWLRLHNSCPVCRKELPVN 282

Query: 294 SASSSHDVDSDDEHGDGARRRCLRLRQLAFLWPFRSRYNRRINPEGDNIAPSQA 347
           S SS+ D D  ++ G    R     RQL+ LWPFR+RY  RI+P G+    SQ 
Sbjct: 283 SESSAQDEDECEDGGGRRGRCSRWRRQLSSLWPFRARYG-RISPHGEVAGTSQG 335

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147783582|emb|CAN68008.1| hypothetical protein VITISV_014950 [Vitis vinifera]

 Score =  318 bits (814), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 182/359 (50%), Positives = 226/359 (62%), Gaps = 40/359 (11%)

Query: 1   MSLSPPRIRINGANDANGDGNGNGANRNYPLYWCYQCHRAVRISSTNPSEIACPRCSGHF 60
           MSLSPPR R NG             +R Y  YWCYQC+R+VRI+S NPS+I CPRC G F
Sbjct: 1   MSLSPPRERNNG-------------DRTYQFYWCYQCNRSVRIASDNPSQIICPRCLGQF 47

Query: 61  VSEIEISRPRLVVDFTAFDPSPEARLLEALSLILDPPIRRFDHGLFDDQEEPTQARRRSW 120
           + EI+ +RPR   +   +DP PEARLLEALSL+LDPP+R  ++G+    E  T+A R   
Sbjct: 48  LQEIDTTRPRAFNEIITWDPFPEARLLEALSLVLDPPLRGLNNGVGRGDEAETEAARNRG 107

Query: 121 --------FRRRNVNIDQEPGI-GRSNVHRRPRRNRSFDGNTNE--ETDALPRPRTWIIL 169
                     R +   + + G+ GR       RRN    G            + RTWI+L
Sbjct: 108 RRWLRRRSHSREHWEAEADTGVPGR-------RRNNELGGRLGWPFGNGLGAQGRTWIVL 160

Query: 170 RHAEPPNPLEPILRPGQNPLPPGVNPRDYFLGQGMQQLIEEITQNDRPGPPPVPEAAIQA 229
           R   PP    P  +  +N  PP    RD+F G G+ +LIEE+TQNDRPGPPP P++AI A
Sbjct: 161 RPTGPPGQNGPFPQ-SENMRPPRFELRDFFSGPGLNELIEELTQNDRPGPPPAPDSAINA 219

Query: 230 IPTVKIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHE 289
           +PTVKI  +HL ND+ CPVCKEEFKVG E REL C H+YHS+CIVPWL+LHNSCPVCRHE
Sbjct: 220 MPTVKITPTHLINDSHCPVCKEEFKVGEEVRELPCNHVYHSDCIVPWLQLHNSCPVCRHE 279

Query: 290 VPVSSASSSHDVDSDDEH-GDGARRRCLRLRQLAFLWPFRSRYNRRINPEGDNIAPSQA 347
           VPV S       +SD+ H G+  R RC+RLRQLA LWPFRSRY RRINP+  ++ P +A
Sbjct: 280 VPVPSD------ESDESHEGEDRRVRCMRLRQLASLWPFRSRY-RRINPQDRDVTPHRA 331

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225459511|ref|XP_002284442.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like [Vitis vinifera]

 Score =  317 bits (813), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 182/361 (50%), Positives = 227/361 (62%), Gaps = 40/361 (11%)

Query: 1   MSLSPPRIRINGANDANGDGNGNGANRNYPLYWCYQCHRAVRISSTNPSEIACPRCSGHF 60
           MSLSPPR R NG             +R Y  YWCYQC+R+VRI+S NPS+I CPRC G F
Sbjct: 1   MSLSPPRERNNG-------------DRTYQFYWCYQCNRSVRIASDNPSQIICPRCLGQF 47

Query: 61  VSEIEISRPRLVVDFTAFDPSPEARLLEALSLILDPPIRRFDHGLFDDQEEPTQARRRSW 120
           + EI+ +RPR   +   +DP PEARLLEALSL+LDPP+R  ++G+    E  T+A R   
Sbjct: 48  LQEIDTTRPRAFNEIITWDPFPEARLLEALSLVLDPPLRGLNNGVGRGDEAETEAARNRG 107

Query: 121 --------FRRRNVNIDQEPGI-GRSNVHRRPRRNRSFDGNTNE--ETDALPRPRTWIIL 169
                     R +   + + G+ GR       RRN    G            + RTWI+L
Sbjct: 108 RRWLRRRSHSREHWEAEADTGVPGR-------RRNNELGGRLGWPFGNGLGAQGRTWIVL 160

Query: 170 RHAEPPNPLEPILRPGQNPLPPGVNPRDYFLGQGMQQLIEEITQNDRPGPPPVPEAAIQA 229
           R   PP    P  +  +N  PP    RD+F G G+ +LIEE+TQNDRPGPPP P++AI A
Sbjct: 161 RPTGPPGQNGPFPQ-SENMRPPRFELRDFFSGPGLNELIEELTQNDRPGPPPAPDSAINA 219

Query: 230 IPTVKIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHE 289
           +PTVKI  +HL ND+ CPVCKEEFKVG E REL C H+YHS+CIVPWL+LHNSCPVCRHE
Sbjct: 220 MPTVKITPTHLINDSHCPVCKEEFKVGEEVRELPCNHVYHSDCIVPWLQLHNSCPVCRHE 279

Query: 290 VPVSSASSSHDVDSDDEH-GDGARRRCLRLRQLAFLWPFRSRYNRRINPEGDNIAPSQAE 348
           VPV S       +SD+ H G+  R RC+RLRQLA LWPFRSRY RRINP+  ++ P + E
Sbjct: 280 VPVPSD------ESDESHEGEDRRVRCMRLRQLASLWPFRSRY-RRINPQDRDVTPHRGE 332

Query: 349 N 349
           +
Sbjct: 333 S 333

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357461573|ref|XP_003601068.1| RING finger protein [Medicago truncatula] gi|355490116|gb|AES71319.1| RING finger protein [Medicago truncatula]

 Score =  312 bits (800), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 176/348 (50%), Positives = 220/348 (63%), Gaps = 40/348 (11%)

Query: 1   MSLSPPRIRINGANDANGDGNGNGANRNYPLYWCYQCHRAVRISSTNPSEIACPRCSGHF 60
           MSLSPPR R N               RN+ LY+C+QC+R VR++  N S++ CPRC G F
Sbjct: 1   MSLSPPRERTNNQR------------RNFQLYYCFQCNRTVRVAPYNSSDLICPRCFGQF 48

Query: 61  VSEIEISRPRLVVDFTAFDPSPEARLLEALSLILDPPIRRFDHGLFDDQEEPTQARRRSW 120
           + EI I RPRLVVDFTA DPSPEARLLEALS++LDPPIRRF+          TQ RR   
Sbjct: 49  ICEINIPRPRLVVDFTAHDPSPEARLLEALSIMLDPPIRRFN--------PETQTRRP-- 98

Query: 121 FRRRNVNIDQEPGIGRSNVHRRPRRNRSFDGNTNEETDALPRPRTWIILRHAEPP----- 175
            RR    +          V RR   +      T  E     RPRTW+IL+  +P      
Sbjct: 99  -RRATQEVP---------VRRRTGDHHPIQTQTEPEPGIQHRPRTWVILQPVDPSSNSDS 148

Query: 176 NPLEPILRPG--QNPLPPGVNPRDYFLGQGMQQLIEEITQNDRPGPPPVPEAAIQAIPTV 233
           N  +P++ PG  Q P+P GV+ RDYF G G  +LI++IT+NDR GPPPVPE  I AIPTV
Sbjct: 149 NTFQPVIYPGGRQGPIPRGVDSRDYFFGPGFNELIDQITENDRQGPPPVPERGINAIPTV 208

Query: 234 KIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVS 293
           KI   +L  ++ CPVC+EEF++GGEAREL CKHIYHS+CIVPWLRLHNSCP+CR E+PVS
Sbjct: 209 KIESKNLKENSHCPVCQEEFEIGGEARELPCKHIYHSDCIVPWLRLHNSCPICRQEIPVS 268

Query: 294 SASSSHDVDSDDEHGDGARRRCLRLRQLAFLWPFRSRYNRRINPEGDN 341
           S     +   +   G G  +RCLR  +++ LWPF  RY RR++P+ DN
Sbjct: 269 SDDDEDECGDEGGGGGGRLQRCLRWTRISSLWPFHGRY-RRVHPQRDN 315

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302141841|emb|CBI19044.3| unnamed protein product [Vitis vinifera]

 Score =  278 bits (711), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 164/350 (46%), Positives = 202/350 (57%), Gaps = 48/350 (13%)

Query: 1   MSLSPPRIRINGANDANGDGNGNGANRNYPLYWCYQCHRAVRISSTNPSEIACPRCSGHF 60
           MSLSPPR R NG             +R Y  YWCYQC+R+VRI+S NPS+I CPRC G F
Sbjct: 1   MSLSPPRERNNG-------------DRTYQFYWCYQCNRSVRIASDNPSQIICPRCLGQF 47

Query: 61  VSEIEISRPRLVVDFTAFDPSPEARLLEALSLILDPPIRRFDHGLFDDQEEPTQARRRSW 120
           + EI+ +RPR   +   +DP PEA                                R  W
Sbjct: 48  LQEIDTTRPRAFNEIITWDPFPEAPARNRGRR----------------WLRRRSHSREHW 91

Query: 121 FRRRNVNIDQEPGIGRSNVHRRPRRNRSFDGNTNEETDALPRPRTWIILRHAEPPNPLEP 180
               +  +   PG  R+N     R    F      +       RTWI+LR   PP    P
Sbjct: 92  EAEADTGV---PGRRRNN-ELGGRLGWPFGNGLGAQG------RTWIVLRPTGPPGQNGP 141

Query: 181 ILRPGQNPLPPGVNPRDYFLGQGMQQLIEEITQNDRPGPPPVPEAAIQAIPTVKIMESHL 240
             +  +N  PP    RD+F G G+ +LIEE+TQNDRPGPPP P++AI A+PTVKI  +HL
Sbjct: 142 FPQ-SENMRPPRFELRDFFSGPGLNELIEELTQNDRPGPPPAPDSAINAMPTVKITPTHL 200

Query: 241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSASSSHD 300
            ND+ CPVCKEEFKVG E REL C H+YHS+CIVPWL+LHNSCPVCRHEVPV S      
Sbjct: 201 INDSHCPVCKEEFKVGEEVRELPCNHVYHSDCIVPWLQLHNSCPVCRHEVPVPSD----- 255

Query: 301 VDSDDEH-GDGARRRCLRLRQLAFLWPFRSRYNRRINPEGDNIAPSQAEN 349
            +SD+ H G+  R RC+RLRQLA LWPFRSRY RRINP+  ++ P + E+
Sbjct: 256 -ESDESHEGEDRRVRCMRLRQLASLWPFRSRY-RRINPQDRDVTPHRGES 303

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356507662|ref|XP_003522583.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like [Glycine max]

 Score =  271 bits (692), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 165/322 (51%), Positives = 199/322 (61%), Gaps = 49/322 (15%)

Query: 1   MSLSPPRIRINGANDANGDGNGNGANRNYPLYWCYQCHRAVRIS--STNPSEIACPRCSG 58
           MSLSPPR R N         NGN   R + LY+C+QC+R VR +  + NP++I CPRC G
Sbjct: 1   MSLSPPRERNN---------NGNAQARTFQLYYCFQCNRTVRAAPDNNNPTQITCPRCFG 51

Query: 59  HFVSEIEISRPRLVVDFTAFDPSPEARLLEALSLILDPPIRRFDHGLFDDQEEPTQARRR 118
            F+ EI + RPRLVVDFT  DPSPEARLLEALSL++DPPIRRF  GL   Q E      R
Sbjct: 52  QFICEINMPRPRLVVDFTTPDPSPEARLLEALSLMMDPPIRRFP-GLIQPQPEELPVYHR 110

Query: 119 SWFRRRNVNIDQEPGIGRSNVHRRPRRNRSFDGNTNEETDALPRPRTWIILRHAEPPNPL 178
                                       R    +   E +   RPRTWI+ +  +P NP 
Sbjct: 111 H--------------------------RRPRRRHPEPEPEPQHRPRTWIVFQPMDPSNPF 144

Query: 179 EPILRPGQNPLPP---------GVNPRDYFLGQGMQQLIEEITQNDRPGPPPVPEAAIQA 229
           EPI  P +    P         G++ RDYF G G+ +LIE+IT+NDR GP P PE AI+A
Sbjct: 145 EPINIPNRRGPGPIHGPGPIPRGLDARDYFFGPGLNELIEQITENDRQGPAPAPERAIEA 204

Query: 230 IPTVKIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHE 289
           IPTVKI  +HL  ++ CPVC+EEF+VGGEAREL CKHIYHS+CIVPWLRLHNSCPVCRHE
Sbjct: 205 IPTVKIESAHLKENSQCPVCQEEFEVGGEARELQCKHIYHSDCIVPWLRLHNSCPVCRHE 264

Query: 290 VPVSSASSSHDVDSDDEHGDGA 311
           VPV S+SSS   + D+  GDG 
Sbjct: 265 VPVPSSSSSS--EGDECVGDGG 284

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15219060|ref|NP_176239.1| RING/U-box domain-containing protein [Arabidopsis thaliana] gi|3249088|gb|AAC24072.1| Contains similarity to goliath protein gb|M97204 from D. melanogster [Arabidopsis thaliana] gi|332195557|gb|AEE33678.1| RING/U-box domain-containing protein [Arabidopsis thaliana]

 Score =  253 bits (646), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 164/344 (47%), Positives = 201/344 (58%), Gaps = 35/344 (10%)

Query: 1   MSLSPPRIRINGANDANGDGNGNGANRNYPLYWCYQCHRAVRISSTNPSEIACPRCSGHF 60
           MSLS P  R + A         NGA R + LYWCY C R VRI+S+NPSEIACPRC   F
Sbjct: 1   MSLSQPITRTDSA--------PNGAFRTFGLYWCYHCDRMVRIASSNPSEIACPRCLRQF 52

Query: 61  VSEIEI-SRPRLVVDFTA--FDPSPEARLLEALSLILDPP-IRRFDHGLFDDQEEPTQAR 116
           V EIE   RPR   +     FD SPEARLLEALSL+ +P  I RF    F          
Sbjct: 53  VVEIETRQRPRFTFNHATPPFDASPEARLLEALSLMFEPATIGRFGADPF---------- 102

Query: 117 RRSWFRRRNVNIDQEPGIGRSNVHRRPRRNRSFDGNTNEETDALPRPRTWIILRHAEPPN 176
                R R+ NI  EP    S    + RR  S D N N     LPR RT++ILR   P +
Sbjct: 103 ----LRARSRNI-LEP---ESRPRPQHRRRHSLD-NVNNGGLPLPR-RTYVILRPNNPTS 152

Query: 177 PLEPILRPGQNPLPPGVNPRDYFLG-QGMQQLIEEITQNDRPGPPPVPEAAIQAIPTVKI 235
           PL  I+ P     P  VN  DYF G   ++QLIE++TQ+DRPGPPP  E  I ++P+VKI
Sbjct: 153 PLGNIIAPPNQAPPRHVNSHDYFTGASSLEQLIEQLTQDDRPGPPPASEPTINSLPSVKI 212

Query: 236 MESHLANDTT-CPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSS 294
              HL ND + C VC EEF VGG+A EL CKHIYH +CIVPWLRL+NSCP+CR ++P+ +
Sbjct: 213 TPQHLTNDMSQCTVCMEEFIVGGDATELPCKHIYHKDCIVPWLRLNNSCPICRRDLPLVN 272

Query: 295 ASSSHDVDSDDEHGDGARRRCLRLRQLAFLWPFRSRYNRRINPE 338
             +     S+    D   RR  R  QL  +WPFR+RY +R++PE
Sbjct: 273 TVAESRERSNPIRQDMPERRRPRWMQLGNIWPFRARY-QRVSPE 315

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297846702|ref|XP_002891232.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata] gi|297337074|gb|EFH67491.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  253 bits (645), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 163/342 (47%), Positives = 202/342 (59%), Gaps = 32/342 (9%)

Query: 1   MSLSPPRIRINGANDANGDGNGNGANRNYPLYWCYQCHRAVRISSTNPSEIACPRCSGHF 60
           MSLS P  R +GA+        NGA R + LYWCY C+R VRI+S+NPSEIACPRC   F
Sbjct: 1   MSLSRPITRTDGAS--------NGAFRTFGLYWCYHCNRMVRIASSNPSEIACPRCLRQF 52

Query: 61  VSEIEISRPRLVVDFTA--FDPSPEARLLEALSLILDPPIRRFDHGLFDDQEEPTQARRR 118
           V EIE  RPR  ++  A  FD SPEARLLEALSL+ +P I     G   D          
Sbjct: 53  VVEIETRRPRFTLNHAAPPFDASPEARLLEALSLMFEPAI---IGGFGAD---------- 99

Query: 119 SWFRRRNVNIDQEPGIGRSNVHRRPRRNRSFDGNTNEETDALPRPRTWIILRHAEPPNPL 178
            + R R+ NI  EP    S    + RR  S D N N     LPR RT++I R       L
Sbjct: 100 PFLRARSRNI-LEP---ESRPRPQHRRRHSLD-NVNNGGLPLPR-RTYVIFRPNNRTREL 153

Query: 179 EPILRPGQNPLPPGVNPRDYFLG-QGMQQLIEEITQNDRPGPPPVPEAAIQAIPTVKIME 237
             I+ P     P  VN  D+F G  G++QLIE++TQ+DRPGP P  E  I+A+P+VKI  
Sbjct: 154 GNIIPPPNQAPPWHVNSNDFFTGASGLEQLIEQLTQDDRPGPLPASEPTIEALPSVKITP 213

Query: 238 SHLANDTT-CPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSAS 296
            HL ND T C VC EEF VGG+A EL CKHIYH +CI+PWLRLHNSCP+CR ++P  +  
Sbjct: 214 QHLTNDLTQCTVCMEEFIVGGDATELPCKHIYHKDCIIPWLRLHNSCPICRSDLPPVNTV 273

Query: 297 SSHDVDSDDEHGDGARRRCLRLRQLAFLWPFRSRYNRRINPE 338
           +     S+    D   RR  R  QL  +WPFR+RY +R++PE
Sbjct: 274 ADSRERSNPTRQDIPERRRPRWIQLGNIWPFRARY-QRVSPE 314

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449449881|ref|XP_004142693.1| PREDICTED: E3 ubiquitin-protein ligase RING1-like [Cucumis sativus]

 Score =  251 bits (641), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 153/337 (45%), Positives = 200/337 (59%), Gaps = 30/337 (8%)

Query: 1   MSLSPPRIRINGANDANGDGNGNGANRNYPLYWCYQCHRAVRISSTNPSEIACPRCSGHF 60
           MSL+PP+   N           N     + LYWC+QCHR V ++S +PSE+ CPRC G F
Sbjct: 1   MSLTPPQSTTN-----------NRHTTTFQLYWCHQCHRTVTLASAHPSELTCPRCFGQF 49

Query: 61  VSEIEISRPRLVVDFTAFDPSPEARLLEALSLILDPPIRRFDHGLFDDQEEPTQARRRSW 120
           + E++++ P        F+PSPE RL EALSL+L+ PIR F++   +         R   
Sbjct: 50  IEEVQLTLPE-------FNPSPEGRLFEALSLMLNQPIRIFNNRTPNGNRHHPPWHRFEE 102

Query: 121 FRRRNVNIDQEPGIGRSNVHRRPRRNRSFDGNTNEETDALPRPRTWIILRHAEPPNPLEP 180
           F RR+ +  +   + +     R R     D N  ++     R RT I+     PP+ L+P
Sbjct: 103 FDRRSFSDPEGDELPQWRRRWRSRSLDERD-NFGQQPPNPNRSRTVIVF---GPPDQLQP 158

Query: 181 ILRPGQNPLPPGVNPRDYFLGQGMQQLIEEITQNDRPGPPPVPEAAIQAIPTVKIMESHL 240
           I    Q  LP  ++PRDYF G  + +LIEE+TQNDRPGP P  E AI+ IPTVKI   HL
Sbjct: 159 I----QPILPRRISPRDYFTGPQLDELIEELTQNDRPGPAPASEEAIERIPTVKIEAEHL 214

Query: 241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSASSSHD 300
            N++ CPVCKEEF+VGGEAREL+CKHIYHSECIVPWLRLHNSCPVCR E+P   + +  +
Sbjct: 215 KNESHCPVCKEEFEVGGEARELSCKHIYHSECIVPWLRLHNSCPVCRQEMP---SFTPEN 271

Query: 301 VDSDDEHGDGARRRCLRLRQLAFLWPFRSRYNRRINP 337
             S     +G  RRC R       WPFR+RY R+I+P
Sbjct: 272 EASSSSEEEGMGRRCARWWSHLVPWPFRNRY-RQISP 307

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	358
TAIR|locus:2195573	327	AT1G60360 [Arabidopsis thalian	0.385	0.422	0.546	1.7e-65
TAIR|locus:2102569	320	RZF1 "AT3G56580" [Arabidopsis	0.449	0.503	0.393	2.5e-39
TAIR|locus:2058465	328	RHC1A "RING-H2 finger C1A" [Ar	0.273	0.298	0.56	4.5e-38
TAIR|locus:2092231	328	AT3G19950 [Arabidopsis thalian	0.293	0.320	0.477	3.4e-34
TAIR|locus:2075175	395	RDUF1 "RING and Domain of Unkn	0.293	0.265	0.429	2.1e-32
TAIR|locus:2148318	407	RDUF2 "RING and Domain of Unkn	0.293	0.257	0.421	7.6e-32
TAIR|locus:1006230278	199	AT3G10815 [Arabidopsis thalian	0.273	0.492	0.465	2.7e-31
TAIR|locus:2063912	401	RHC2A "RING-H2 finger C2A" [Ar	0.293	0.261	0.444	6.7e-31
TAIR|locus:2161058	396	ATCRT1 [Arabidopsis thaliana (	0.310	0.280	0.454	1.6e-30
UNIPROTKB|Q9BV68	326	RNF126 "RING finger protein 12	0.298	0.328	0.447	4.7e-29

TAIR|locus:2195573 AT1G60360 [Arabidopsis thaliana (taxid:3702)]

 Score = 414 (150.8 bits), Expect = 1.7e-65, Sum P(3) = 1.7e-65
 Identities = 77/141 (54%), Positives = 96/141 (68%)

Query:   154 NEETDALPRPR-TWIILRHAEPPNPLEPILRPGQNPLPPGVNPRDYFLG-QGMQQLIEEI 211
             N     LP PR T++ILR   P +PL  I+ P     P  VN  DYF G   ++QLIE++
Sbjct:   129 NVNNGGLPLPRRTYVILRPNNPTSPLGNIIAPPNQAPPRHVNSHDYFTGASSLEQLIEQL 188

Query:   212 TQNDRPGPPPVPEAAIQAIPTVKIMESHLANDTT-CPVCKEEFKVGGEARELACKHIYHS 270
             TQ+DRPGPPP  E  I ++P+VKI   HL ND + C VC EEF VGG+A EL CKHIYH 
Sbjct:   189 TQDDRPGPPPASEPTINSLPSVKITPQHLTNDMSQCTVCMEEFIVGGDATELPCKHIYHK 248

Query:   271 ECIVPWLRLHNSCPVCRHEVP 291
             +CIVPWLRL+NSCP+CR ++P
Sbjct:   249 DCIVPWLRLNNSCPICRRDLP 269

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

TAIR|locus:2102569 RZF1 "AT3G56580" [Arabidopsis thaliana (taxid:3702)]

 Score = 349 (127.9 bits), Expect = 2.5e-39, Sum P(2) = 2.5e-39
 Identities = 65/165 (39%), Positives = 91/165 (55%)

Query:   192 GVNPRDYFLGQGMQQLIEEITQNDRP-GPPPVPEAAIQAIPTVKIMESHL-ANDTTCPVC 249
             G N  DYF G G+++LIE+++      GPPP P+++I A+PT+KI + HL ++D+ CPVC
Sbjct:   130 GTNAGDYFFGPGLEELIEQLSSGTHHRGPPPAPKSSIDALPTIKITQKHLKSSDSHCPVC 189

Query:   250 KEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPXXXXXXXXXXXXXXXXXX 309
             K+EF++  EA+++ C HIYHS+CIVPWL  HNSCPVCR E+P                  
Sbjct:   190 KDEFELKSEAKQMPCHHIYHSDCIVPWLVQHNSCPVCRKELPSRGSSSSTQSSQNRSTNG 249

Query:   310 XXXXXXXXXXXXAFLWPFRSRYNRRINPEGDNIAPSQAENSGWRH 354
                           LWPFRS  +       D    + AE   + H
Sbjct:   250 RENSRRRNIFSN--LWPFRSSSSSSTQNRRDTNNTATAEEGHYHH 292

GO:0005575 "cellular_component" evidence=ND

GO:0008270 "zinc ion binding" evidence=ISS

GO:0004842 "ubiquitin-protein ligase activity" evidence=IDA

GO:0009414 "response to water deprivation" evidence=IEP

GO:1902006 "negative regulation of proline biosynthetic process" evidence=IMP

TAIR|locus:2058465 RHC1A "RING-H2 finger C1A" [Arabidopsis thaliana (taxid:3702)]

 Score = 340 (124.7 bits), Expect = 4.5e-38, Sum P(2) = 4.5e-38
 Identities = 56/100 (56%), Positives = 77/100 (77%)

Query:   194 NPRDYFLGQGMQQLIEEITQND-RPGPPPVPEAAIQAIPTVKIMESHL-ANDTTCPVCKE 251
             N  DYF G G+++L E+++    R GPPP P +AI A+PT+KI + HL ++D+ CPVCK+
Sbjct:   136 NTGDYFFGPGLEELFEQLSAGTTRRGPPPAPRSAIDALPTIKIAQRHLRSSDSNCPVCKD 195

Query:   252 EFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVP 291
             EF++G EA+++ C HIYHS+CIVPWL  HNSCPVCR E+P
Sbjct:   196 EFELGSEAKQMPCNHIYHSDCIVPWLVQHNSCPVCRQELP 235

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

GO:0005618 "cell wall" evidence=IDA

TAIR|locus:2092231 AT3G19950 [Arabidopsis thaliana (taxid:3702)]

 Score = 299 (110.3 bits), Expect = 3.4e-34, Sum P(2) = 3.4e-34
 Identities = 53/111 (47%), Positives = 79/111 (71%)

Query:   184 PGQNPLPPGVNPRDYFLGQGMQQLIEEITQND--RPGPPPVPEAAIQAIPTVKIMESHLA 241
             PG N +P G N  DYF G G++QLI+++ +ND  R G PP  ++AI A+PTVK+ +  L 
Sbjct:   154 PG-NRMP-G-NFGDYFFGPGLEQLIQQLAENDPNRYGTPPASKSAIDALPTVKVTKDMLK 210

Query:   242 NDTT-CPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVP 291
             ++   C VC +EF+ G + +++ CKH++H +C++PWL LHNSCPVCR E+P
Sbjct:   211 SEMNQCAVCMDEFEDGSDVKQMPCKHVFHQDCLLPWLELHNSCPVCRFELP 261

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

GO:0010200 "response to chitin" evidence=RCA

TAIR|locus:2075175 RDUF1 "RING and Domain of Unknown Function 1117 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 272 (100.8 bits), Expect = 2.1e-32, Sum P(2) = 2.1e-32
 Identities = 49/114 (42%), Positives = 73/114 (64%)

Query:   185 GQNPLPPGVNPRDYFLGQGMQQLIEEITQND-------RPGPPPVPEAAIQAIPTVKIME 237
             G  PLP  V+  +  +G G ++L+E+++Q +       R G PP  ++AI+++P V+I +
Sbjct:   149 GLRPLPDSVS--EILMGSGFERLLEQLSQIEASGNGIGRSGNPPASKSAIESLPRVEISD 206

Query:   238 SHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVP 291
              H   +  C VC E F+ G E RE+ CKHI+H +CIVPWL + NSCPVCR E+P
Sbjct:   207 CHTKAEANCAVCTEVFEAGIEGREMPCKHIFHGDCIVPWLSIRNSCPVCRFELP 260

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

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

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0004842 "ubiquitin-protein ligase activity" evidence=IDA

GO:0009414 "response to water deprivation" evidence=IMP

GO:0009737 "response to abscisic acid stimulus" evidence=IMP

GO:0051865 "protein autoubiquitination" evidence=IDA

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

GO:0009611 "response to wounding" evidence=RCA

GO:0009612 "response to mechanical stimulus" evidence=RCA

GO:0009693 "ethylene biosynthetic process" evidence=RCA

GO:0009873 "ethylene mediated signaling pathway" evidence=RCA

GO:0035556 "intracellular signal transduction" evidence=RCA

TAIR|locus:2148318 RDUF2 "RING and Domain of Unknown Function 1117 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 274 (101.5 bits), Expect = 7.6e-32, Sum P(2) = 7.6e-32
 Identities = 48/114 (42%), Positives = 75/114 (65%)

Query:   185 GQNPLPPGVNPRDYFLGQGMQQLIEEITQND-------RPGPPPVPEAAIQAIPTVKIME 237
             G  PLP  V+  +  +G G ++L+E+++Q +       R G PP  ++AI+++P V+I +
Sbjct:   133 GLRPLPDSVS--EILMGSGFERLLEQLSQIEASATGIGRSGNPPASKSAIESLPRVEISD 190

Query:   238 SHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVP 291
              H+ ++  C VC E F+   EARE+ CKH++H +CIVPWL + NSCPVCR E+P
Sbjct:   191 CHIGSEANCAVCTEIFETETEAREMPCKHLFHDDCIVPWLSIRNSCPVCRFELP 244

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0004842 "ubiquitin-protein ligase activity" evidence=IDA

GO:0009414 "response to water deprivation" evidence=IMP

GO:0009737 "response to abscisic acid stimulus" evidence=IMP

GO:0051865 "protein autoubiquitination" evidence=IDA

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

GO:0009693 "ethylene biosynthetic process" evidence=RCA

GO:0009873 "ethylene mediated signaling pathway" evidence=RCA

GO:0030968 "endoplasmic reticulum unfolded protein response" evidence=RCA

GO:0035556 "intracellular signal transduction" evidence=RCA

TAIR|locus:1006230278 AT3G10815 [Arabidopsis thaliana (taxid:3702)]

 Score = 269 (99.8 bits), Expect = 2.7e-31, Sum P(3) = 2.7e-31
 Identities = 47/101 (46%), Positives = 68/101 (67%)

Query:   194 NPRDYFLGQGM--QQLIEEITQ-NDRPGPPPVPEAAIQAIPTVKIMESHLANDTTCPVCK 250
             N R   +G+ +  ++L   +    DR GPPP   AAI ++  +KI + HL  D  CPVC+
Sbjct:    66 NNRRSVIGEQLSFEELFNRLPALQDRRGPPPASLAAINSLQKIKIRQKHLGLDPYCPVCQ 125

Query:   251 EEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVP 291
             ++F++G +AR++ CKHIYHSECI+PWL   N+CPVCR E+P
Sbjct:   126 DQFEIGSDARKMPCKHIYHSECILPWLVQRNTCPVCRKELP 166

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2063912 RHC2A "RING-H2 finger C2A" [Arabidopsis thaliana (taxid:3702)]

 Score = 270 (100.1 bits), Expect = 6.7e-31, Sum P(2) = 6.7e-31
 Identities = 52/117 (44%), Positives = 75/117 (64%)

Query:   185 GQNPLPPGVNPRDYFLGQGMQQLIEEITQ-------NDRPGP-PPVPEAAIQAIPTVKIM 236
             G  PLPP +   ++ LG G  +L+++I+Q       N R    PP  ++AI+A+P ++I 
Sbjct:   132 GLRPLPPSMT--EFLLGSGFDRLLDQISQIELNTNRNLRSCEHPPASKSAIEALPLIEID 189

Query:   237 ESHLANDTT--CPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVP 291
              +HL +D+   C VCKE F +   ARE+ C HIYH +CI+PWL + NSCPVCRHE+P
Sbjct:   190 PTHLLSDSQSHCAVCKENFVLKSSAREMPCNHIYHPDCILPWLAIRNSCPVCRHELP 246

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

TAIR|locus:2161058 ATCRT1 [Arabidopsis thaliana (taxid:3702)]

 Score = 278 (102.9 bits), Expect = 1.6e-30, Sum P(2) = 1.6e-30
 Identities = 55/121 (45%), Positives = 77/121 (63%)

Query:   176 NPL-EPILRPG-QNPLPPGVNPR-DYFLGQGMQQLIEEITQND--RPGPPPVPEAAIQAI 230
             NP  + ++ P  QN   P +    DYF+G G+  L++ + +ND  R G PP  + A++A+
Sbjct:   189 NPYNQSLVVPSDQNQNHPSLTSLGDYFIGPGLDLLLQHLAENDPNRQGTPPARKEAVEAL 248

Query:   231 PTVKIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEV 290
             PTVKIME        C VC ++F+ G EA+E+ CKH +H  CIVPWL LH+SCPVCR E+
Sbjct:   249 PTVKIMEP-----LQCSVCLDDFEKGTEAKEMPCKHKFHVRCIVPWLELHSSCPVCRFEL 303

Query:   291 P 291
             P
Sbjct:   304 P 304

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

UNIPROTKB|Q9BV68 RNF126 "RING finger protein 126" [Homo sapiens (taxid:9606)]

 Score = 267 (99.0 bits), Expect = 4.7e-29, Sum P(2) = 4.7e-29
 Identities = 51/114 (44%), Positives = 70/114 (61%)

Query:   181 ILRPGQNP-LPP-GV---NPRDYFLG-QGMQQLIEEI-TQNDRPGPPPVPEAAIQAIPTV 233
             I+ P   P L P GV   NP DY  G  G+  +I ++  Q +  GPPP  +  IQA+PTV
Sbjct:   157 IITPATIPSLGPWGVLHSNPMDYAWGANGLDAIITQLLNQFENTGPPPADKEKIQALPTV 216

Query:   234 KIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCR 287
              + E H+ +   CPVCK+++ +G   R+L C H++H  CIVPWL  H+SCPVCR
Sbjct:   217 PVTEEHVGSGLECPVCKDDYALGERVRQLPCNHLFHDGCIVPWLEQHDSCPVCR 270

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

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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

Prediction Level	EC number	Confidence of Prediction
3rd Layer	6.3.2	LOW CONFIDENCE prediction!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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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	358
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	2e-14
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	7e-11
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	4e-09
pfam14369	34	pfam14369, zf-RING_3, zinc-finger	1e-08
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	4e-08
smart00184	40	smart00184, RING, Ring finger	2e-07
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	1e-06
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	5e-06
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	2e-05
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	2e-05
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	1e-04
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	4e-04

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

 Score = 66.6 bits (163), Expect = 2e-14
 Identities = 21/45 (46%), Positives = 29/45 (64%)

Query: 245 TCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHE 289
            CP+C +EF+ G E   L C H++H EC+  WLR  N+CP+CR  
Sbjct: 2   ECPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

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

 Score = 56.3 bits (136), Expect = 7e-11
 Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 3/47 (6%)

Query: 245 TCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL-HNSCPVCRHEV 290
            CP+C EEF+       L C H++   CI  WL+   N+CP+CR  +
Sbjct: 1   ECPICLEEFRE--PVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 52.0 bits (125), Expect = 4e-09
 Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 10/62 (16%)

Query: 236 MESHLANDTTCPVCKEEF-------KVGGEARELA---CKHIYHSECIVPWLRLHNSCPV 285
           + S    D  C +C+  F       K  G+   +    C H +H  CI  WL+  N+CP+
Sbjct: 12  LWSWDIEDDVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPL 71

Query: 286 CR 287
           CR
Sbjct: 72  CR 73

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

>gnl|CDD|222714 pfam14369, zf-RING_3, zinc-finger

 Score = 49.9 bits (120), Expect = 1e-08
 Identities = 20/33 (60%), Positives = 22/33 (66%), Gaps = 1/33 (3%)

Query: 32 YWCYQCHRAVRISSTNPSEIACPRCSGHFVSEI 64
          YWCYQC R VRI+ +  S   CPRC G FV EI
Sbjct: 3  YWCYQCDRFVRIAPSGDS-DVCPRCGGGFVEEI 34

Length = 34

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

 Score = 48.6 bits (116), Expect = 4e-08
 Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRH 288
            +  CP+C +  +         C H++  ECI+ +L+  + CP+CR 
Sbjct: 1   EELECPICLDLLR--DPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 46.3 bits (110), Expect = 2e-07
 Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 3/42 (7%)

Query: 246 CPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN-SCPVC 286
           CP+C EE+    +   L C H +   CI  WL   N +CP+C
Sbjct: 1   CPICLEEYLK--DPVILPCGHTFCRSCIRKWLESGNNTCPIC 40

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

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

 Score = 49.6 bits (118), Expect = 1e-06
 Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 246 CPVCKEEFKVGGEARELACKHIYHSECIVPWLRLH-NSCPVCRHEVP 291
           C +C   F      R L C H +H  C+  WL  + N CPVCR  +P
Sbjct: 326 CAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372

Length = 374

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

 Score = 42.5 bits (100), Expect = 5e-06
 Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 3/42 (7%)

Query: 246 CPVCKEEFKVGGEARELACKHIYHSECIVPWLRL-HNSCPVC 286
           CP+C EE K       L C H++ S+CI+ WL   + +CP+C
Sbjct: 1   CPICLEEPKD--PVTILPCGHLFCSKCILSWLESGNVTCPLC 40

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

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

 Score = 45.7 bits (108), Expect = 2e-05
 Identities = 22/66 (33%), Positives = 28/66 (42%), Gaps = 11/66 (16%)

Query: 233 VKIMESHLAN-DTTCPVCKEE-FKVGGEA---------RELACKHIYHSECIVPWLRLHN 281
               E  L N D TC +C +E F    E          + L C HI H  C+  WL    
Sbjct: 276 PTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQ 335

Query: 282 SCPVCR 287
           +CP+CR
Sbjct: 336 TCPICR 341

Length = 491

>gnl|CDD|227521 COG5194, APC11, Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]

 Score = 42.1 bits (99), Expect = 2e-05
 Identities = 16/49 (32%), Positives = 20/49 (40%), Gaps = 2/49 (4%)

Query: 243 DTTCPVCKEEFKVGGEAREL--ACKHIYHSECIVPWLRLHNSCPVCRHE 289
             TCP C+     G E   +   C H +H  CI  WL     CP+ R  
Sbjct: 31  MGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQT 79

Length = 88

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

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 13/64 (20%)

Query: 239 HLANDTTCPVCKEEF-------KVGGEARELA---CKHIYHSECIVPWLRLHNS---CPV 285
              +D  C +C+  F       K  G+   L    CKH +H  CI+ WL    S   CP+
Sbjct: 17  DTPSDDVCGICRVSFDGTCPQCKFPGDDCPLVWGKCKHNFHMHCILKWLATETSKGLCPM 76

Query: 286 CRHE 289
           CR  
Sbjct: 77  CRQT 80

Apc11 is one of the subunits of the anaphase-promoting complex or cyclosome. The APC subunits are cullin family proteins with ubiquitin ligase activity. Polyubiquitination marks proteins for degradation by the 26S proteasome and is carried out by a cascade of enzymes that includes ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and is responsible for recruiting E2s to the APC and for mediating the subsequent transfer of ubiquitin to APC substrates in vivo. In Saccharomyces cerevisiae this RING-H2 finger protein defines the minimal ubiquitin ligase activity of the APC, and the integrity of the RING-H2 finger is essential for budding yeast cell viability. Length = 85

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

 Score = 42.3 bits (99), Expect = 4e-04
 Identities = 10/30 (33%), Positives = 16/30 (53%), Gaps = 2/30 (6%)

Query: 264  CKHIYHSECIVPWLRLHNS--CPVCRHEVP 291
            CK+ +H+ C+  W        CP+CR E+ 
Sbjct: 1494 CKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523

Length = 1525

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	358
PF14369	35	zf-RING_3: zinc-finger	99.6
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.55
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.45
PHA02929	238	N1R/p28-like protein; Provisional	99.2
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.18
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.17
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.04
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.94
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	98.91
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	98.87
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	98.87
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.81
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.81
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.75
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.7
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.68
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.67
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.65
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.58
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.57
PF14634	44	zf-RING_5: zinc-RING finger domain	98.55
PHA02926	242	zinc finger-like protein; Provisional	98.54
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.5
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.32
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.24
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.18
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.17
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.15
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.13
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.1
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.08
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.08
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.02
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	97.97
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	97.97
COG5219	1525	Uncharacterized conserved protein, contains RING Z	97.91
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.9
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	97.88
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	97.85
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	97.78
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.78
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.53
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.46
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.45
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.4
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.38
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.38
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.15
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.0
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	96.97
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	96.9
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	96.9
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	96.82
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	96.82
KOG2660	331	consensus Locus-specific chromosome binding protei	96.78
KOG0297	391	consensus TNF receptor-associated factor [Signal t	96.75
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	96.35
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	96.31
COG5152	259	Uncharacterized conserved protein, contains RING a	96.15
KOG1941	518	consensus Acetylcholine receptor-associated protei	95.98
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	95.9
KOG1002	791	consensus Nucleotide excision repair protein RAD16	95.88
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	95.88
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	95.73
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	95.71
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.47
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	95.39
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	95.24
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	95.11
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	95.02
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	95.01
PF04641	260	Rtf2: Rtf2 RING-finger	94.94
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	94.91
KOG3039	303	consensus Uncharacterized conserved protein [Funct	94.88
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	94.85
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	94.74
PHA02862	156	5L protein; Provisional	94.46
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	94.33
PHA02825	162	LAP/PHD finger-like protein; Provisional	93.89
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	93.87
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	93.81
COG5222	427	Uncharacterized conserved protein, contains RING Z	93.19
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	93.08
KOG4739	233	consensus Uncharacterized protein involved in syna	92.42
PHA03096	284	p28-like protein; Provisional	92.04
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	91.97
COG5236	493	Uncharacterized conserved protein, contains RING Z	91.49
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	90.79
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	90.54
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	90.37
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	90.37
KOG1940	276	consensus Zn-finger protein [General function pred	90.05
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	89.82
KOG0298	1394	consensus DEAD box-containing helicase-like transc	89.41
PRK00398	46	rpoP DNA-directed RNA polymerase subunit P; Provis	89.4
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	89.28
COG0375	115	HybF Zn finger protein HypA/HybF (possibly regulat	89.26
KOG1001	674	consensus Helicase-like transcription factor HLTF/	89.12
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	88.14
KOG3899	381	consensus Uncharacterized conserved protein [Funct	87.01
PF03604	32	DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa	86.43
TIGR00100	115	hypA hydrogenase nickel insertion protein HypA. In	86.19
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	86.01
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	84.89
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	84.81
PRK12380	113	hydrogenase nickel incorporation protein HybF; Pro	84.56
PRK06266	178	transcription initiation factor E subunit alpha; V	83.48
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	83.34
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	83.29
COG5175	480	MOT2 Transcriptional repressor [Transcription]	83.17
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	83.09
PF01155	113	HypA: Hydrogenase expression/synthesis hypA family	82.69
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	82.37
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	82.31
KOG3002	299	consensus Zn finger protein [General function pred	81.8
smart00659	44	RPOLCX RNA polymerase subunit CX. present in RNA p	81.67
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	81.33
PRK00762	124	hypA hydrogenase nickel incorporation protein; Pro	80.91
PRK00564	117	hypA hydrogenase nickel incorporation protein; Pro	80.8
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	80.2

>PF14369 zf-RING_3: zinc-finger

Probab=99.60  E-value=5e-16  Score=103.43  Aligned_cols=35  Identities=57%  Similarity=1.228  Sum_probs=30.7

Q ss_pred             CeeeeeccCcceeecCCCCCCccCCCCCCCceEEE
Q 018299           30 PLYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEI   64 (358)
Q Consensus        30 ~~YwCh~C~r~V~i~~~~~~ei~CP~C~~gFvEEi   64 (358)
                      ++||||+|+++|++.+...++++||+|++||||||
T Consensus         1 ~~ywCh~C~~~V~~~~~~~~~~~CP~C~~gFvEei   35 (35)
T PF14369_consen    1 QRYWCHQCNRFVRIAPSPDSDVACPRCHGGFVEEI   35 (35)
T ss_pred             CCEeCccCCCEeEeCcCCCCCcCCcCCCCcEeEeC
Confidence            47999999999999866555677999999999997

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

Probab=99.55  E-value=3.2e-15  Score=145.94  Aligned_cols=80  Identities=28%  Similarity=0.701  Sum_probs=67.9

Q ss_pred             CCCCCCCHHHHHhCCceeeeccccCCC-ccccccccccccCCccEEeccCCeeChhhHHHHHhcCCC-CCccceeccCCC
Q 018299          217 PGPPPVPEAAIQAIPTVKIMESHLAND-TTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNS-CPVCRHEVPVSS  294 (358)
Q Consensus       217 ~~~ppas~~~i~~lp~~~~~~~~~~~~-~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~s-CPvCR~~l~~~~  294 (358)
                      .....+.+..++++|...++....... ..|+||+|+|+.|++++.|||+|.||..||++||.++.+ ||+||+++....
T Consensus       202 ~~~~r~~k~~l~~~p~~~f~~~~~~~~~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~  281 (348)
T KOG4628|consen  202 LRRNRLIKRLLKKLPVRTFTKGDDEDATDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDS  281 (348)
T ss_pred             hhhhhhHHHHHhhCCcEEeccccccCCCceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCCC
Confidence            355578999999999999977654332 499999999999999999999999999999999999865 999999876654


Q ss_pred             CC
Q 018299          295 AS  296 (358)
Q Consensus       295 ~~  296 (358)
                      ..
T Consensus       282 ~~  283 (348)
T KOG4628|consen  282 GS  283 (348)
T ss_pred             CC
Confidence            43

>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A

Probab=99.45  E-value=2.8e-14  Score=99.71  Aligned_cols=44  Identities=50%  Similarity=1.234  Sum_probs=40.7

Q ss_pred             ccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccc
Q 018299          244 TTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCR  287 (358)
Q Consensus       244 ~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR  287 (358)
                      ++|+||++.|..++.++.++|+|.||.+||..|++.+.+||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence            37999999999899999999999999999999999999999997

...

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.20  E-value=1.5e-11  Score=115.29  Aligned_cols=70  Identities=29%  Similarity=0.576  Sum_probs=55.4

Q ss_pred             CCHHHHHhCCceeeecccc---CCCccccccccccccCCc-----cEEeccCCeeChhhHHHHHhcCCCCCccceecc
Q 018299          222 VPEAAIQAIPTVKIMESHL---ANDTTCPVCKEEFKVGGE-----ARELACKHIYHSECIVPWLRLHNSCPVCRHEVP  291 (358)
Q Consensus       222 as~~~i~~lp~~~~~~~~~---~~~~~C~ICle~~~~~~~-----~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~  291 (358)
                      .++..++.+|.+.......   ..+.+|+||++.+...+.     ++.++|+|.||..||..|++.+.+||+||..+.
T Consensus       150 ~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~  227 (238)
T PHA02929        150 NYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI  227 (238)
T ss_pred             hhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence            3888999999886543322   346899999999875431     344569999999999999999999999999875

>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.18  E-value=1e-11  Score=96.27  Aligned_cols=45  Identities=38%  Similarity=0.959  Sum_probs=36.2

Q ss_pred             Ccccccccccccc----------CCccEEeccCCeeChhhHHHHHhcCCCCCccc
Q 018299          243 DTTCPVCKEEFKV----------GGEARELACKHIYHSECIVPWLRLHNSCPVCR  287 (358)
Q Consensus       243 ~~~C~ICle~~~~----------~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR  287 (358)
                      +..|+||++.|..          .-.+...+|+|.||..||..||+.+++||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            4569999999932          12445567999999999999999999999997

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....

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

Probab=99.17  E-value=8.6e-12  Score=118.42  Aligned_cols=50  Identities=36%  Similarity=0.927  Sum_probs=46.5

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHh-cCCCCCccceeccC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLR-LHNSCPVCRHEVPV  292 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~-~~~sCPvCR~~l~~  292 (358)
                      ..+|+||++.|..+++++.|||+|.||..||.+|+. -++.||+||.+++.
T Consensus       323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            579999999999999999999999999999999999 56789999999875

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

Probab=99.04  E-value=1e-10  Score=113.83  Aligned_cols=52  Identities=37%  Similarity=0.924  Sum_probs=44.8

Q ss_pred             CCCccccccccc-cccC---------CccEEeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          241 ANDTTCPVCKEE-FKVG---------GEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       241 ~~~~~C~ICle~-~~~~---------~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      ..|..|.||+|+ |..+         .+++.|||||++|.+|++.|++++.+||+||.++.-
T Consensus       285 n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~if  346 (491)
T COG5243         285 NSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVIF  346 (491)
T ss_pred             CCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCcccc
Confidence            357899999999 4433         367999999999999999999999999999999643

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

Probab=98.94  E-value=5e-10  Score=103.34  Aligned_cols=57  Identities=25%  Similarity=0.623  Sum_probs=48.1

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhcCC---CCCccceeccCCCCCCCCCC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN---SCPVCRHEVPVSSASSSHDV  301 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~---sCPvCR~~l~~~~~~~~~~~  301 (358)
                      ...+|.||||..+   +++++.|||+||+.||.+||..+.   .|||||.+|..++.......
T Consensus        46 ~~FdCNICLd~ak---dPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlYGr  105 (230)
T KOG0823|consen   46 GFFDCNICLDLAK---DPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLYGR  105 (230)
T ss_pred             CceeeeeeccccC---CCEEeecccceehHHHHHHHhhcCCCeeCCccccccccceEEeeecc
Confidence            3679999999988   889999999999999999998654   49999999988776554433

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=98.91  E-value=7.4e-10  Score=100.37  Aligned_cols=52  Identities=25%  Similarity=0.724  Sum_probs=43.4

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHhc----------------CCCCCccceeccCCCC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL----------------HNSCPVCRHEVPVSSA  295 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~----------------~~sCPvCR~~l~~~~~  295 (358)
                      .++.+|+||++.++   .++.++|+|.||..||..|+..                ...||+||..+.....
T Consensus        16 ~~~~~CpICld~~~---dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~L   83 (193)
T PLN03208         16 GGDFDCNICLDQVR---DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATL   83 (193)
T ss_pred             CCccCCccCCCcCC---CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcE
Confidence            35689999999987   7788999999999999999863                2369999999966443

>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A

Probab=98.87  E-value=1.3e-09  Score=78.12  Aligned_cols=46  Identities=33%  Similarity=0.886  Sum_probs=40.7

Q ss_pred             CccccccccccccCCccEEeccCCe-eChhhHHHHHhcCCCCCccceecc
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHI-YHSECIVPWLRLHNSCPVCRHEVP  291 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~-FH~~CI~~WL~~~~sCPvCR~~l~  291 (358)
                      +..|.||++...   .+..+||+|. ||..|+..|++....||+||.++.
T Consensus         2 ~~~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPR---DVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBS---SEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCC---ceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            568999999977   7899999999 999999999999999999999874

...

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

Probab=98.87  E-value=1.2e-09  Score=103.52  Aligned_cols=50  Identities=28%  Similarity=0.742  Sum_probs=45.2

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccCCC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSS  294 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~  294 (358)
                      ....|.|||+...   .+..+||||+||..||..|+..+..||+||..+....
T Consensus       238 a~~kC~LCLe~~~---~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~psk  287 (293)
T KOG0317|consen  238 ATRKCSLCLENRS---NPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSK  287 (293)
T ss_pred             CCCceEEEecCCC---CCCcCcCcchHHHHHHHHHHccccCCCcccccCCCcc
Confidence            4679999999987   7889999999999999999999999999999886543

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

Probab=98.81  E-value=3e-09  Score=72.58  Aligned_cols=44  Identities=41%  Similarity=1.106  Sum_probs=36.5

Q ss_pred             cccccccccccCCccEEeccCCeeChhhHHHHHhc-CCCCCccceec
Q 018299          245 TCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL-HNSCPVCRHEV  290 (358)
Q Consensus       245 ~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~-~~sCPvCR~~l  290 (358)
                      .|+||++.+.  +....++|+|.||..|+..|++. ...||+|+..+
T Consensus         1 ~C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhh--CceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            5999999983  34445559999999999999998 67799999764

>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A

Probab=98.81  E-value=2.7e-09  Score=72.60  Aligned_cols=39  Identities=36%  Similarity=0.942  Sum_probs=33.2

Q ss_pred             ccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCcc
Q 018299          246 CPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVC  286 (358)
Q Consensus       246 C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvC  286 (358)
                      |+||++.+..  .++.++|||.||..||..|++.+.+||+|
T Consensus         1 C~iC~~~~~~--~~~~~~CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTPCGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC--cCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence            8999999882  44788999999999999999998899998

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

Probab=98.75  E-value=5.6e-09  Score=72.42  Aligned_cols=38  Identities=34%  Similarity=0.932  Sum_probs=31.3

Q ss_pred             ccccccccccCCccEEeccCCeeChhhHHHHHhcCC----CCCcc
Q 018299          246 CPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN----SCPVC  286 (358)
Q Consensus       246 C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~----sCPvC  286 (358)
                      |+||++.|+   +++.|+|+|.|+..||..|++...    .||+|
T Consensus         1 CpiC~~~~~---~Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFK---DPVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-S---SEEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhC---CccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            899999999   899999999999999999998642    59988

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

Probab=98.70  E-value=6.8e-09  Score=82.23  Aligned_cols=54  Identities=33%  Similarity=0.804  Sum_probs=41.4

Q ss_pred             cCCCcccccccccccc--------CC--ccEEeccCCeeChhhHHHHHhcC---CCCCccceeccCC
Q 018299          240 LANDTTCPVCKEEFKV--------GG--EARELACKHIYHSECIVPWLRLH---NSCPVCRHEVPVS  293 (358)
Q Consensus       240 ~~~~~~C~ICle~~~~--------~~--~~~~lpC~H~FH~~CI~~WL~~~---~sCPvCR~~l~~~  293 (358)
                      +.+++.|.||...|+.        |+  .++.-.|+|.||..||.+||..+   ..||+||+++..+
T Consensus        18 ~~~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k   84 (85)
T PF12861_consen   18 VANDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKFK   84 (85)
T ss_pred             cCCCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeeeC
Confidence            4458899999998862        22  23334599999999999999864   5699999987543

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

Probab=98.68  E-value=7.2e-09  Score=92.12  Aligned_cols=50  Identities=28%  Similarity=0.715  Sum_probs=42.6

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccCC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      ...|+|||+.+... .++.+.|||+||+.||+.-|+..+.||+|++.|..+
T Consensus       131 ~~~CPiCl~~~sek-~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k  180 (187)
T KOG0320|consen  131 TYKCPICLDSVSEK-VPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHK  180 (187)
T ss_pred             ccCCCceecchhhc-cccccccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence            47999999999832 225578999999999999999999999999987654

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

Probab=98.67  E-value=8.3e-09  Score=108.01  Aligned_cols=52  Identities=33%  Similarity=0.883  Sum_probs=45.7

Q ss_pred             CCccccccccccccCCc--cEEeccCCeeChhhHHHHHhcCCCCCccceeccCC
Q 018299          242 NDTTCPVCKEEFKVGGE--ARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~--~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      .+..|+||+|.+..+..  ++.|+|+|+||..|+..|+++.++||+||..+...
T Consensus       290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~~~~  343 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVLYDY  343 (543)
T ss_pred             cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhhhcc
Confidence            37899999999996554  89999999999999999999999999999955443

>smart00504 Ubox Modified RING finger domain

Probab=98.65  E-value=2.2e-08  Score=74.42  Aligned_cols=46  Identities=26%  Similarity=0.468  Sum_probs=41.6

Q ss_pred             ccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          244 TTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       244 ~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      ..|+||++.+.   .++.++|||+|+..||..|++.+.+||+|+..+..
T Consensus         2 ~~Cpi~~~~~~---~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~   47 (63)
T smart00504        2 FLCPISLEVMK---DPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTH   47 (63)
T ss_pred             cCCcCCCCcCC---CCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence            57999999998   57889999999999999999998899999988743

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

>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=98.58  E-value=3.3e-08  Score=67.53  Aligned_cols=38  Identities=37%  Similarity=1.072  Sum_probs=32.9

Q ss_pred             ccccccccccCCccE-EeccCCeeChhhHHHHHh--cCCCCCcc
Q 018299          246 CPVCKEEFKVGGEAR-ELACKHIYHSECIVPWLR--LHNSCPVC  286 (358)
Q Consensus       246 C~ICle~~~~~~~~~-~lpC~H~FH~~CI~~WL~--~~~sCPvC  286 (358)
                      |+||++.+.   ... .++|+|.||..||..|++  ....||+|
T Consensus         1 C~iC~~~~~---~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFE---DPVILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCS---SEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCcccc---CCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            899999988   444 889999999999999999  34569998

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

>smart00184 RING Ring finger

Probab=98.57  E-value=3.9e-08  Score=64.71  Aligned_cols=38  Identities=45%  Similarity=1.197  Sum_probs=33.6

Q ss_pred             ccccccccccCCccEEeccCCeeChhhHHHHHh-cCCCCCcc
Q 018299          246 CPVCKEEFKVGGEARELACKHIYHSECIVPWLR-LHNSCPVC  286 (358)
Q Consensus       246 C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~-~~~sCPvC  286 (358)
                      |+||++...   .+..++|+|.||..|+..|++ ....||+|
T Consensus         1 C~iC~~~~~---~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELK---DPVVLPCGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCC---CcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence            789999854   788999999999999999998 56679987

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

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.55  E-value=3.8e-08  Score=68.72  Aligned_cols=44  Identities=27%  Similarity=0.748  Sum_probs=38.5

Q ss_pred             cccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccce
Q 018299          245 TCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRH  288 (358)
Q Consensus       245 ~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~  288 (358)
                      .|.||++.|.....+..++|+|+||..||..+......||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            59999999965667889999999999999999856668999985

>PHA02926 zinc finger-like protein; Provisional

Probab=98.54  E-value=4.1e-08  Score=90.34  Aligned_cols=51  Identities=27%  Similarity=0.668  Sum_probs=38.8

Q ss_pred             CCccccccccccccCC-----c-cEEeccCCeeChhhHHHHHhcC------CCCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVGG-----E-ARELACKHIYHSECIVPWLRLH------NSCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~-----~-~~~lpC~H~FH~~CI~~WL~~~------~sCPvCR~~l~~  292 (358)
                      .+.+|+||++......     . ....+|+|.||..||..|.+.+      .+||+||..+..
T Consensus       169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~  231 (242)
T PHA02926        169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRN  231 (242)
T ss_pred             CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeee
Confidence            4789999999864321     1 2344699999999999999753      359999998754

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.50  E-value=5.4e-08  Score=97.61  Aligned_cols=51  Identities=33%  Similarity=0.662  Sum_probs=44.6

Q ss_pred             cCCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccCC
Q 018299          240 LANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       240 ~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      +.....|+||++.|.   .++.++|+|.||..||..|+.....||+|+..+...
T Consensus        23 Le~~l~C~IC~d~~~---~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~   73 (397)
T TIGR00599        23 LDTSLRCHICKDFFD---VPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES   73 (397)
T ss_pred             cccccCCCcCchhhh---CccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence            344689999999998   667899999999999999999988999999987653

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

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

Probab=98.32  E-value=3.6e-07  Score=71.04  Aligned_cols=50  Identities=28%  Similarity=0.743  Sum_probs=37.4

Q ss_pred             cccccccccc-----------ccCCcc--EEeccCCeeChhhHHHHHhcCCCCCccceeccCC
Q 018299          244 TTCPVCKEEF-----------KVGGEA--RELACKHIYHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       244 ~~C~ICle~~-----------~~~~~~--~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      +.|+||...+           ..+++.  ..-.|.|.||..||..||..++.||++|++....
T Consensus        21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~   83 (88)
T COG5194          21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLA   83 (88)
T ss_pred             chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEe
Confidence            5677776554           233332  2334999999999999999999999999987543

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

Probab=98.24  E-value=4.2e-07  Score=92.36  Aligned_cols=53  Identities=28%  Similarity=0.725  Sum_probs=44.3

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhcC-----CCCCccceeccCCCCCCC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLH-----NSCPVCRHEVPVSSASSS  298 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~-----~sCPvCR~~l~~~~~~~~  298 (358)
                      +..|+|||+...   .+..+.|||+||..||..++...     ..||+|+..+..+.....
T Consensus       186 ~~~CPICL~~~~---~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~pv  243 (513)
T KOG2164|consen  186 DMQCPICLEPPS---VPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLPV  243 (513)
T ss_pred             CCcCCcccCCCC---cccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccceeee
Confidence            679999999988   77788899999999999998764     369999998877554443

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

Probab=98.18  E-value=5.9e-07  Score=84.55  Aligned_cols=50  Identities=28%  Similarity=0.693  Sum_probs=43.6

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHH-HHhcCCC-CCccceeccCCC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVP-WLRLHNS-CPVCRHEVPVSS  294 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~-WL~~~~s-CPvCR~~l~~~~  294 (358)
                      .+..|+||++..+   .+..++|+|+||..||.. |-+.+.. ||+||+.+..+.
T Consensus       214 ~d~kC~lC~e~~~---~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~  265 (271)
T COG5574         214 ADYKCFLCLEEPE---VPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK  265 (271)
T ss_pred             cccceeeeecccC---CcccccccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence            3789999999988   889999999999999999 9877766 999999876543

>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=98.17  E-value=3.3e-07  Score=70.70  Aligned_cols=51  Identities=33%  Similarity=0.855  Sum_probs=38.6

Q ss_pred             CCcccccccccccc--------C-CccEEec-cCCeeChhhHHHHHhcCC---CCCccceeccC
Q 018299          242 NDTTCPVCKEEFKV--------G-GEARELA-CKHIYHSECIVPWLRLHN---SCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~--------~-~~~~~lp-C~H~FH~~CI~~WL~~~~---sCPvCR~~l~~  292 (358)
                      .+++|-||.-.|..        | +-+..+. |.|.||..||.+||....   .||+||+++..
T Consensus        19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~   82 (84)
T KOG1493|consen   19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQF   82 (84)
T ss_pred             CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence            46699999988852        2 2333333 999999999999997644   59999998754

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

Probab=98.15  E-value=1.4e-06  Score=60.80  Aligned_cols=34  Identities=29%  Similarity=0.819  Sum_probs=22.2

Q ss_pred             cccccccccc-CCccEEeccCCeeChhhHHHHHhcC
Q 018299          246 CPVCKEEFKV-GGEARELACKHIYHSECIVPWLRLH  280 (358)
Q Consensus       246 C~ICle~~~~-~~~~~~lpC~H~FH~~CI~~WL~~~  280 (358)
                      |+||++ |.. ...++.|+|||+|+.+||..+++..
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~   35 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKS   35 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcC
Confidence            899999 753 4468999999999999999999854

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

Probab=98.13  E-value=5.7e-07  Score=87.13  Aligned_cols=47  Identities=30%  Similarity=0.603  Sum_probs=43.7

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      ...|-||.+.|.   .++++||+|.||.-||..+|..+..||.|++++..
T Consensus        23 lLRC~IC~eyf~---ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~E   69 (442)
T KOG0287|consen   23 LLRCGICFEYFN---IPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTE   69 (442)
T ss_pred             HHHHhHHHHHhc---CceeccccchHHHHHHHHHhccCCCCCceecccch
Confidence            579999999999   88999999999999999999999999999988744

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

Probab=98.10  E-value=1.9e-06  Score=61.77  Aligned_cols=42  Identities=24%  Similarity=0.807  Sum_probs=33.6

Q ss_pred             cccccccccccCCccEEeccC-----CeeChhhHHHHHhcCC--CCCccc
Q 018299          245 TCPVCKEEFKVGGEARELACK-----HIYHSECIVPWLRLHN--SCPVCR  287 (358)
Q Consensus       245 ~C~ICle~~~~~~~~~~lpC~-----H~FH~~CI~~WL~~~~--sCPvCR  287 (358)
                      .|.||++ ...++.+..+||.     |.+|..|+..|+..+.  +||+|+
T Consensus         1 ~CrIC~~-~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHD-EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCC-CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            4899999 4444566788985     8999999999997654  799995

Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class

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

Probab=98.08  E-value=1.3e-06  Score=83.15  Aligned_cols=47  Identities=30%  Similarity=0.589  Sum_probs=43.3

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      -..|-||.+.|.   .+..++|+|.||+-||...|..+.-||+||.+...
T Consensus        25 ~lrC~IC~~~i~---ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~e   71 (391)
T COG5432          25 MLRCRICDCRIS---IPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPCE   71 (391)
T ss_pred             HHHhhhhhheee---cceecccccchhHHHHHHHhcCCCCCccccccHHh
Confidence            569999999999   88899999999999999999999999999987644

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

Probab=98.08  E-value=1.9e-06  Score=66.66  Aligned_cols=48  Identities=25%  Similarity=0.495  Sum_probs=39.0

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhc-CCCCCccceeccCC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL-HNSCPVCRHEVPVS  293 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~-~~sCPvCR~~l~~~  293 (358)
                      ...|+||.+.|.   .++.++|||.|...||..||+. +.+||+|+..+...
T Consensus         4 ~f~CpIt~~lM~---dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~   52 (73)
T PF04564_consen    4 EFLCPITGELMR---DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSES   52 (73)
T ss_dssp             GGB-TTTSSB-S---SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGG
T ss_pred             ccCCcCcCcHhh---CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcc
Confidence            578999999999   8999999999999999999999 78899999887543

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

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

Probab=98.02  E-value=1.2e-06  Score=82.58  Aligned_cols=52  Identities=31%  Similarity=0.860  Sum_probs=43.0

Q ss_pred             CCccccccccccccCC-------ccEEeccCCeeChhhHHHHHh--cCCCCCccceeccCC
Q 018299          242 NDTTCPVCKEEFKVGG-------EARELACKHIYHSECIVPWLR--LHNSCPVCRHEVPVS  293 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~-------~~~~lpC~H~FH~~CI~~WL~--~~~sCPvCR~~l~~~  293 (358)
                      ++..|+||-..+....       +..+|.|+|+||..||.-|-.  .+.+||.|+..+..+
T Consensus       223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl~  283 (328)
T KOG1734|consen  223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLK  283 (328)
T ss_pred             CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhHh
Confidence            4789999988776544       678899999999999999975  466899999987544

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

Probab=97.97  E-value=2.2e-06  Score=86.57  Aligned_cols=50  Identities=28%  Similarity=0.840  Sum_probs=39.8

Q ss_pred             CccccccccccccCC--------------ccEEeccCCeeChhhHHHHHhcCC-CCCccceeccC
Q 018299          243 DTTCPVCKEEFKVGG--------------EARELACKHIYHSECIVPWLRLHN-SCPVCRHEVPV  292 (358)
Q Consensus       243 ~~~C~ICle~~~~~~--------------~~~~lpC~H~FH~~CI~~WL~~~~-sCPvCR~~l~~  292 (358)
                      ..+|+||+..+..-.              .-..+||.|+||..|+..|...-+ .||+||..|+.
T Consensus       571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             cccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            579999999874311              134559999999999999999554 89999999874

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

Probab=97.97  E-value=1.2e-06  Score=67.31  Aligned_cols=51  Identities=22%  Similarity=0.589  Sum_probs=24.2

Q ss_pred             Cccccccccccc-cCCccEEe----ccCCeeChhhHHHHHhc----CC-------CCCccceeccCC
Q 018299          243 DTTCPVCKEEFK-VGGEAREL----ACKHIYHSECIVPWLRL----HN-------SCPVCRHEVPVS  293 (358)
Q Consensus       243 ~~~C~ICle~~~-~~~~~~~l----pC~H~FH~~CI~~WL~~----~~-------sCPvCR~~l~~~  293 (358)
                      +.+|.||+..+. .++.+...    .|++.||..||..||..    +.       .||.|+.+|..+
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~   68 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS   68 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence            468999999875 33333222    49999999999999974    11       399999998653

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

Probab=97.91  E-value=2.6e-06  Score=91.33  Aligned_cols=52  Identities=25%  Similarity=0.833  Sum_probs=39.4

Q ss_pred             cCCCccccccccccccCC---ccEEec-cCCeeChhhHHHHHhcC--CCCCccceecc
Q 018299          240 LANDTTCPVCKEEFKVGG---EARELA-CKHIYHSECIVPWLRLH--NSCPVCRHEVP  291 (358)
Q Consensus       240 ~~~~~~C~ICle~~~~~~---~~~~lp-C~H~FH~~CI~~WL~~~--~sCPvCR~~l~  291 (358)
                      .....+|+||+..+..-+   .-+..+ |+|.||..|+.+|++..  ++||+||.+++
T Consensus      1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            445689999998775211   223334 99999999999999975  46999998775

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

Probab=97.90  E-value=4.9e-06  Score=83.36  Aligned_cols=49  Identities=35%  Similarity=0.861  Sum_probs=39.7

Q ss_pred             CCCccccccccccccCC-ccEEeccCCeeChhhHHHHHhcCCCCCccceecc
Q 018299          241 ANDTTCPVCKEEFKVGG-EARELACKHIYHSECIVPWLRLHNSCPVCRHEVP  291 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~-~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~  291 (358)
                      .+..+|+|||+.+.... .++.+.|.|.||..|+..|  ...+|||||+-..
T Consensus       173 tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w--~~~scpvcR~~q~  222 (493)
T KOG0804|consen  173 TELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKW--WDSSCPVCRYCQS  222 (493)
T ss_pred             ccCCCcchhHhhcCccccceeeeecccccchHHHhhc--ccCcChhhhhhcC
Confidence            34679999999987544 3355569999999999999  5678999999765

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

Probab=97.88  E-value=4.1e-06  Score=77.97  Aligned_cols=44  Identities=39%  Similarity=0.830  Sum_probs=38.9

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccc
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCR  287 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR  287 (358)
                      .+...|+||++.|.   .++.++|+|.||..||..++.....||.||
T Consensus        11 ~~~~~C~iC~~~~~---~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr   54 (386)
T KOG2177|consen   11 QEELTCPICLEYFR---EPVLLPCGHNFCRACLTRSWEGPLSCPVCR   54 (386)
T ss_pred             cccccChhhHHHhh---cCccccccchHhHHHHHHhcCCCcCCcccC
Confidence            35789999999999   458999999999999999998555799999

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=97.85  E-value=1e-05  Score=78.63  Aligned_cols=52  Identities=23%  Similarity=0.519  Sum_probs=38.9

Q ss_pred             CccccccccccccCCccEEe--ccCCeeChhhHHHHHhc-CCCCCccceeccCCC
Q 018299          243 DTTCPVCKEEFKVGGEAREL--ACKHIYHSECIVPWLRL-HNSCPVCRHEVPVSS  294 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~l--pC~H~FH~~CI~~WL~~-~~sCPvCR~~l~~~~  294 (358)
                      +..|+||+..-......+.|  +|+|.||..||...+.. ...||+|+..+....
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~   57 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNN   57 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence            56899999964444333233  79999999999996644 457999999886654

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

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

Probab=97.78  E-value=1.1e-05  Score=65.79  Aligned_cols=50  Identities=26%  Similarity=0.644  Sum_probs=37.3

Q ss_pred             Cccccccccccc-------------cCC-ccEEeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          243 DTTCPVCKEEFK-------------VGG-EARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       243 ~~~C~ICle~~~-------------~~~-~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      -+.|+||..-+-             .++ .+..--|.|.||..||..||+..+.||+|.++...
T Consensus        46 vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~~  109 (114)
T KOG2930|consen   46 VDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWVF  109 (114)
T ss_pred             echhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcceeE
Confidence            578999865441             112 22233499999999999999999999999887643

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

Probab=97.78  E-value=2.5e-06  Score=83.25  Aligned_cols=59  Identities=25%  Similarity=0.575  Sum_probs=46.5

Q ss_pred             eeeccccCCCccccccccccccCCccEEec-cCCeeChhhHHHHHhc-CCCCCccceeccCCCC
Q 018299          234 KIMESHLANDTTCPVCKEEFKVGGEARELA-CKHIYHSECIVPWLRL-HNSCPVCRHEVPVSSA  295 (358)
Q Consensus       234 ~~~~~~~~~~~~C~ICle~~~~~~~~~~lp-C~H~FH~~CI~~WL~~-~~sCPvCR~~l~~~~~  295 (358)
                      .+....+..+..|+|||+.++   ..+..+ |.|.||.+||..-++. .++||.||+.+..+-.
T Consensus        34 ~~~l~~~~~~v~c~icl~llk---~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Skrs   94 (381)
T KOG0311|consen   34 MVDLAMFDIQVICPICLSLLK---KTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRS   94 (381)
T ss_pred             eecHHHhhhhhccHHHHHHHH---hhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcccccc
Confidence            333444556789999999998   555555 9999999999999986 4679999998876543

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

Probab=97.53  E-value=3.1e-05  Score=74.36  Aligned_cols=48  Identities=23%  Similarity=0.507  Sum_probs=42.0

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhcCC-CCCccceeccCC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN-SCPVCRHEVPVS  293 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~-sCPvCR~~l~~~  293 (358)
                      +.+|+||+....   .++.|+|+|.||.-||+--.+... +|++||++++..
T Consensus         7 ~~eC~IC~nt~n---~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    7 KKECLICYNTGN---CPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDST   55 (324)
T ss_pred             CCcceeeeccCC---cCccccccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence            679999999877   778999999999999998877655 599999999764

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

Probab=97.46  E-value=1.9e-05  Score=59.33  Aligned_cols=46  Identities=30%  Similarity=0.686  Sum_probs=24.1

Q ss_pred             CCccccccccccccCCccE-EeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVGGEAR-ELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~-~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      +...|++|.+.++   +++ ...|.|+||+.||..-+.  ..||+|+.+.-.
T Consensus         6 ~lLrCs~C~~~l~---~pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~   52 (65)
T PF14835_consen    6 ELLRCSICFDILK---EPVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWI   52 (65)
T ss_dssp             HTTS-SSS-S--S---S-B---SSS--B-TTTGGGGTT--TB-SSS--B-S-
T ss_pred             HhcCCcHHHHHhc---CCceeccCccHHHHHHhHHhcC--CCCCCcCChHHH
Confidence            3568999999988   554 456999999999988544  349999887643

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

Probab=97.45  E-value=7.6e-05  Score=73.26  Aligned_cols=50  Identities=26%  Similarity=0.640  Sum_probs=42.8

Q ss_pred             CccccccccccccCCccEEeccCCe-eChhhHHHHHhcCCCCCccceeccCCCC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHI-YHSECIVPWLRLHNSCPVCRHEVPVSSA  295 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~-FH~~CI~~WL~~~~sCPvCR~~l~~~~~  295 (358)
                      ..+|.||+.+-.   ....|||.|. .|..|-+..--+++.||+||+.+...-.
T Consensus       290 gkeCVIClse~r---dt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ll~  340 (349)
T KOG4265|consen  290 GKECVICLSESR---DTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEELLE  340 (349)
T ss_pred             CCeeEEEecCCc---ceEEecchhhehhHhHHHHHHHhhcCCCccccchHhhhe
Confidence            579999999988   8899999997 6889998887788999999998855433

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

Probab=97.40  E-value=3.2e-05  Score=81.91  Aligned_cols=50  Identities=30%  Similarity=0.600  Sum_probs=44.6

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      ...|++|+..+.++......+|+|+||..||..|-+.-++||+||.++..
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~  172 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGE  172 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhhe
Confidence            57899999999877777777899999999999999999999999998744

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

Probab=97.38  E-value=4.2e-05  Score=73.29  Aligned_cols=55  Identities=27%  Similarity=0.639  Sum_probs=45.8

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhc-----------------------CCCCCccceeccCCCCC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL-----------------------HNSCPVCRHEVPVSSAS  296 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~-----------------------~~sCPvCR~~l~~~~~~  296 (358)
                      ..-.|.|||--|..++....++|.|.||..|+..+|..                       ...|||||..|..+..+
T Consensus       114 p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~~s  191 (368)
T KOG4445|consen  114 PNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEENS  191 (368)
T ss_pred             CCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccccc
Confidence            35799999999999998999999999999999988721                       12499999999776554

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

Probab=97.38  E-value=6.9e-05  Score=74.06  Aligned_cols=48  Identities=25%  Similarity=0.821  Sum_probs=37.4

Q ss_pred             ccccccccccccCCccEEec-cCCeeChhhHHHHHhcC---CCCCccceecc
Q 018299          244 TTCPVCKEEFKVGGEARELA-CKHIYHSECIVPWLRLH---NSCPVCRHEVP  291 (358)
Q Consensus       244 ~~C~ICle~~~~~~~~~~lp-C~H~FH~~CI~~WL~~~---~sCPvCR~~l~  291 (358)
                      ..|.||.+-+.....+.-+. |||+||..|+..|++..   ..||+|+-.++
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~   56 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQ   56 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeeccc
Confidence            58999966666555565555 99999999999999864   36999995443

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

Probab=97.15  E-value=0.00021  Score=70.99  Aligned_cols=50  Identities=26%  Similarity=0.736  Sum_probs=41.9

Q ss_pred             ccccccccccccCCccEEeccCCeeChhhHHHHHhc--CCCCCccceeccCCCCC
Q 018299          244 TTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL--HNSCPVCRHEVPVSSAS  296 (358)
Q Consensus       244 ~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~--~~sCPvCR~~l~~~~~~  296 (358)
                      .-|.||-|.-+   .+++-||||..|..|+..|-..  .++||.||.+++-....
T Consensus       370 eLCKICaendK---dvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~v  421 (563)
T KOG1785|consen  370 ELCKICAENDK---DVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPV  421 (563)
T ss_pred             HHHHHhhccCC---CcccccccchHHHHHHHhhcccCCCCCCCceeeEeccccce
Confidence            46999988766   7888899999999999999854  46899999999776543

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

Probab=97.00  E-value=0.00027  Score=70.02  Aligned_cols=52  Identities=27%  Similarity=0.671  Sum_probs=38.3

Q ss_pred             CCccccccccccccCC----ccEEec-cCCeeChhhHHHHH--hc-----CCCCCccceeccCC
Q 018299          242 NDTTCPVCKEEFKVGG----EARELA-CKHIYHSECIVPWL--RL-----HNSCPVCRHEVPVS  293 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~----~~~~lp-C~H~FH~~CI~~WL--~~-----~~sCPvCR~~l~~~  293 (358)
                      .+.+|.||++......    ...+|| |.|.||..||..|-  ++     ...||.||......
T Consensus       160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v  223 (344)
T KOG1039|consen  160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFV  223 (344)
T ss_pred             ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccc
Confidence            4789999999876322    012334 99999999999998  34     35699999866443

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

Probab=96.97  E-value=0.00037  Score=70.30  Aligned_cols=49  Identities=27%  Similarity=0.604  Sum_probs=43.7

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      ..+..|.||+.-+.   .++.+||+|.||..||..-+.....||.||.++..
T Consensus        82 ~sef~c~vc~~~l~---~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   82 RSEFECCVCSRALY---PPVVTPCGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cchhhhhhhHhhcC---CCccccccccccHHHHHHHhccCCCCccccccccc
Confidence            35789999999998   88888999999999999988877789999999975

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

Probab=96.90  E-value=0.00024  Score=75.63  Aligned_cols=47  Identities=26%  Similarity=0.671  Sum_probs=40.6

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhc-CCCCCccceeccC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL-HNSCPVCRHEVPV  292 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~-~~sCPvCR~~l~~  292 (358)
                      -..|++|-..++   .+++..|+|+||..||.+-+.. +..||.|...+-.
T Consensus       643 ~LkCs~Cn~R~K---d~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga  690 (698)
T KOG0978|consen  643 LLKCSVCNTRWK---DAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA  690 (698)
T ss_pred             ceeCCCccCchh---hHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence            468999998888   7778889999999999999985 5679999887754

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

Probab=96.90  E-value=0.00074  Score=49.90  Aligned_cols=41  Identities=24%  Similarity=0.728  Sum_probs=28.7

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhcCC--CCCc
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN--SCPV  285 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~--sCPv  285 (358)
                      ...|+|.+..|+  +.++...|+|+|-...|..||+.+.  .||+
T Consensus        11 ~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   11 SLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             -SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             ccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            579999999998  3555568999999999999995443  4998

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

Probab=96.82  E-value=0.00023  Score=51.73  Aligned_cols=46  Identities=26%  Similarity=0.696  Sum_probs=35.9

Q ss_pred             CccccccccccccCCccEEeccCCe-eChhhHHHHHh-cCCCCCccceecc
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHI-YHSECIVPWLR-LHNSCPVCRHEVP  291 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~-FH~~CI~~WL~-~~~sCPvCR~~l~  291 (358)
                      +.+|.||+|.-.   ..+..-|+|. .|..|-...++ .+..||+||.++.
T Consensus         7 ~dECTICye~pv---dsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    7 SDECTICYEHPV---DSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             ccceeeeccCcc---hHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            479999999865   3445569996 57888777666 7889999999874

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

Probab=96.82  E-value=0.00078  Score=67.20  Aligned_cols=48  Identities=35%  Similarity=0.965  Sum_probs=36.6

Q ss_pred             Ccccccccccccc-CC-ccEEeccCCeeChhhHHHHHhcC--CCCCccceec
Q 018299          243 DTTCPVCKEEFKV-GG-EARELACKHIYHSECIVPWLRLH--NSCPVCRHEV  290 (358)
Q Consensus       243 ~~~C~ICle~~~~-~~-~~~~lpC~H~FH~~CI~~WL~~~--~sCPvCR~~l  290 (358)
                      ...|+||++.++. ++ ....+.|+|.|..+||..||...  ..||.|..+-
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~ka   55 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKA   55 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChh
Confidence            5689999998864 33 34555699999999999999522  2499997643

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

Probab=96.78  E-value=0.0003  Score=68.43  Aligned_cols=50  Identities=26%  Similarity=0.654  Sum_probs=42.5

Q ss_pred             CCCccccccccccccCCccEEec-cCCeeChhhHHHHHhcCCCCCccceeccCC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELA-CKHIYHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lp-C~H~FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      .....|.+|...|.   .+.++. |-|.||..||...|+..++||+|...+-..
T Consensus        13 n~~itC~LC~GYli---DATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   13 NPHITCRLCGGYLI---DATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             ccceehhhccceee---cchhHHHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence            34679999999998   455555 999999999999999999999999877554

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

Probab=96.75  E-value=0.00064  Score=68.74  Aligned_cols=53  Identities=28%  Similarity=0.784  Sum_probs=45.0

Q ss_pred             cCCCccccccccccccCCccEE-eccCCeeChhhHHHHHhcCCCCCccceeccCCCC
Q 018299          240 LANDTTCPVCKEEFKVGGEARE-LACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSA  295 (358)
Q Consensus       240 ~~~~~~C~ICle~~~~~~~~~~-lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~~  295 (358)
                      +.++..|+||...+.   .+.. ..|+|.||..||..|+..+..||.|+..+.....
T Consensus        18 ~~~~l~C~~C~~vl~---~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~   71 (391)
T KOG0297|consen   18 LDENLLCPICMSVLR---DPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEE   71 (391)
T ss_pred             CcccccCcccccccc---CCCCCCCCCCcccccccchhhccCcCCcccccccchhhc
Confidence            456789999999998   5555 5899999999999999999999999988765443

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

Probab=96.35  E-value=0.0033  Score=59.95  Aligned_cols=49  Identities=35%  Similarity=0.693  Sum_probs=38.9

Q ss_pred             CCCccccccccccccCCccEEe-ccCCeeChhhHHHHHhcC--CCCCccceeccC
Q 018299          241 ANDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLH--NSCPVCRHEVPV  292 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~~~--~sCPvCR~~l~~  292 (358)
                      ..+.+|++|-+.-.   .+.++ +|+|+||..||..=+...  .+||.|-.++..
T Consensus       237 t~~~~C~~Cg~~Pt---iP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~  288 (298)
T KOG2879|consen  237 TSDTECPVCGEPPT---IPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEP  288 (298)
T ss_pred             cCCceeeccCCCCC---CCeeeccccceeehhhhhhhhcchhhcccCccCCCCcc
Confidence            45789999998866   44444 599999999999977654  579999887764

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

Probab=96.31  E-value=0.0013  Score=58.03  Aligned_cols=40  Identities=28%  Similarity=0.670  Sum_probs=31.2

Q ss_pred             CceeeeccccC-CCccccccccccccCCccEEeccCCeeCh
Q 018299          231 PTVKIMESHLA-NDTTCPVCKEEFKVGGEARELACKHIYHS  270 (358)
Q Consensus       231 p~~~~~~~~~~-~~~~C~ICle~~~~~~~~~~lpC~H~FH~  270 (358)
                      |.+.|....+. ..-+|.||||+++.+++...|||-.+||+
T Consensus       164 PrlsYNdDVL~ddkGECvICLEdL~~GdtIARLPCLCIYHK  204 (205)
T KOG0801|consen  164 PRLSYNDDVLKDDKGECVICLEDLEAGDTIARLPCLCIYHK  204 (205)
T ss_pred             cccccccchhcccCCcEEEEhhhccCCCceeccceEEEeec
Confidence            33444444443 34699999999999999999999999996

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

Probab=96.15  E-value=0.0015  Score=59.50  Aligned_cols=46  Identities=22%  Similarity=0.565  Sum_probs=41.3

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceecc
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVP  291 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~  291 (358)
                      ...|.||..+|+   .++.+.|+|.||..|...-.+....|-+|-+...
T Consensus       196 PF~C~iCKkdy~---spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~  241 (259)
T COG5152         196 PFLCGICKKDYE---SPVVTECGHSFCSLCAIRKYQKGDECGVCGKATY  241 (259)
T ss_pred             ceeehhchhhcc---chhhhhcchhHHHHHHHHHhccCCcceecchhhc
Confidence            468999999999   8889999999999999999999999999977553

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

Probab=95.98  E-value=0.002  Score=64.03  Aligned_cols=48  Identities=31%  Similarity=0.743  Sum_probs=39.4

Q ss_pred             CccccccccccccCC-ccEEeccCCeeChhhHHHHHhcCC--CCCccceec
Q 018299          243 DTTCPVCKEEFKVGG-EARELACKHIYHSECIVPWLRLHN--SCPVCRHEV  290 (358)
Q Consensus       243 ~~~C~ICle~~~~~~-~~~~lpC~H~FH~~CI~~WL~~~~--sCPvCR~~l  290 (358)
                      +..|-.|-+.+...+ ..--|||.|+||..|+...|+.+.  +||-||+-.
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crklr  415 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLR  415 (518)
T ss_pred             hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHH
Confidence            578999999886543 566789999999999999998754  699999533

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

Probab=95.90  E-value=0.0055  Score=60.32  Aligned_cols=48  Identities=27%  Similarity=0.474  Sum_probs=43.2

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      ++..|+||+..-.   .++..||+|.-|+.||.+-|-..+.|=.|+..+..
T Consensus       421 Ed~lCpICyA~pi---~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  421 EDNLCPICYAGPI---NAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             ccccCcceecccc---hhhccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            5789999988766   78889999999999999999999999999998764

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

Probab=95.88  E-value=0.0053  Score=63.19  Aligned_cols=82  Identities=20%  Similarity=0.425  Sum_probs=55.2

Q ss_pred             hHHHHHHHHHhcCCCCCCCCCHHHHHhCCceeeeccccCCCccccccccccccCCccEEeccCCeeChhhHHHHHhc---
Q 018299          203 GMQQLIEEITQNDRPGPPPVPEAAIQAIPTVKIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL---  279 (358)
Q Consensus       203 ~l~~li~~l~~~~~~~~ppas~~~i~~lp~~~~~~~~~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~---  279 (358)
                      .+.+||..|.|....+--. ..++...++..      -....+|-+|-+.-+   ..+...|.|.||..||..++..   
T Consensus       503 nIF~LitRmRQ~aDHP~LV-l~S~~~n~~~e------nk~~~~C~lc~d~ae---d~i~s~ChH~FCrlCi~eyv~~f~~  572 (791)
T KOG1002|consen  503 NIFTLITRMRQAADHPDLV-LYSANANLPDE------NKGEVECGLCHDPAE---DYIESSCHHKFCRLCIKEYVESFME  572 (791)
T ss_pred             HHHHHHHHHHHhccCccee-eehhhcCCCcc------ccCceeecccCChhh---hhHhhhhhHHHHHHHHHHHHHhhhc
Confidence            3667888876654332211 11122222221      124579999999877   7888999999999999998864   


Q ss_pred             --CCCCCccceeccCCC
Q 018299          280 --HNSCPVCRHEVPVSS  294 (358)
Q Consensus       280 --~~sCPvCR~~l~~~~  294 (358)
                        +-+||+|-..|..+.
T Consensus       573 ~~nvtCP~C~i~LsiDl  589 (791)
T KOG1002|consen  573 NNNVTCPVCHIGLSIDL  589 (791)
T ss_pred             ccCCCCccccccccccc
Confidence              336999998887653

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

Probab=95.88  E-value=0.0058  Score=43.28  Aligned_cols=40  Identities=28%  Similarity=0.744  Sum_probs=27.4

Q ss_pred             ccccccccccCCccEEecc--CC---eeChhhHHHHHhc--CCCCCcc
Q 018299          246 CPVCKEEFKVGGEARELAC--KH---IYHSECIVPWLRL--HNSCPVC  286 (358)
Q Consensus       246 C~ICle~~~~~~~~~~lpC--~H---~FH~~CI~~WL~~--~~sCPvC  286 (358)
                      |-||++.-...+ ....||  +-   ..|..|+..|+..  ..+|++|
T Consensus         1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            779999877554 566775  44   7899999999985  3469887

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

Probab=95.73  E-value=0.007  Score=59.03  Aligned_cols=46  Identities=22%  Similarity=0.523  Sum_probs=37.7

Q ss_pred             CCccccccccccccCCccEEec-cCCeeChhhHHHHHhcCCCCCccceec
Q 018299          242 NDTTCPVCKEEFKVGGEARELA-CKHIYHSECIVPWLRLHNSCPVCRHEV  290 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lp-C~H~FH~~CI~~WL~~~~sCPvCR~~l  290 (358)
                      ....|+||+....   .+..+. -|-+||..||...+..++.|||--.+.
T Consensus       299 ~~~~CpvClk~r~---Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~  345 (357)
T KOG0826|consen  299 DREVCPVCLKKRQ---NPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPA  345 (357)
T ss_pred             ccccChhHHhccC---CCceEEecceEEeHHHHHHHHHhcCCCCccCCcc
Confidence            4679999999877   344444 699999999999999999999976654

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

Probab=95.71  E-value=0.0061  Score=68.67  Aligned_cols=51  Identities=31%  Similarity=0.686  Sum_probs=42.1

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhcCC----------CCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN----------SCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~----------sCPvCR~~l~~  292 (358)
                      .++.|.||..+--.....++|.|+|+||..|....|+..-          +||+|+.++..
T Consensus      3485 ~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred             cCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence            4689999998876666889999999999999998887532          59999988754

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

Probab=95.47  E-value=0.0084  Score=60.11  Aligned_cols=47  Identities=21%  Similarity=0.472  Sum_probs=38.6

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhcCC--------CCCcccee
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN--------SCPVCRHE  289 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~--------sCPvCR~~  289 (358)
                      ...|.||+++..-....+.+||.|+||..|+..++..+.        .||-|...
T Consensus       184 lf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C~  238 (445)
T KOG1814|consen  184 LFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKCG  238 (445)
T ss_pred             cccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCCc
Confidence            579999999987557888999999999999999987533        38876553

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

Probab=95.39  E-value=0.0099  Score=55.26  Aligned_cols=51  Identities=24%  Similarity=0.650  Sum_probs=41.4

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhcC--------CCCCccceeccCC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLH--------NSCPVCRHEVPVS  293 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~--------~sCPvCR~~l~~~  293 (358)
                      ....|..|.-.+..++. +.|.|-|+||.+|+..|-..-        ..||.|..++...
T Consensus        49 Y~pNC~LC~t~La~gdt-~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp  107 (299)
T KOG3970|consen   49 YNPNCRLCNTPLASGDT-TRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP  107 (299)
T ss_pred             CCCCCceeCCccccCcc-eeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence            35789999999987764 578899999999999998541        2499999998554

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

Probab=95.24  E-value=0.012  Score=58.21  Aligned_cols=44  Identities=32%  Similarity=0.668  Sum_probs=34.0

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceecc
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVP  291 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~  291 (358)
                      ....|.||+++.+   ..+.+||||.-|  |+.--.. -.+||+||..+.
T Consensus       304 ~p~lcVVcl~e~~---~~~fvpcGh~cc--ct~cs~~-l~~CPvCR~rI~  347 (355)
T KOG1571|consen  304 QPDLCVVCLDEPK---SAVFVPCGHVCC--CTLCSKH-LPQCPVCRQRIR  347 (355)
T ss_pred             CCCceEEecCCcc---ceeeecCCcEEE--chHHHhh-CCCCchhHHHHH
Confidence            3578999999998   689999999976  6555322 234999998763

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

Probab=95.11  E-value=0.012  Score=63.53  Aligned_cols=49  Identities=29%  Similarity=0.767  Sum_probs=36.6

Q ss_pred             CCccccccccccccCCccEEe-ccCCeeChhhHHHHHhcCC-------CCCccceec
Q 018299          242 NDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHN-------SCPVCRHEV  290 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~~~~-------sCPvCR~~l  290 (358)
                      ...+|.||++.+.....+-.- .|-|+||..||..|-+...       .||.|....
T Consensus       190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~  246 (950)
T KOG1952|consen  190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVS  246 (950)
T ss_pred             CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchh
Confidence            357999999998854433222 3999999999999987522       399998543

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

Probab=95.02  E-value=0.0081  Score=57.88  Aligned_cols=46  Identities=20%  Similarity=0.484  Sum_probs=41.7

Q ss_pred             ccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          244 TTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       244 ~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      ..|-||...|.   .++.+.|+|.||..|-..-++....|.+|-+....
T Consensus       242 f~c~icr~~f~---~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g  287 (313)
T KOG1813|consen  242 FKCFICRKYFY---RPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG  287 (313)
T ss_pred             ccccccccccc---cchhhcCCceeehhhhccccccCCcceeccccccc
Confidence            57999999999   88999999999999999998888999999887644

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

Probab=95.01  E-value=0.0083  Score=51.70  Aligned_cols=39  Identities=15%  Similarity=0.447  Sum_probs=31.3

Q ss_pred             CccccccccccccCCccEEeccC------CeeChhhHHHHHhcCC
Q 018299          243 DTTCPVCKEEFKVGGEARELACK------HIYHSECIVPWLRLHN  281 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~------H~FH~~CI~~WL~~~~  281 (358)
                      ..+|.||++.+...+.++.++|+      |.||.+|+..|-+.++
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~   70 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRERN   70 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhhcc
Confidence            46999999999875567777776      8999999999944333

The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.

>PF04641 Rtf2: Rtf2 RING-finger

Probab=94.94  E-value=0.043  Score=52.48  Aligned_cols=93  Identities=15%  Similarity=0.337  Sum_probs=60.6

Q ss_pred             HHHHHHHHHhcCCCCCCCCC---HHHHHhCCceeeeccc------------cCCCccccccccccccCCccEEe-ccCCe
Q 018299          204 MQQLIEEITQNDRPGPPPVP---EAAIQAIPTVKIMESH------------LANDTTCPVCKEEFKVGGEAREL-ACKHI  267 (358)
Q Consensus       204 l~~li~~l~~~~~~~~ppas---~~~i~~lp~~~~~~~~------------~~~~~~C~ICle~~~~~~~~~~l-pC~H~  267 (358)
                      .+.+|+.|......+..+..   ...++.|-.++++...            ......|||...+|......+.| +|||+
T Consensus        59 Keaile~Ll~~~~~~~~~~~~~hI~~LKDl~~l~~~~n~~~~~~~~~~~~~~~~~~~CPvt~~~~~~~~~fv~l~~cG~V  138 (260)
T PF04641_consen   59 KEAILEFLLDKKKNKDLPKTFSHIKSLKDLVELKFTKNPSYKEEDKSSGDNSEGRFICPVTGKEFNGKHKFVYLRPCGCV  138 (260)
T ss_pred             HHHHHHHHHhcCcCCCCccccccccCccceeeEEeEecCccccccccccccCCceeECCCCCcccCCceeEEEEcCCCCE
Confidence            67888888765432222222   2234555555555432            23357999999999644444444 79999


Q ss_pred             eChhhHHHHHhcCCCCCccceeccCCCCCC
Q 018299          268 YHSECIVPWLRLHNSCPVCRHEVPVSSASS  297 (358)
Q Consensus       268 FH~~CI~~WL~~~~sCPvCR~~l~~~~~~~  297 (358)
                      |...+|... .....||+|-.++...+...
T Consensus       139 ~s~~alke~-k~~~~Cp~c~~~f~~~DiI~  167 (260)
T PF04641_consen  139 FSEKALKEL-KKSKKCPVCGKPFTEEDIIP  167 (260)
T ss_pred             eeHHHHHhh-cccccccccCCccccCCEEE
Confidence            999999997 33557999999987554433

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

Probab=94.91  E-value=0.013  Score=41.72  Aligned_cols=44  Identities=27%  Similarity=0.590  Sum_probs=22.1

Q ss_pred             ccccccccccCCccEEec--cCCeeChhhHHHHHh-cCCCCCccceec
Q 018299          246 CPVCKEEFKVGGEARELA--CKHIYHSECIVPWLR-LHNSCPVCRHEV  290 (358)
Q Consensus       246 C~ICle~~~~~~~~~~lp--C~H~FH~~CI~~WL~-~~~sCPvCR~~l  290 (358)
                      |++|.+++... ....+|  |++.++..|...-++ ....||-||.+.
T Consensus         1 cp~C~e~~d~~-d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDET-DKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CC-CTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccC-CCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            78999998433 334455  899999999888876 467899999864

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.88  E-value=0.03  Score=52.81  Aligned_cols=54  Identities=19%  Similarity=0.319  Sum_probs=46.2

Q ss_pred             CccccccccccccCCccEEe-ccCCeeChhhHHHHHhcCCCCCccceeccCCCCC
Q 018299          243 DTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSAS  296 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~~~  296 (358)
                      ...|+||.+.+........| ||+|+|+.+|+.+.++....||+|-.++...+..
T Consensus       221 ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI  275 (303)
T KOG3039|consen  221 RYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDII  275 (303)
T ss_pred             ceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceE
Confidence            46899999999877766666 5999999999999999999999999988766543

>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1

Probab=94.85  E-value=0.014  Score=47.35  Aligned_cols=33  Identities=27%  Similarity=0.615  Sum_probs=27.8

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHH
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIV  274 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~  274 (358)
                      .++..|+||...+.. ......||+|+||..|+.
T Consensus        76 ~~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   76 TESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence            456789999999875 567788999999999974

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

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

Probab=94.74  E-value=0.015  Score=52.24  Aligned_cols=52  Identities=23%  Similarity=0.585  Sum_probs=38.0

Q ss_pred             CccccccccccccCCcc----EEeccCCeeChhhHHHHHhcCC-----------CCCccceeccCCC
Q 018299          243 DTTCPVCKEEFKVGGEA----RELACKHIYHSECIVPWLRLHN-----------SCPVCRHEVPVSS  294 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~----~~lpC~H~FH~~CI~~WL~~~~-----------sCPvCR~~l~~~~  294 (358)
                      ...|-||+..--.|..+    --..|+..||.-|+..||+.--           .||+|..++..+.
T Consensus       165 ~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKm  231 (234)
T KOG3268|consen  165 LGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKM  231 (234)
T ss_pred             hhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeec
Confidence            35799998765554433    2335999999999999997421           2999999886654

>PHA02862 5L protein; Provisional

Probab=94.46  E-value=0.024  Score=49.36  Aligned_cols=47  Identities=17%  Similarity=0.651  Sum_probs=35.5

Q ss_pred             CccccccccccccCCccEEeccC-----CeeChhhHHHHHhcCC--CCCccceeccCC
Q 018299          243 DTTCPVCKEEFKVGGEARELACK-----HIYHSECIVPWLRLHN--SCPVCRHEVPVS  293 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~-----H~FH~~CI~~WL~~~~--sCPvCR~~l~~~  293 (358)
                      +..|-||+++-++  .  .-||.     ...|..|+..|++...  +|++|+.+...+
T Consensus         2 ~diCWIC~~~~~e--~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik   55 (156)
T PHA02862          2 SDICWICNDVCDE--R--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIK   55 (156)
T ss_pred             CCEEEEecCcCCC--C--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEE
Confidence            4689999998542  2  35654     6889999999997543  599999988554

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

Probab=94.33  E-value=0.01  Score=57.04  Aligned_cols=42  Identities=26%  Similarity=0.721  Sum_probs=33.4

Q ss_pred             CccccccccccccCCccEEeccCCee-ChhhHHHHHhcCCCCCccceecc
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIY-HSECIVPWLRLHNSCPVCRHEVP  291 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~F-H~~CI~~WL~~~~sCPvCR~~l~  291 (358)
                      ..-|+||++.-.   ....|+|||.. |..|-...    +.||+||+.+.
T Consensus       300 ~~LC~ICmDaP~---DCvfLeCGHmVtCt~CGkrm----~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDAPR---DCVFLECGHMVTCTKCGKRM----NECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcCCc---ceEEeecCcEEeehhhcccc----ccCchHHHHHH
Confidence            568999999887   88999999964 66675443    47999998764

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=93.89  E-value=0.044  Score=48.55  Aligned_cols=49  Identities=29%  Similarity=0.737  Sum_probs=36.2

Q ss_pred             CCCccccccccccccCCccEEeccC--C---eeChhhHHHHHhcCC--CCCccceeccCC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACK--H---IYHSECIVPWLRLHN--SCPVCRHEVPVS  293 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~--H---~FH~~CI~~WL~~~~--sCPvCR~~l~~~  293 (358)
                      ..+..|-||.++..  +  ..-||.  .   ..|..|+..|+....  +|++|+++....
T Consensus         6 ~~~~~CRIC~~~~~--~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          6 LMDKCCWICKDEYD--V--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCCCeeEecCCCCC--C--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            34789999998843  2  234654  4   569999999998654  599999987553

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

Probab=93.87  E-value=0.0048  Score=61.34  Aligned_cols=51  Identities=29%  Similarity=0.666  Sum_probs=44.4

Q ss_pred             CccccccccccccC-CccEEeccCCeeChhhHHHHHhcCCCCCccceeccCC
Q 018299          243 DTTCPVCKEEFKVG-GEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       243 ~~~C~ICle~~~~~-~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      ...|+||.+.++.. ++...+-|+|.+|.+||.+||.....||.|+.+|+..
T Consensus       196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~  247 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPKN  247 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhhh
Confidence            36899999988755 5777888999999999999999988999999998654

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

Probab=93.81  E-value=0.023  Score=39.56  Aligned_cols=41  Identities=29%  Similarity=0.783  Sum_probs=23.9

Q ss_pred             ccccccccccCCccEEeccCCeeChhhHHHHHhcCC--CCCcc
Q 018299          246 CPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN--SCPVC  286 (358)
Q Consensus       246 C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~--sCPvC  286 (358)
                      |.+|.+.+..|..-..-.|.-.+|..|+..+++...  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            778888887554333334999999999999998766  69987

; PDB: 3NW0_A 2CT0_A.

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

Probab=93.19  E-value=0.054  Score=52.41  Aligned_cols=43  Identities=28%  Similarity=0.692  Sum_probs=35.5

Q ss_pred             CccccccccccccCCccEEec-cCCeeChhhHHHHHh-cCCCCCccce
Q 018299          243 DTTCPVCKEEFKVGGEARELA-CKHIYHSECIVPWLR-LHNSCPVCRH  288 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lp-C~H~FH~~CI~~WL~-~~~sCPvCR~  288 (358)
                      ...|+.|..-+.   .+..++ |+|.||..||..-|. ....||.|..
T Consensus       274 ~LkCplc~~Llr---np~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         274 SLKCPLCHCLLR---NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             cccCcchhhhhh---CcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            479999998887   566666 999999999997665 5668999976

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=93.08  E-value=0.061  Score=39.38  Aligned_cols=46  Identities=22%  Similarity=0.496  Sum_probs=34.1

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccCC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      ...|..|...-.   +...+||+|+.+..|..-+  .-+.||+|-+++...
T Consensus         7 ~~~~~~~~~~~~---~~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~~~   52 (55)
T PF14447_consen    7 EQPCVFCGFVGT---KGTVLPCGHLICDNCFPGE--RYNGCPFCGTPFEFD   52 (55)
T ss_pred             ceeEEEcccccc---ccccccccceeeccccChh--hccCCCCCCCcccCC
Confidence            345666655433   6789999999999997653  667899999887543

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

Probab=92.42  E-value=0.043  Score=51.62  Aligned_cols=45  Identities=20%  Similarity=0.563  Sum_probs=34.8

Q ss_pred             cccccccccccCCccEEeccCCeeChhhHHHHHhcCC-CCCccceeccCC
Q 018299          245 TCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN-SCPVCRHEVPVS  293 (358)
Q Consensus       245 ~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~-sCPvCR~~l~~~  293 (358)
                      .|-.|.-.-. ++....+.|.|+||..|...   .+. .||+|++.+...
T Consensus         5 hCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~---~~~~~C~lCkk~ir~i   50 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLTACRHVFCEPCLKA---SSPDVCPLCKKSIRII   50 (233)
T ss_pred             EeccccccCC-CCceeeeechhhhhhhhccc---CCccccccccceeeee
Confidence            6777766544 66778888999999999766   233 799999987554

>PHA03096 p28-like protein; Provisional

Probab=92.04  E-value=0.065  Score=52.02  Aligned_cols=36  Identities=28%  Similarity=0.494  Sum_probs=28.0

Q ss_pred             ccccccccccccCC----ccEEec-cCCeeChhhHHHHHhc
Q 018299          244 TTCPVCKEEFKVGG----EARELA-CKHIYHSECIVPWLRL  279 (358)
Q Consensus       244 ~~C~ICle~~~~~~----~~~~lp-C~H~FH~~CI~~WL~~  279 (358)
                      ..|.||++......    .-..|+ |.|.||..||..|-..
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~  219 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTE  219 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHh
Confidence            58999999776432    334555 9999999999999865

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

Probab=91.97  E-value=0.1  Score=50.41  Aligned_cols=48  Identities=27%  Similarity=0.644  Sum_probs=40.0

Q ss_pred             CccccccccccccCC---ccEEeccCCeeChhhHHHHHhcCC-CCCccceec
Q 018299          243 DTTCPVCKEEFKVGG---EARELACKHIYHSECIVPWLRLHN-SCPVCRHEV  290 (358)
Q Consensus       243 ~~~C~ICle~~~~~~---~~~~lpC~H~FH~~CI~~WL~~~~-sCPvCR~~l  290 (358)
                      -..|-||-++|...+   .++.|.|+|.|+..|+.+.+.... .||.||...
T Consensus         3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CCceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence            358999999997653   577888999999999999887654 599999985

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

Probab=91.49  E-value=0.14  Score=50.53  Aligned_cols=47  Identities=26%  Similarity=0.684  Sum_probs=39.0

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHH--HhcCCCCCccceecc
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPW--LRLHNSCPVCRHEVP  291 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~W--L~~~~sCPvCR~~l~  291 (358)
                      +...|.||.+.+.   -...+||+|..|.-|-...  |-....||+||.+..
T Consensus        60 en~~C~ICA~~~T---Ys~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~e  108 (493)
T COG5236          60 ENMNCQICAGSTT---YSARYPCGHQICHACAVRLRALYMQKGCPLCRTETE  108 (493)
T ss_pred             ccceeEEecCCce---EEEeccCCchHHHHHHHHHHHHHhccCCCccccccc
Confidence            4578999999988   7889999999999997764  445778999998763

>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function

Probab=90.79  E-value=0.22  Score=44.16  Aligned_cols=34  Identities=35%  Similarity=0.747  Sum_probs=23.9

Q ss_pred             CCccccccccccccCCccEEec------------cCC-eeChhhHHHHHh
Q 018299          242 NDTTCPVCKEEFKVGGEARELA------------CKH-IYHSECIVPWLR  278 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lp------------C~H-~FH~~CI~~WL~  278 (358)
                      ++..|+||||.-.   .++.|-            |+. .-|..|++++-+
T Consensus         1 ed~~CpICme~PH---NAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    1 EDVTCPICMEHPH---NAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CCccCceeccCCC---ceEEEEeccccCCccccccCCccchhHHHHHHHH
Confidence            3678999999876   556663            333 347789998853

The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.

>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=90.54  E-value=0.1  Score=37.05  Aligned_cols=44  Identities=25%  Similarity=0.642  Sum_probs=25.9

Q ss_pred             cccccccccccCCccEEecc-CCeeChhhHHHHHhcCCCCCccceeccCC
Q 018299          245 TCPVCKEEFKVGGEARELAC-KHIYHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       245 ~C~ICle~~~~~~~~~~lpC-~H~FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      .|.-|+-..+     ....| .|..|..|+...|.....||+|.++||.+
T Consensus         4 nCKsCWf~~k-----~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen    4 NCKSCWFANK-----GLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK   48 (50)
T ss_dssp             ---SS-S--S-----SEEE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred             cChhhhhcCC-----CeeeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence            4666665533     34456 49999999999999999999999999874

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.

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

Probab=90.37  E-value=0.11  Score=56.39  Aligned_cols=43  Identities=26%  Similarity=0.743  Sum_probs=34.6

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceec
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEV  290 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l  290 (358)
                      ...|..|--.++.  +.+...|+|.||.+|+.   .....||-|+.++
T Consensus       840 ~skCs~C~~~Ldl--P~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  840 VSKCSACEGTLDL--PFVHFLCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeeecccCCcccc--ceeeeecccHHHHHhhc---cCcccCCccchhh
Confidence            3689999887763  56777899999999998   4556799998844

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

Probab=90.37  E-value=0.25  Score=49.62  Aligned_cols=49  Identities=24%  Similarity=0.451  Sum_probs=42.2

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCC---CCCcccee
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN---SCPVCRHE  289 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~---sCPvCR~~  289 (358)
                      .....|||=.+.-.+.+.++.|.|||+...+-|.+..+...   .||+|=.+
T Consensus       332 HSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e  383 (394)
T KOG2817|consen  332 HSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVE  383 (394)
T ss_pred             cceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence            34579999999998889999999999999999999887655   59999543

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

Probab=90.05  E-value=0.14  Score=49.34  Aligned_cols=46  Identities=33%  Similarity=0.754  Sum_probs=38.7

Q ss_pred             CccccccccccccCC-ccEEeccCCeeChhhHHHHHhcCCCCCccce
Q 018299          243 DTTCPVCKEEFKVGG-EARELACKHIYHSECIVPWLRLHNSCPVCRH  288 (358)
Q Consensus       243 ~~~C~ICle~~~~~~-~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~  288 (358)
                      ...|+||.+.+.... .+..++|+|.-|..|.......+-+||+|.+
T Consensus       158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             cCCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc
Confidence            345999999876554 6778899999999999998888888999988

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

Probab=89.82  E-value=0.13  Score=50.08  Aligned_cols=42  Identities=29%  Similarity=0.738  Sum_probs=29.8

Q ss_pred             cccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceec
Q 018299          245 TCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEV  290 (358)
Q Consensus       245 ~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l  290 (358)
                      .|.-|--.+..  --+.+||+|+||.+|-..  ...+.||.|-..|
T Consensus        92 fCd~Cd~PI~I--YGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen   92 FCDRCDFPIAI--YGRMIPCKHVFCLECARS--DSDKICPLCDDRV  133 (389)
T ss_pred             eecccCCccee--eecccccchhhhhhhhhc--CccccCcCcccHH
Confidence            56667554441  346779999999999654  3456899997655

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

Probab=89.41  E-value=0.15  Score=57.68  Aligned_cols=44  Identities=23%  Similarity=0.680  Sum_probs=38.2

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccce
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRH  288 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~  288 (358)
                      ...|.||++.+.  ....+..|+|.+|..|+..|+..+..||+|+.
T Consensus      1153 ~~~c~ic~dil~--~~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1153 HFVCEICLDILR--NQGGIAGCGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred             ccchHHHHHHHH--hcCCeeeechhHhhhHHHHHHHHhccCcchhh
Confidence            459999999987  24456679999999999999999999999974

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

Probab=89.40  E-value=0.41  Score=33.41  Aligned_cols=34  Identities=24%  Similarity=0.582  Sum_probs=26.9

Q ss_pred             CeeeeeccCcceeecCCCCCCccCCCCCCCceEEE
Q 018299           30 PLYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEI   64 (358)
Q Consensus        30 ~~YwCh~C~r~V~i~~~~~~ei~CP~C~~gFvEEi   64 (358)
                      ..|=|-.|...+.+..... .+.||+|++-++...
T Consensus         2 ~~y~C~~CG~~~~~~~~~~-~~~Cp~CG~~~~~~~   35 (46)
T PRK00398          2 AEYKCARCGREVELDEYGT-GVRCPYCGYRILFKE   35 (46)
T ss_pred             CEEECCCCCCEEEECCCCC-ceECCCCCCeEEEcc
Confidence            4688999999998765432 689999999888543

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

Probab=89.28  E-value=0.6  Score=46.78  Aligned_cols=30  Identities=27%  Similarity=0.876  Sum_probs=23.6

Q ss_pred             cCCeeChhhHHHHHhcCC-------------CCCccceeccCC
Q 018299          264 CKHIYHSECIVPWLRLHN-------------SCPVCRHEVPVS  293 (358)
Q Consensus       264 C~H~FH~~CI~~WL~~~~-------------sCPvCR~~l~~~  293 (358)
                      |...+|.+|+-+|+..+.             .||+||+.+...
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCil  353 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCIL  353 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceee
Confidence            667789999999985432             499999987654

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

>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]

Probab=89.26  E-value=0.26  Score=41.54  Aligned_cols=36  Identities=22%  Similarity=0.609  Sum_probs=27.7

Q ss_pred             CCCeeeeeccCcceeecCCCCCCccCCCCCCCceEEEcc
Q 018299           28 NYPLYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEIEI   66 (358)
Q Consensus        28 t~~~YwCh~C~r~V~i~~~~~~ei~CP~C~~gFvEEi~~   66 (358)
                      -....||..|++.+....   .+..||.|++..+.-+..
T Consensus        67 ~p~~~~C~~C~~~~~~e~---~~~~CP~C~s~~~~i~~G  102 (115)
T COG0375          67 EPAECWCLDCGQEVELEE---LDYRCPKCGSINLRIIGG  102 (115)
T ss_pred             eccEEEeccCCCeecchh---heeECCCCCCCceEEecC
Confidence            357899999999887443   346899999998876653

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

Probab=89.12  E-value=0.15  Score=55.23  Aligned_cols=49  Identities=20%  Similarity=0.527  Sum_probs=40.5

Q ss_pred             ccccccccccccCCccEEeccCCeeChhhHHHHHhcCC--CCCccceeccCCCCC
Q 018299          244 TTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN--SCPVCRHEVPVSSAS  296 (358)
Q Consensus       244 ~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~--sCPvCR~~l~~~~~~  296 (358)
                      ..|.||++ .   +.+...+|+|.||..|+..-++...  .||+||..+..+...
T Consensus       455 ~~c~ic~~-~---~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l~  505 (674)
T KOG1001|consen  455 HWCHICCD-L---DSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKLL  505 (674)
T ss_pred             cccccccc-c---ccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHHh
Confidence            79999999 3   3788889999999999999987643  499999988665443

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=88.14  E-value=0.42  Score=34.93  Aligned_cols=33  Identities=33%  Similarity=0.771  Sum_probs=29.0

Q ss_pred             CccccccccccccCCccEEec-cCCeeChhhHHH
Q 018299          243 DTTCPVCKEEFKVGGEARELA-CKHIYHSECIVP  275 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lp-C~H~FH~~CI~~  275 (358)
                      ...|.+|-+.|+.++.+++-| |+-.||..|...
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            568999999999888888888 999999999544

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.01  E-value=0.88  Score=44.14  Aligned_cols=100  Identities=20%  Similarity=0.436  Sum_probs=52.0

Q ss_pred             CCCCCCCCccccchhHHHHHHHHHhcCCCCCCCCCHHHHHhC---CceeeeccccCCCccccccc-ccc--ccCCccEEe
Q 018299          189 LPPGVNPRDYFLGQGMQQLIEEITQNDRPGPPPVPEAAIQAI---PTVKIMESHLANDTTCPVCK-EEF--KVGGEAREL  262 (358)
Q Consensus       189 ~~~~~~~~d~~~~~~l~~li~~l~~~~~~~~ppas~~~i~~l---p~~~~~~~~~~~~~~C~ICl-e~~--~~~~~~~~l  262 (358)
                      +|+.+++.--|+..-.+..+++++++.-.....+++.-..-.   +.+|+       +..|.-=- ..+  ..|....-.
T Consensus       251 vp~~i~~~~~~~~~~~~~f~~~ia~n~v~~~~~~sekcfac~~~e~~~ki-------~~~c~~~~~~~~~~~~ga~c~nc  323 (381)
T KOG3899|consen  251 VPPHINVPLTFMEELKEDFIQRIASNTVTHRVKASEKCFACGTEENMVKI-------ERSCDGQEQRVFFHDIGAPCENC  323 (381)
T ss_pred             cCCcccccHHHHHHHHHHHHHHHhcCCCCcccchhhhhHhhccCCCchhh-------hhcccchhhcccccccCCccccc
Confidence            466666665566666677777777776433333333322221   11111       22231000 000  011111112


Q ss_pred             ccCCeeChhhHHHHHh-------------cCCCCCccceeccCCCC
Q 018299          263 ACKHIYHSECIVPWLR-------------LHNSCPVCRHEVPVSSA  295 (358)
Q Consensus       263 pC~H~FH~~CI~~WL~-------------~~~sCPvCR~~l~~~~~  295 (358)
                      -|...+|..|+..|+.             .+-+||+||+.+...+.
T Consensus       324 ~crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~dv  369 (381)
T KOG3899|consen  324 ICRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRDV  369 (381)
T ss_pred             ccccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEeee
Confidence            2677889999999873             34469999999876543

>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Probab=86.43  E-value=0.72  Score=30.10  Aligned_cols=29  Identities=28%  Similarity=0.773  Sum_probs=22.0

Q ss_pred             eeeeccCcceeecCCCCCCccCCCCCCCceE
Q 018299           32 YWCYQCHRAVRISSTNPSEIACPRCSGHFVS   62 (358)
Q Consensus        32 YwCh~C~r~V~i~~~~~~ei~CP~C~~gFvE   62 (358)
                      |-|-.|...|.+...+  .|.||+|+...+.
T Consensus         1 Y~C~~Cg~~~~~~~~~--~irC~~CG~RIly   29 (32)
T PF03604_consen    1 YICGECGAEVELKPGD--PIRCPECGHRILY   29 (32)
T ss_dssp             EBESSSSSSE-BSTSS--TSSBSSSS-SEEB
T ss_pred             CCCCcCCCeeEcCCCC--cEECCcCCCeEEE
Confidence            7799999999987665  4899999986553

Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....

>TIGR00100 hypA hydrogenase nickel insertion protein HypA

Probab=86.19  E-value=0.63  Score=39.12  Aligned_cols=34  Identities=21%  Similarity=0.408  Sum_probs=25.7

Q ss_pred             CCCeeeeeccCcceeecCCCCCCccCCCCCCCceEEE
Q 018299           28 NYPLYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEI   64 (358)
Q Consensus        28 t~~~YwCh~C~r~V~i~~~~~~ei~CP~C~~gFvEEi   64 (358)
                      .....||..|...+.+...   ...||.|++..++-+
T Consensus        67 ~p~~~~C~~Cg~~~~~~~~---~~~CP~Cgs~~~~i~  100 (115)
T TIGR00100        67 EPVECECEDCSEEVSPEID---LYRCPKCHGIMLQVR  100 (115)
T ss_pred             eCcEEEcccCCCEEecCCc---CccCcCCcCCCcEEe
Confidence            4678999999987775432   368999999876544

In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.

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

Probab=86.01  E-value=0.48  Score=40.85  Aligned_cols=49  Identities=31%  Similarity=0.581  Sum_probs=37.9

Q ss_pred             CccccccccccccCCccEEe-c---cCCeeChhhHHHHHhc---CCCCCccceeccCCC
Q 018299          243 DTTCPVCKEEFKVGGEAREL-A---CKHIYHSECIVPWLRL---HNSCPVCRHEVPVSS  294 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~l-p---C~H~FH~~CI~~WL~~---~~sCPvCR~~l~~~~  294 (358)
                      -.+|.||.|...   +.+.| |   ||-..|.-|-...++.   +..||+|+..++...
T Consensus        80 lYeCnIC~etS~---ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~  135 (140)
T PF05290_consen   80 LYECNICKETSA---EERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS  135 (140)
T ss_pred             ceeccCcccccc---hhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence            579999999876   44455 3   9999999988877765   456999999886543

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=84.89  E-value=0.73  Score=39.87  Aligned_cols=35  Identities=14%  Similarity=0.426  Sum_probs=24.8

Q ss_pred             CCCeeeeeccCcceeecC--C----------------CCCCccCCCCCCCceE
Q 018299           28 NYPLYWCYQCHRAVRISS--T----------------NPSEIACPRCSGHFVS   62 (358)
Q Consensus        28 t~~~YwCh~C~r~V~i~~--~----------------~~~ei~CP~C~~gFvE   62 (358)
                      ....|||..|...+.+..  .                ......||.|++.-++
T Consensus        67 ~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~  119 (135)
T PRK03824         67 EEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFE  119 (135)
T ss_pred             cceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcE
Confidence            458899999998877641  0                0123579999987655

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=84.81  E-value=0.82  Score=38.39  Aligned_cols=35  Identities=23%  Similarity=0.698  Sum_probs=25.0

Q ss_pred             CCCeeeeeccCcceeecCCCCCCccCCCCCCCceEEE
Q 018299           28 NYPLYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEI   64 (358)
Q Consensus        28 t~~~YwCh~C~r~V~i~~~~~~ei~CP~C~~gFvEEi   64 (358)
                      .....||..|...+.+....  -..||.|++..++-+
T Consensus        67 ~p~~~~C~~Cg~~~~~~~~~--~~~CP~Cgs~~~~i~  101 (114)
T PRK03681         67 QEAECWCETCQQYVTLLTQR--VRRCPQCHGDMLRIV  101 (114)
T ss_pred             eCcEEEcccCCCeeecCCcc--CCcCcCcCCCCcEEc
Confidence            47899999999877643221  256999998765543

>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional

Probab=84.56  E-value=0.86  Score=38.21  Aligned_cols=34  Identities=26%  Similarity=0.762  Sum_probs=25.0

Q ss_pred             CCCeeeeeccCcceeecCCCCCCccCCCCCCCceEEE
Q 018299           28 NYPLYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEI   64 (358)
Q Consensus        28 t~~~YwCh~C~r~V~i~~~~~~ei~CP~C~~gFvEEi   64 (358)
                      ....+||..|.....+...   ...||.|++.-++-+
T Consensus        67 vp~~~~C~~Cg~~~~~~~~---~~~CP~Cgs~~~~i~  100 (113)
T PRK12380         67 KPAQAWCWDCSQVVEIHQH---DAQCPHCHGERLRVD  100 (113)
T ss_pred             eCcEEEcccCCCEEecCCc---CccCcCCCCCCcEEc
Confidence            4688999999987765432   357999998765543

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=83.48  E-value=0.6  Score=42.28  Aligned_cols=35  Identities=20%  Similarity=0.593  Sum_probs=26.5

Q ss_pred             CCCeeeeeccCcceeecCCCCCCccCCCCCCCceE
Q 018299           28 NYPLYWCYQCHRAVRISSTNPSEIACPRCSGHFVS   62 (358)
Q Consensus        28 t~~~YwCh~C~r~V~i~~~~~~ei~CP~C~~gFvE   62 (358)
                      +...|.|-.|.+.+...--...++.||.|++-+++
T Consensus       114 ~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~  148 (178)
T PRK06266        114 NNMFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEE  148 (178)
T ss_pred             CCCEEECCCCCcEEeHHHHhhcCCcCCCCCCCCee
Confidence            34789999999877753222347999999998877

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

Probab=83.34  E-value=0.67  Score=50.43  Aligned_cols=55  Identities=22%  Similarity=0.596  Sum_probs=41.5

Q ss_pred             CCccccccccccccCCccEEeccC-----CeeChhhHHHHHhcCC--CCCccceeccCCCCCC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACK-----HIYHSECIVPWLRLHN--SCPVCRHEVPVSSASS  297 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~-----H~FH~~CI~~WL~~~~--sCPvCR~~l~~~~~~~  297 (358)
                      ++..|-||..+-..++ +..-||+     ...|..|+..|+.-..  .|-+|..++.-++-..
T Consensus        11 d~~~CRICr~e~~~d~-pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~IY~   72 (1175)
T COG5183          11 DKRSCRICRTEDIRDD-PLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDIYK   72 (1175)
T ss_pred             cchhceeecCCCCCCC-cCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeeecc
Confidence            4689999998866444 4455776     4589999999998654  4999999987765433

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

Probab=83.29  E-value=0.51  Score=51.78  Aligned_cols=38  Identities=18%  Similarity=0.586  Sum_probs=30.5

Q ss_pred             ccCCCccccccccccccCCccEEeccCCeeChhhHHHHH
Q 018299          239 HLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWL  277 (358)
Q Consensus       239 ~~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL  277 (358)
                      .++..+.|.+|...+-. ..-...||+|.||.+||..-.
T Consensus       813 v~ep~d~C~~C~~~ll~-~pF~vf~CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  813 VLEPQDSCDHCGRPLLI-KPFYVFPCGHCFHRDCLIRHV  850 (911)
T ss_pred             EecCccchHHhcchhhc-CcceeeeccchHHHHHHHHHH
Confidence            34567899999887763 366777999999999998875

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=83.17  E-value=0.7  Score=45.66  Aligned_cols=53  Identities=21%  Similarity=0.505  Sum_probs=37.1

Q ss_pred             CCccccccccccccCCcc-EEeccCCeeChhhHHHHHh-cCCCCCccceeccCCC
Q 018299          242 NDTTCPVCKEEFKVGGEA-RELACKHIYHSECIVPWLR-LHNSCPVCRHEVPVSS  294 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~-~~lpC~H~FH~~CI~~WL~-~~~sCPvCR~~l~~~~  294 (358)
                      +++.|+.|++.+...++- .-.+||-..|.-|...--+ .+..||-||.......
T Consensus        13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~den   67 (480)
T COG5175          13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDEN   67 (480)
T ss_pred             ccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccc
Confidence            456699999999876643 3346888888888655433 3557999999775443

>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=83.09  E-value=0.67  Score=28.76  Aligned_cols=23  Identities=35%  Similarity=0.745  Sum_probs=17.9

Q ss_pred             eeccCcceeecCCCCCCccCCCCCCCce
Q 018299           34 CYQCHRAVRISSTNPSEIACPRCSGHFV   61 (358)
Q Consensus        34 Ch~C~r~V~i~~~~~~ei~CP~C~~gFv   61 (358)
                      |-.|...|.+..     .+||+|+-.|.
T Consensus         3 CP~C~~~V~~~~-----~~Cp~CG~~F~   25 (26)
T PF10571_consen    3 CPECGAEVPESA-----KFCPHCGYDFE   25 (26)
T ss_pred             CCCCcCCchhhc-----CcCCCCCCCCc
Confidence            778999886433     59999998874

Several members are annotated as putative helicases.

>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation

Probab=82.69  E-value=0.69  Score=38.71  Aligned_cols=34  Identities=24%  Similarity=0.461  Sum_probs=22.6

Q ss_pred             CCCeeeeeccCcceeecCCCCCCccCCCCCCCceEEE
Q 018299           28 NYPLYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEI   64 (358)
Q Consensus        28 t~~~YwCh~C~r~V~i~~~~~~ei~CP~C~~gFvEEi   64 (358)
                      .....||..|.....+...   ...||.|++..++-+
T Consensus        67 ~p~~~~C~~Cg~~~~~~~~---~~~CP~Cgs~~~~i~  100 (113)
T PF01155_consen   67 VPARARCRDCGHEFEPDEF---DFSCPRCGSPDVEII  100 (113)
T ss_dssp             E--EEEETTTS-EEECHHC---CHH-SSSSSS-EEEE
T ss_pred             cCCcEECCCCCCEEecCCC---CCCCcCCcCCCcEEc
Confidence            3678999999998875543   378999999977544

The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.

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

Probab=82.37  E-value=0.96  Score=43.80  Aligned_cols=48  Identities=23%  Similarity=0.571  Sum_probs=36.3

Q ss_pred             cccccccccccCCccEEe--ccCCeeChhhHHHHHhcCC-CCCccceeccC
Q 018299          245 TCPVCKEEFKVGGEAREL--ACKHIYHSECIVPWLRLHN-SCPVCRHEVPV  292 (358)
Q Consensus       245 ~C~ICle~~~~~~~~~~l--pC~H~FH~~CI~~WL~~~~-sCPvCR~~l~~  292 (358)
                      .|++|..+....-.++.|  +|+|..|..|+..-+.... .||.|-..|-.
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk   52 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRK   52 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhh
Confidence            599998866544444443  6999999999999887654 69999876644

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

Probab=82.31  E-value=0.32  Score=52.24  Aligned_cols=47  Identities=28%  Similarity=0.734  Sum_probs=39.3

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhcCC---CCCccceeccC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN---SCPVCRHEVPV  292 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~---sCPvCR~~l~~  292 (358)
                      ..+|+||+..+.   ....+.|.|.|+..|+..-|...+   .||+|+..+..
T Consensus        21 ~lEc~ic~~~~~---~p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK   70 (684)
T KOG4362|consen   21 ILECPICLEHVK---EPSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIEK   70 (684)
T ss_pred             hccCCceeEEee---ccchhhhhHHHHhhhhhceeeccCccccchhhhhhhhh
Confidence            679999999998   557888999999999998887655   49999965543

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

Probab=81.80  E-value=0.99  Score=44.23  Aligned_cols=44  Identities=27%  Similarity=0.591  Sum_probs=33.7

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceecc
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVP  291 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~  291 (358)
                      -.+|+||.+.+..  ...+-.=||+-|..|-.   +..+.||.||.++.
T Consensus        48 lleCPvC~~~l~~--Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   48 LLDCPVCFNPLSP--PIFQCDNGHLACSSCRT---KVSNKCPTCRLPIG   91 (299)
T ss_pred             hccCchhhccCcc--cceecCCCcEehhhhhh---hhcccCCccccccc
Confidence            4799999999882  22333347999999876   46788999999886

>smart00659 RPOLCX RNA polymerase subunit CX

Probab=81.67  E-value=1.3  Score=30.91  Aligned_cols=33  Identities=24%  Similarity=0.590  Sum_probs=26.8

Q ss_pred             eeeeeccCcceeecCCCCCCccCCCCCCCceEEEc
Q 018299           31 LYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEIE   65 (358)
Q Consensus        31 ~YwCh~C~r~V~i~~~~~~ei~CP~C~~gFvEEi~   65 (358)
                      .|=|-.|...|.+...  ..+.||+|+...+...-
T Consensus         2 ~Y~C~~Cg~~~~~~~~--~~irC~~CG~rIlyK~R   34 (44)
T smart00659        2 IYICGECGRENEIKSK--DVVRCRECGYRILYKKR   34 (44)
T ss_pred             EEECCCCCCEeecCCC--CceECCCCCceEEEEeC
Confidence            4889999999997743  35999999998886654

present in RNA polymerase I, II and III

>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=81.33  E-value=0.45  Score=50.52  Aligned_cols=43  Identities=28%  Similarity=0.598  Sum_probs=33.1

Q ss_pred             CccccccccccccCC-ccEEeccCCeeChhhHHHHHhcCCCCCccce
Q 018299          243 DTTCPVCKEEFKVGG-EARELACKHIYHSECIVPWLRLHNSCPVCRH  288 (358)
Q Consensus       243 ~~~C~ICle~~~~~~-~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~  288 (358)
                      -..|.||+..|.... .++.|-|+|..|..|+..-  .+.+|| |++
T Consensus        11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~   54 (861)
T KOG3161|consen   11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKR   54 (861)
T ss_pred             HhhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCc
Confidence            468999988876443 5677789999999999875  456788 554

>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional

Probab=80.91  E-value=1.1  Score=38.14  Aligned_cols=36  Identities=17%  Similarity=0.278  Sum_probs=24.3

Q ss_pred             CCCeeeeeccCcceeecCCCC--C--CccCCCCCCCceEEE
Q 018299           28 NYPLYWCYQCHRAVRISSTNP--S--EIACPRCSGHFVSEI   64 (358)
Q Consensus        28 t~~~YwCh~C~r~V~i~~~~~--~--ei~CP~C~~gFvEEi   64 (358)
                      -....|| .|.....+.....  -  -..||.|++..++-+
T Consensus        67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~  106 (124)
T PRK00762         67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHIL  106 (124)
T ss_pred             cCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEe
Confidence            4678999 9998766532111  0  146999998876644

>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional

Probab=80.80  E-value=1.3  Score=37.40  Aligned_cols=35  Identities=14%  Similarity=0.266  Sum_probs=24.9

Q ss_pred             CCCeeeeeccCcceeecCCCCCCccCCCCCCCceEEE
Q 018299           28 NYPLYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEI   64 (358)
Q Consensus        28 t~~~YwCh~C~r~V~i~~~~~~ei~CP~C~~gFvEEi   64 (358)
                      ....+||..|...+.+...  ....||.|++..++-+
T Consensus        68 vp~~~~C~~Cg~~~~~~~~--~~~~CP~Cgs~~~~i~  102 (117)
T PRK00564         68 EKVELECKDCSHVFKPNAL--DYGVCEKCHSKNVIIT  102 (117)
T ss_pred             cCCEEEhhhCCCccccCCc--cCCcCcCCCCCceEEe
Confidence            4688999999976654322  1235999999877644

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

Probab=80.20  E-value=0.99  Score=48.87  Aligned_cols=28  Identities=29%  Similarity=0.782  Sum_probs=24.2

Q ss_pred             ccEEeccCCeeChhhHHHHHhcCCCCCc
Q 018299          258 EARELACKHIYHSECIVPWLRLHNSCPV  285 (358)
Q Consensus       258 ~~~~lpC~H~FH~~CI~~WL~~~~sCPv  285 (358)
                      ......|+|+.|.+|...|++....||.
T Consensus      1042 s~~Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1042 SNFCGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             chhhccccccccHHHHHHHHhcCCcCCC
Confidence            3445579999999999999999999986

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	358
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		2e-12
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		6e-09
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		7e-06
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		6e-05
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		7e-05
4ayc_B	138	Rnf8 Ring Domain Structure Length = 138		9e-04

>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring Finger) Domain Of Ring Finger Protein 126 Length = 78

Iteration: 1
 Score = 70.1 bits (170), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 37/55 (67%)
Query: 236 MESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEV 290
            E H+ +   CPVCKE++ +G   R+L C H++H  CIVPWL  H+SCPVCR  +
Sbjct: 8   TEEHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSL 62

>pdb|2L0B|A Chain A, Solution Nmr Structure Of Zinc Finger Domain Of E3 Ubiquitin-Protein Ligase Praja-1 From Homo Sapiens, Northeast Structural Genomics Consortium (Nesg) Target Hr4710b Length = 91

Iteration: 1
 Score = 58.5 bits (140), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 220 PPVPEAAIQAIPTVKIMESH--LANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWL 277
           PP  + +I A+P + + E H  +  +  CP+C  E+  G  A EL C H +H  C+  WL
Sbjct: 15  PPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWL 74
Query: 278 RLHNSCPVCRHEVP 291
           +   +CPVCR   P
Sbjct: 75  QKSGTCPVCRCMFP 88

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 22/46 (47%), Positives = 29/46 (63%), Gaps = 1/46 (2%)
Query: 246 CPVCKEEFKVGGEARELA-CKHIYHSECIVPWLRLHNSCPVCRHEV 290
           C VC  E + G EAR L  C H +H+EC+  WL  H++CP+CR  V
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger Protein 24 Length = 74

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 18/45 (40%), Positives = 25/45 (55%)
Query: 246 CPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEV 290
           C VC E+FK   E     CKH +H +C++ WL +   CP+C   V
Sbjct: 18  CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPV 62

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 18/52 (34%), Positives = 31/52 (59%)
Query: 238 SHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHE 289
           +H +  T C VC  +F+     R L C H +H++C+  WL+ + +CP+CR +
Sbjct: 18  NHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRAD 69

>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure Length = 138

Iteration: 1
 Score = 41.2 bits (95), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 236 MESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVP 291
           M   L N+  C +C E F    EA  L C H + S CI  W++    CP+CR ++ 
Sbjct: 46  MNDVLENELQCIICSEYF---IEAVTLNCAHSFCSYCINEWMKRKIECPICRKDIK 98

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	358
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	8e-38
2ect_A	78	Ring finger protein 126; metal binding protein, st	4e-28
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	5e-24
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	2e-22
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	3e-22
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	4e-19
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	9e-18
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	2e-17
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	9e-16
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-13
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	3e-12
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	3e-12
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	5e-12
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	1e-10
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	3e-09
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	3e-09
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	7e-09
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	2e-08
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	8e-08
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	8e-08
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	1e-07
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	2e-07
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	4e-07
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	4e-07
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	5e-06
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	5e-07
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	5e-07
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	2e-06
1z6u_A	150	NP95-like ring finger protein isoform B; structura	2e-06
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	3e-06
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	3e-06
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	7e-06
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	2e-05
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	2e-05
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	3e-05
3nw0_A	238	Non-structural maintenance of chromosomes element	3e-05
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	9e-05
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	1e-04
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	1e-04
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	1e-04
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	2e-04
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	2e-04
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	4e-04
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	6e-04
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	7e-04

>2l0b_A E3 ubiquitin-protein ligase praja-1; zinc finger, NESG, structural genomics, PSI-2, protein struc initiative; NMR {Homo sapiens} Length = 91

 Score =  129 bits (327), Expect = 8e-38
 Identities = 29/90 (32%), Positives = 42/90 (46%), Gaps = 4/90 (4%)

Query: 204 MQQLIEEITQNDRPGPPPVPEAAIQAIPTVKIMESHLA--NDTTCPVCKEEFKVGGEARE 261
           M         +     PP  + +I A+P + + E H A   +  CP+C  E+  G  A E
Sbjct: 1   MGHHHH--HHSHMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATE 58

Query: 262 LACKHIYHSECIVPWLRLHNSCPVCRHEVP 291
           L C H +H  C+  WL+   +CPVCR   P
Sbjct: 59  LPCHHYFHKPCVSIWLQKSGTCPVCRCMFP 88

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 78

 Score =  104 bits (260), Expect = 4e-28
 Identities = 27/62 (43%), Positives = 41/62 (66%)

Query: 237 ESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSAS 296
           E H+ +   CPVCKE++ +G   R+L C H++H  CIVPWL  H+SCPVCR  +   + +
Sbjct: 9   EEHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTA 68

Query: 297 SS 298
           ++
Sbjct: 69  TN 70

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

 Score = 93.2 bits (232), Expect = 5e-24
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 225 AAIQAIPTVKI-MESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSC 283
            +   +P+ +    +H +  T C VC  +F+     R L C H +H++C+  WL+ + +C
Sbjct: 4   GSSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTC 63

Query: 284 PVCRHEVPVSSA 295
           P+CR +   SS 
Sbjct: 64  PICRADSGPSSG 75

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

 Score = 88.2 bits (219), Expect = 2e-22
 Identities = 17/57 (29%), Positives = 28/57 (49%)

Query: 242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSASSS 298
            +  C +C    + G + R L C H++H  C+  WL  +  CP+CR ++     S S
Sbjct: 13  TEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQLPSES 69

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

 Score = 88.3 bits (219), Expect = 3e-22
 Identities = 20/62 (32%), Positives = 28/62 (45%)

Query: 237 ESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSAS 296
              L     C VC E+FK   E     CKH +H +C++ WL +   CP+C   V   +  
Sbjct: 9   VKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQL 68

Query: 297 SS 298
           S 
Sbjct: 69  SG 70

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

 Score = 79.4 bits (196), Expect = 4e-19
 Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 4/62 (6%)

Query: 237 ESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSAS 296
              L ++  C +C +          L C H +  +CI  W   H +CP+CR ++  ++ S
Sbjct: 9   VKQLTDEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANES 64

Query: 297 SS 298
           S 
Sbjct: 65  SG 66

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A Length = 55

 Score = 75.4 bits (186), Expect = 9e-18
 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 1/51 (1%)

Query: 241 ANDTTCPVCKEEFKVGGE-ARELACKHIYHSECIVPWLRLHNSCPVCRHEV 290
           +  + CP+C E+       A  L C H+ H  C    L+    CP+C    
Sbjct: 3   SGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPS 53

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

 Score = 74.2 bits (183), Expect = 2e-17
 Identities = 23/52 (44%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 242 NDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHNSCPVCRHEVPV 292
           +   C VC  E + G EAR L  C H +H+EC+  WL  H++CP+CR  V V
Sbjct: 4   DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV 55

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

 Score = 70.1 bits (172), Expect = 9e-16
 Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 6/69 (8%)

Query: 241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSASSSHD 300
                CP+C E+      +  L C H +   CI  W+R + +CP+C+  V     S  H 
Sbjct: 3   TVAERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNPTCPLCKVPV----ESVVHT 56

Query: 301 VDSDDEHGD 309
           ++SD E GD
Sbjct: 57  IESDSEFGD 65

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

 Score = 63.8 bits (155), Expect = 2e-13
 Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 4/54 (7%)

Query: 241 ANDTTCPVCKEEFK----VGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEV 290
           +   +CP+C + +      G       C H++ S+C+   L+  N+CP CR ++
Sbjct: 13  SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66

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

 Score = 60.2 bits (146), Expect = 3e-12
 Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 4/56 (7%)

Query: 243 DTTCPVCKEEFKVGGEARE----LACKHIYHSECIVPWLRLHNSCPVCRHEVPVSS 294
             +CP+C + +    +         C H++ S+C+   L+  N+CP CR ++    
Sbjct: 3   MVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR 58

>3ng2_A RNF4, snurf, ring finger protein 4; ring domain, E3 ligase, ubiquitylation, sumoylation, zinc-FI metal binding protein; 1.80A {Rattus norvegicus} Length = 71

 Score = 60.2 bits (146), Expect = 3e-12
 Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 4/58 (6%)

Query: 241 ANDTTCPVCKEEFKVGGEARE----LACKHIYHSECIVPWLRLHNSCPVCRHEVPVSS 294
           +   +CP+C + +    +         C H++ S+C+   L+  N+CP CR ++    
Sbjct: 8   SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR 65

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

 Score = 60.3 bits (146), Expect = 5e-12
 Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 243 DTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHNSCPVCRHE 289
              C  C+ E K          C H +H+ C+  W++ +N CP+C+ +
Sbjct: 26  MDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQD 73

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

 Score = 55.9 bits (135), Expect = 1e-10
 Identities = 18/78 (23%), Positives = 29/78 (37%), Gaps = 12/78 (15%)

Query: 225 AAIQAIPTVKIMESHLANDTTCPVCKEEFKVGGEARELA-CKHIYHSECIVPWLRLHNSC 283
            +  +   +  +  ++     C +CK       +A  +  C H +   CIV      N C
Sbjct: 1   GSSGSSGNLSELTPYI----LCSICKGYLI---DATTITECLHTFCKSCIVRHFYYSNRC 53

Query: 284 PVCRHEV----PVSSASS 297
           P C   V    P+S  SS
Sbjct: 54  PKCNIVVHQTQPLSGPSS 71

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

 Score = 52.5 bits (126), Expect = 3e-09
 Identities = 9/46 (19%), Positives = 17/46 (36%), Gaps = 3/46 (6%)

Query: 245 TCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEV 290
            C +C++ F+         C+H +   C +   R    C +C    
Sbjct: 17  RCFICRQAFQ---NPVVTKCRHYFCESCALEHFRATPRCYICDQPT 59

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

 Score = 52.9 bits (127), Expect = 3e-09
 Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 4/60 (6%)

Query: 232 TVKIMESHLANDTTCPVCKEEFKVGGEARELA-CKHIYHSECIVPWLRLHNSCPVCRHEV 290
           T +I  + L     C +C   F    +A  +  C H +   CIV +L     CP+C  +V
Sbjct: 4   TTRIKITELNPHLMCVLCGGYFI---DATTIIECLHSFCKTCIVRYLETSKYCPICDVQV 60

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

 Score = 51.0 bits (122), Expect = 7e-09
 Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 3/52 (5%)

Query: 240 LANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVP 291
                 C +C +          L CKH++   C+     L   C +CR E+P
Sbjct: 12  SLTVPECAICLQTCV---HPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIP 60

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens} Length = 100

 Score = 50.7 bits (121), Expect = 2e-08
 Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 5/59 (8%)

Query: 238 SHLANDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHN-SCPVCRHEVPVSS 294
             +A    C +C E+ +   +AR    C  +    CI  WL      CP CR  + +  
Sbjct: 17  ESIAEVFRCFICMEKLR---DARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRE 72

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

 Score = 50.0 bits (119), Expect = 8e-08
 Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 3/56 (5%)

Query: 236 MESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVP 291
           M   L N+  C +C E F    EA  L C H + S CI  W++    CP+CR ++ 
Sbjct: 57  MNDVLENELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIECPICRKDIK 109

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

 Score = 49.0 bits (117), Expect = 8e-08
 Identities = 18/76 (23%), Positives = 25/76 (32%), Gaps = 8/76 (10%)

Query: 220 PPVPEAAIQAIPTVKIMESHLANDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLR 278
                     +  +K ++  L     C +C E F     A  +  C H Y S CI  +L 
Sbjct: 3   SLAESRWPPGLAVMKTIDDLL----RCGICFEYFN---IAMIIPQCSHNYCSLCIRKFLS 55

Query: 279 LHNSCPVCRHEVPVSS 294
               CP C   V    
Sbjct: 56  YKTQCPTCCVTVTEPD 71

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 74

 Score = 47.6 bits (113), Expect = 1e-07
 Identities = 15/59 (25%), Positives = 21/59 (35%), Gaps = 8/59 (13%)

Query: 245 TCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNS--CPVCR----HEVPVSSASS 297
            C +C      G       C    H  C+  + + +    CP C     HE+P S  SS
Sbjct: 17  ICNICHSLLIQGQSCET--CGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIPKSGPSS 73

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

 Score = 51.8 bits (123), Expect = 2e-07
 Identities = 18/145 (12%), Positives = 40/145 (27%), Gaps = 30/145 (20%)

Query: 186 QNPLPPGVNPRDYFLG--QGMQQLIEEITQNDRPGPP------------PVPEAAIQAIP 231
            +P     +     +G  + + +L   ++                     +    +    
Sbjct: 237 ADPFACIASMSLKIIGPTEEVARLRHVLSDGLSNWDSEMNIHKNLLRMFDLCYFPMPDWS 296

Query: 232 TVKIMESHLANDTTCPVCKEEFKVGGEARE-----LACKHIYHSECIVPWLR-------- 278
               ++     +  C +C      GGE          C    H+ C+  W +        
Sbjct: 297 DGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTF 356

Query: 279 ---LHNSCPVCRHEVPVSSASSSHD 300
                  CP C+ ++  S A+  +D
Sbjct: 357 LEVSFGQCPFCKAKLSTSFAALLND 381

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1 Length = 114

 Score = 47.1 bits (111), Expect = 4e-07
 Identities = 18/92 (19%), Positives = 28/92 (30%), Gaps = 24/92 (26%)

Query: 217 PGPPPVPEAAIQAIPTVKIMESHLANDTTCPVCKEEFKVGGEARE--------------- 261
            G    PE  I+        E  +A +  C +C E+  V     +               
Sbjct: 3   SGSSGEPEQVIRKYTE----ELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRL 58

Query: 262 LACKHIYHSECIVPWLRLHN-----SCPVCRH 288
             C H +H  C++      N      CP C+ 
Sbjct: 59  TKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKT 90

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

 Score = 47.5 bits (112), Expect = 4e-07
 Identities = 13/55 (23%), Positives = 27/55 (49%), Gaps = 4/55 (7%)

Query: 241 ANDTTCPVCKEEFKVGGEARE----LACKHIYHSECIVPWLRLHNSCPVCRHEVP 291
           +   +CP+C + +    +         C H++ S+C+   L+  N+CP CR ++ 
Sbjct: 5   SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKIN 59

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

 Score = 44.4 bits (104), Expect = 5e-06
 Identities = 15/72 (20%), Positives = 30/72 (41%), Gaps = 4/72 (5%)

Query: 223 PEAAIQAIPTVKIMESHLANDTTCPVCKEEFKVGGEARELA----CKHIYHSECIVPWLR 278
           P    +            +   +CP+C + +    +   L     C H++ S+C+   L+
Sbjct: 52  PTCRKKINHKRYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK 111

Query: 279 LHNSCPVCRHEV 290
             N+CP CR ++
Sbjct: 112 NANTCPTCRKKI 123

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

 Score = 50.1 bits (119), Expect = 5e-07
 Identities = 20/114 (17%), Positives = 36/114 (31%), Gaps = 12/114 (10%)

Query: 180 PILRPGQNPLPPGVNPRDYFL--GQGMQQLIEEITQNDRPGPPPVPEAAIQAIPTVKIME 237
           P  +P    L  G     Y    G+     +  + +        V +   +      +  
Sbjct: 273 PHNKPLFQALIDGFREGFYLFPDGRNQNPDLTGLCEPTPQDHIKVTQEQYE------LYC 326

Query: 238 SHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN-SCPVCRHEV 290
              +    C +C E  K   + +   C H+  + C+  W       CP CR E+
Sbjct: 327 EMGSTFQLCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEI 377

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A Length = 106

 Score = 46.7 bits (110), Expect = 5e-07
 Identities = 13/93 (13%), Positives = 24/93 (25%), Gaps = 22/93 (23%)

Query: 219 PPPVPEAAIQAIPTVKI-------MESHLANDTTCPVCKEEFKVGGEARE---------- 261
             P    +       ++       + +       C +C+          +          
Sbjct: 6   DTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEE 65

Query: 262 -----LACKHIYHSECIVPWLRLHNSCPVCRHE 289
                  C H +H  CI  WL+    CP+   E
Sbjct: 66  CTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 98

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

 Score = 45.2 bits (106), Expect = 2e-06
 Identities = 12/67 (17%), Positives = 19/67 (28%), Gaps = 15/67 (22%)

Query: 238 SHLANDTTCPVCKEEFKVGGEARE---------------LACKHIYHSECIVPWLRLHNS 282
           +       C +C+          +                 C H +H  CI  WL+    
Sbjct: 43  AWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQV 102

Query: 283 CPVCRHE 289
           CP+   E
Sbjct: 103 CPLDNRE 109

>1z6u_A NP95-like ring finger protein isoform B; structural genomics consortium, ligase, ubiquitin-protein ligase, cell cycle regulation, SGC; 2.10A {Homo sapiens} Length = 150

 Score = 45.8 bits (108), Expect = 2e-06
 Identities = 21/118 (17%), Positives = 34/118 (28%), Gaps = 9/118 (7%)

Query: 175 PNPLEPILRPGQNPLPPGVNPRDYFLGQGMQQLIEEITQNDRPGPPPVPEAAIQAIPTVK 234
                P                 + L    Q LI E  QN +     + +  +  +    
Sbjct: 15  VPRGSPSASKVYKASDSAEAIEAFQLTPQQQHLIREDCQNQK-----LWDEVLSHLVEGP 69

Query: 235 IMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN-SCPVCRHEVP 291
                L     C  C+E      +     C H    +C+    +    SCP CRH++ 
Sbjct: 70  NFLKKLEQSFMCVCCQELVY---QPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLG 124

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

 Score = 43.1 bits (102), Expect = 3e-06
 Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 6/50 (12%)

Query: 245 TCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSS 294
            C  C+ E K     + L C H   S C+         CP+C+   P+ +
Sbjct: 8   RCQQCQAEAK---CPKLLPCLHTLCSGCLE---ASGMQCPICQAPWPLGA 51

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 66

 Score = 43.2 bits (102), Expect = 3e-06
 Identities = 8/47 (17%), Positives = 15/47 (31%), Gaps = 4/47 (8%)

Query: 245 TCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN-SCPVCRHEV 290
            C  C          ++  C H +   C+   L   +  C  C+  +
Sbjct: 17  KCEKCHLVLC---SPKQTECGHRFCESCMAALLSSSSPKCTACQESI 60

>1rmd_A RAG1; V(D)J recombination, antibody, MAD, ring finger, zinc binuclear cluster, zinc finger, DNA-binding protein; 2.10A {Mus musculus} SCOP: g.37.1.1 g.44.1.1 Length = 116

 Score = 43.8 bits (103), Expect = 7e-06
 Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 4/54 (7%)

Query: 238 SHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNS-CPVCRHEV 290
           +H     +C +C+       +  E +CKH++   CI+  L++  S CP CR+  
Sbjct: 18  AHFVKSISCQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPC 68

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens} Length = 124

 Score = 43.0 bits (101), Expect = 2e-05
 Identities = 19/97 (19%), Positives = 31/97 (31%), Gaps = 6/97 (6%)

Query: 198 YFLGQGMQQLIEEITQN--DRPGPPPVPEAAIQAIPTVKIMESHLANDTTCPVCKEEFKV 255
           Y L      LI E   N           +    +    ++  S +     C  C+E    
Sbjct: 5   YSLTAQQSSLIREDKSNAKLWNEVLASLKDRPASGSPFQLFLSKVEETFQCICCQELVF- 63

Query: 256 GGEARELACKHIYHSECIVPWLRLH-NSCPVCRHEVP 291
                   C+H    +C+    R    SCP CR+++ 
Sbjct: 64  --RPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLG 98

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

 Score = 42.2 bits (99), Expect = 2e-05
 Identities = 17/76 (22%), Positives = 26/76 (34%), Gaps = 10/76 (13%)

Query: 220 PPVPEAAIQAIPTVKIMESHLANDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLR 278
           P    A   +   +  +E  L     C  C    +   E   L  C+HI+ S C+   + 
Sbjct: 3   PDGRGAWAHSRAALDRLEKLL----RCSRCTNILR---EPVCLGGCEHIFCSNCVSDCIG 55

Query: 279 LHNSCPVCRHEVPVSS 294
               CPVC     +  
Sbjct: 56  --TGCPVCYTPAWIQD 69

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A Length = 118

 Score = 42.1 bits (99), Expect = 3e-05
 Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 4/55 (7%)

Query: 237 ESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNS-CPVCRHEV 290
           +  L +   CP+C    +   EA +  C H +   CI+  +R     CPV    +
Sbjct: 12  DPPLESKYECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEIL 63

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

 Score = 44.0 bits (103), Expect = 3e-05
 Identities = 14/63 (22%), Positives = 22/63 (34%), Gaps = 8/63 (12%)

Query: 235 IMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNS--CPVCR----H 288
           I E++      C +C      G       C    H  C+  + + +    CP C     H
Sbjct: 172 IRETYPDAVKICNICHSLLIQGQSCET--CGIRMHLPCVAKYFQSNAEPRCPHCNDYWPH 229

Query: 289 EVP 291
           E+P
Sbjct: 230 EIP 232

>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} Length = 170

 Score = 41.6 bits (97), Expect = 9e-05
 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 4/56 (7%)

Query: 237 ESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNS-CPVCRHEVP 291
           +  L +   CP+C    +   EA +  C H +   CI+  +R     CPV    + 
Sbjct: 12  DPPLESKYECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILL 64

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

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 14/57 (24%), Positives = 21/57 (36%), Gaps = 4/57 (7%)

Query: 245 TCPVCKEEFKVGGEA-RELACKHIYHSECIVPWLRLHN---SCPVCRHEVPVSSASS 297
            CP+C E F       + L C H    +C+   L        CP C     ++S + 
Sbjct: 17  ECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITSLTQ 73

>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B Length = 165

 Score = 41.5 bits (97), Expect = 1e-04
 Identities = 22/109 (20%), Positives = 41/109 (37%), Gaps = 12/109 (11%)

Query: 184 PGQNPLPPGVNPRDYFLGQGMQQLIEEITQNDRPGPPPVPEAAIQAIPTVKIMESHLAND 243
           P  + +   V        Q + +  E      +  P       ++ + + + + S L   
Sbjct: 2   PLGSHMSQAVQTNG---TQPLSKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSEL--- 55

Query: 244 TTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHN-SCPVCRHEV 290
             CP+C +  K          C H + ++CI+  LR  N  CP CR ++
Sbjct: 56  -MCPICLDMLK---NTMTTKECLHRFCADCIITALRSGNKECPTCRKKL 100

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens} Length = 141

 Score = 40.9 bits (95), Expect = 1e-04
 Identities = 17/85 (20%), Positives = 27/85 (31%), Gaps = 6/85 (7%)

Query: 233 VKIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNS-CPVCRHEVP 291
             ++ + L     C  C+   +      +  C H Y S C+   L      C  C H   
Sbjct: 21  KTLLGTKLEAKYLCSACRNVLR---RPFQAQCGHRYCSFCLASILSSGPQNCAACVH--E 75

Query: 292 VSSASSSHDVDSDDEHGDGARRRCL 316
                    ++S     D A RR +
Sbjct: 76  GIYEEGISILESSSAFPDNAARREV 100

>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA damage, chromatin regulator, chromosomal protein, DNA repair, metal-binding; 2.12A {Homo sapiens} Length = 115

 Score = 39.5 bits (92), Expect = 2e-04
 Identities = 13/62 (20%), Positives = 20/62 (32%), Gaps = 4/62 (6%)

Query: 240 LANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN-SCPVCRHEVPVSSASSS 298
             ++  C +C E      E   L C H     C    +   +  CP CR  V   +   +
Sbjct: 12  SLSECQCGICMEILV---EPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSSWTRYHT 68

Query: 299 HD 300
             
Sbjct: 69  RR 70

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

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 6/50 (12%)

Query: 245 TCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHN--SCPVCRHEVP 291
            C +CK+      +A  +  C + Y  ECI   L   +  +CP C     
Sbjct: 17  LCLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV 63

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

 Score = 37.8 bits (87), Expect = 4e-04
 Identities = 12/52 (23%), Positives = 17/52 (32%), Gaps = 2/52 (3%)

Query: 242 NDTTCPVCKEEFKVGGEA-RELACKHIYHSECIVPWLRLHN-SCPVCRHEVP 291
           +   CP+C E  ++         C +     C        N  CP CR   P
Sbjct: 10  DPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYP 61

>3htk_C E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae} Length = 267

 Score = 39.9 bits (92), Expect = 6e-04
 Identities = 11/64 (17%), Positives = 25/64 (39%), Gaps = 6/64 (9%)

Query: 235 IMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNS--CPV--CRHEV 290
           +       + TCP+  + ++         C H++  + I  +L+ + +  CP   C   V
Sbjct: 173 LQIEGGKIELTCPITCKPYEA--PLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVV 230

Query: 291 PVSS 294
            +  
Sbjct: 231 SMRD 234

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

 Score = 37.4 bits (87), Expect = 7e-04
 Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 6/50 (12%)

Query: 245 TCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHN--SCPVCRHEVP 291
            C +CK+      +A  +  C + Y  ECI   L   +  +CP C     
Sbjct: 15  LCLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV 61

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	358
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.65
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.57
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.47
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.46
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.45
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.45
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.35
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.34
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.33
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.32
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.32
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.31
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.3
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.28
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.27
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.26
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.25
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.22
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.22
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.21
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.21
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.2
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.19
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.17
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.17
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.14
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.14
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.13
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.12
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.12
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.12
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.1
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.08
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.07
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.07
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.07
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.07
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.04
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.04
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.02
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	98.98
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	98.96
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	98.95
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	98.95
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	98.95
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.95
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.92
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.91
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.9
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	98.89
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.89
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	98.85
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.82
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.78
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.77
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.76
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.75
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.68
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.65
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.64
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.52
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.49
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.47
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.45
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.45
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.38
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.32
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.31
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.24
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.23
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	97.86
3nw0_A	238	Non-structural maintenance of chromosomes element	97.62
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	95.36
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	92.26
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	91.7
4ayb_P	48	DNA-directed RNA polymerase; transferase, multi-su	88.93
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	88.48
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	88.25
1we9_A	64	PHD finger family protein; structural genomics, PH	87.75
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	85.83
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	84.87
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	83.69
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	82.69
3a43_A	139	HYPD, hydrogenase nickel incorporation protein HYP	82.23
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	82.2
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	82.09
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	81.23
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	80.35
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	80.1
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	80.05

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

Probab=99.65  E-value=1.3e-16  Score=127.10  Aligned_cols=77  Identities=35%  Similarity=0.869  Sum_probs=67.9

Q ss_pred             CCCCCCCCHHHHHhCCceeeeccc--cCCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          216 RPGPPPVPEAAIQAIPTVKIMESH--LANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       216 ~~~~ppas~~~i~~lp~~~~~~~~--~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      .....+++++.|++||.+.+....  ...+..|+||++.|..++.++.|+|+|.||..||..||+.+.+||+||+.+..
T Consensus        11 ~~~~~~~s~~~i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           11 MVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFPP   89 (91)
T ss_dssp             SSCCCCCCHHHHHTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTCBCTTTCCBSSC
T ss_pred             CcCCCCCCHHHHHhCCCeeecccccccCCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCCcCcCcCccCCC
Confidence            456778999999999999887654  33567899999999988889999999999999999999999999999998864

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

Probab=99.57  E-value=1e-15  Score=117.11  Aligned_cols=70  Identities=26%  Similarity=0.692  Sum_probs=59.7

Q ss_pred             CHHHHHhCCceeeecccc-CCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          223 PEAAIQAIPTVKIMESHL-ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       223 s~~~i~~lp~~~~~~~~~-~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      +.+.++.||.+++..... .++..|+||++.|..++.++.++|+|.||..||..||+.+.+||+||+++..
T Consensus         2 s~~~i~~lp~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~   72 (75)
T 1x4j_A            2 SSGSSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGP   72 (75)
T ss_dssp             CCCCCSSCCCEEBCSSSCSSSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCSSCTTTCCCCCC
T ss_pred             cHhhHhhCCcEEecCccccCCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCCcCcCcCCcCCC
Confidence            345677888888765433 3568999999999988888999999999999999999999999999998864

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

Probab=99.47  E-value=2.5e-14  Score=102.48  Aligned_cols=51  Identities=43%  Similarity=0.944  Sum_probs=46.9

Q ss_pred             CCCccccccccccccCCccEEec-cCCeeChhhHHHHHhcCCCCCccceecc
Q 018299          241 ANDTTCPVCKEEFKVGGEARELA-CKHIYHSECIVPWLRLHNSCPVCRHEVP  291 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lp-C~H~FH~~CI~~WL~~~~sCPvCR~~l~  291 (358)
                      +++.+|+||++.|..++.+..++ |+|.||..||..|++.+.+||+||+++.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            35679999999999888899998 9999999999999999999999999874

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

Probab=99.46  E-value=4.5e-14  Score=105.93  Aligned_cols=55  Identities=27%  Similarity=0.850  Sum_probs=49.2

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccCCCC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSA  295 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~~  295 (358)
                      ..+..|+||++.|..++.++.++|+|.||..||..|++.+.+||+||..+.....
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   66 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQLP   66 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCSCCC
T ss_pred             CCCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccCcCC
Confidence            3467999999999888889999999999999999999999999999999876543

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

Probab=99.45  E-value=7.6e-14  Score=106.11  Aligned_cols=54  Identities=33%  Similarity=0.807  Sum_probs=48.7

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccCCC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSS  294 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~  294 (358)
                      ..+..|+||++.|.....++.|+|+|.||..||..|++.+.+||+||+++....
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQLA   66 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCSBCTTTCCBCSSCC
T ss_pred             CCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCCcCCCcCccccccc
Confidence            447899999999998888889999999999999999999999999999986543

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

Probab=99.45  E-value=7.5e-14  Score=107.18  Aligned_cols=56  Identities=45%  Similarity=1.161  Sum_probs=49.8

Q ss_pred             cCCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccCCCC
Q 018299          240 LANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSA  295 (358)
Q Consensus       240 ~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~~  295 (358)
                      ...+..|+||++.|.....++.++|+|.||..||..|++.+.+||+||..+.....
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   67 (78)
T 2ect_A           12 VGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNT   67 (78)
T ss_dssp             SSSSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCCCSCS
T ss_pred             CCCCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccCCccc
Confidence            34578999999999988888899999999999999999999999999999876543

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

Probab=99.35  E-value=3.6e-13  Score=104.85  Aligned_cols=51  Identities=25%  Similarity=0.733  Sum_probs=42.3

Q ss_pred             CCcccccccccccc-----------CCccEEec-cCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          242 NDTTCPVCKEEFKV-----------GGEARELA-CKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~-----------~~~~~~lp-C~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      ++..|+||++.|..           ++.++.++ |+|.||..||.+||+.+++||+||+++..
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   76 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVV   76 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcch
Confidence            36678888888853           44466666 99999999999999999999999998754

>2ecm_A Ring finger and CHY zinc finger domain- containing protein 1; RCHY1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2jrj_A

Probab=99.34  E-value=5.2e-13  Score=95.42  Aligned_cols=50  Identities=28%  Similarity=0.695  Sum_probs=43.8

Q ss_pred             CCccccccccccccC-CccEEeccCCeeChhhHHHHHhcCCCCCccceecc
Q 018299          242 NDTTCPVCKEEFKVG-GEARELACKHIYHSECIVPWLRLHNSCPVCRHEVP  291 (358)
Q Consensus       242 ~~~~C~ICle~~~~~-~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~  291 (358)
                      .+..|+||++.|..+ +.++.++|+|.||..||..|++.+.+||+||+++.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECTTSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecCCCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            467999999999643 35788899999999999999999999999999874

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

Probab=99.33  E-value=6e-13  Score=99.16  Aligned_cols=52  Identities=25%  Similarity=0.701  Sum_probs=44.7

Q ss_pred             CCCccccccccccccC----CccEEeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          241 ANDTTCPVCKEEFKVG----GEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~----~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      .+...|+||++.|...    ..++.++|+|.||..||..|++.+.+||+||.++..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            4578999999999843    234889999999999999999999999999998854

>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1

Probab=99.32  E-value=8.8e-13  Score=108.37  Aligned_cols=52  Identities=23%  Similarity=0.558  Sum_probs=42.5

Q ss_pred             CCccccccccccccCC---------------ccEEeccCCeeChhhHHHHHh-----cCCCCCccceeccCC
Q 018299          242 NDTTCPVCKEEFKVGG---------------EARELACKHIYHSECIVPWLR-----LHNSCPVCRHEVPVS  293 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~---------------~~~~lpC~H~FH~~CI~~WL~-----~~~sCPvCR~~l~~~  293 (358)
                      .+..|+||++.|....               .++.++|+|.||..||..||.     .+.+||+||..+...
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCCCCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            3579999999997542               344788999999999999994     466899999988654

>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 4f52_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A

Probab=99.32  E-value=9.1e-13  Score=108.13  Aligned_cols=50  Identities=24%  Similarity=0.572  Sum_probs=43.2

Q ss_pred             CCccccccccccccC---------------CccEEeccCCeeChhhHHHHHhcCCCCCccceecc
Q 018299          242 NDTTCPVCKEEFKVG---------------GEARELACKHIYHSECIVPWLRLHNSCPVCRHEVP  291 (358)
Q Consensus       242 ~~~~C~ICle~~~~~---------------~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~  291 (358)
                      ++..|+||++.|...               ..++.++|+|.||..||.+||+.+.+||+||+++.
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  100 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecccCcEECHHHHHHHHHcCCcCcCCCCcce
Confidence            478999999998743               13567889999999999999999999999999864

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

Probab=99.31  E-value=8.7e-13  Score=99.05  Aligned_cols=53  Identities=25%  Similarity=0.688  Sum_probs=45.6

Q ss_pred             CCCccccccccccccC----CccEEeccCCeeChhhHHHHHhcCCCCCccceeccCC
Q 018299          241 ANDTTCPVCKEEFKVG----GEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~----~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      .++..|+||++.+...    +.++.++|+|.||..||..|++.+.+||+||..+...
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK   64 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCCC
T ss_pred             CCCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccChh
Confidence            3568999999999742    3458899999999999999999999999999998654

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

Probab=99.30  E-value=1.8e-12  Score=96.67  Aligned_cols=50  Identities=30%  Similarity=0.782  Sum_probs=44.0

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccCC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      .+..|+||++.+.  +.++.++|+|.||..||..|++.+.+||+||..+...
T Consensus         4 ~~~~C~IC~~~~~--~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   53 (68)
T 1chc_A            4 VAERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVESV   53 (68)
T ss_dssp             CCCCCSSCCSCCC--SCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCCCE
T ss_pred             CCCCCeeCCcccc--CCcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhHhh
Confidence            4679999999987  2458899999999999999999999999999988643

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

Probab=99.28  E-value=3.4e-12  Score=96.64  Aligned_cols=53  Identities=28%  Similarity=0.631  Sum_probs=45.5

Q ss_pred             cCCCccccccccccccCCccEEe-ccCCeeChhhHHHHHhcCCCCCccceeccCCCC
Q 018299          240 LANDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSA  295 (358)
Q Consensus       240 ~~~~~~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~~  295 (358)
                      +.++..|+||++.+.   .++.+ +|+|.||..||..|++.+.+||+||..+.....
T Consensus        12 ~~~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~   65 (72)
T 2djb_A           12 LTPYILCSICKGYLI---DATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQP   65 (72)
T ss_dssp             CCGGGSCTTTSSCCS---SCEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSCS
T ss_pred             cCCCCCCCCCChHHH---CcCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCcccc
Confidence            345789999999998   56666 899999999999999999999999999866543

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

Probab=99.27  E-value=2.2e-12  Score=94.66  Aligned_cols=52  Identities=25%  Similarity=0.671  Sum_probs=44.7

Q ss_pred             CCccccccccccccC----CccEEeccCCeeChhhHHHHHhcCCCCCccceeccCC
Q 018299          242 NDTTCPVCKEEFKVG----GEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       242 ~~~~C~ICle~~~~~----~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      ++..|+||++.+...    ..++.++|+|.||..||..|++.+.+||+||..+...
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   57 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK   57 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTTT
T ss_pred             CCCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCcc
Confidence            367999999999742    3458889999999999999999999999999988653

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

Probab=99.26  E-value=1.8e-12  Score=97.94  Aligned_cols=48  Identities=27%  Similarity=0.679  Sum_probs=43.7

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      ++..|+||++.+.   .++.++|+|.||..||..|++.+.+||+||..+..
T Consensus        14 ~~~~C~IC~~~~~---~~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   61 (71)
T 2d8t_A           14 TVPECAICLQTCV---HPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPE   61 (71)
T ss_dssp             SCCBCSSSSSBCS---SEEEETTTEEEEHHHHHHCTTCSSBCSSSCCBCCH
T ss_pred             CCCCCccCCcccC---CCEEccCCCHHHHHHHHHHHHCCCcCcCcCchhCH
Confidence            4679999999998   67889999999999999999999999999998854

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

Probab=99.25  E-value=2.4e-12  Score=96.65  Aligned_cols=51  Identities=25%  Similarity=0.716  Sum_probs=44.9

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccCCCC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSA  295 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~~  295 (358)
                      .+...|+||++.+..    +.++|+|.||..||..|++.+.+||+||..+.....
T Consensus        13 ~~~~~C~IC~~~~~~----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   63 (70)
T 2ecn_A           13 TDEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANE   63 (70)
T ss_dssp             CCCCCCSSSCCSCCS----EEETTTEEECHHHHHHSSCCCSSCHHHHHCTTCCCC
T ss_pred             CCCCCCeeCCcCccC----cccCCCCcccHHHHHHHHHCcCcCCCcCCcccCCCc
Confidence            456899999999983    889999999999999999999999999999875543

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

Probab=99.22  E-value=1.1e-11  Score=94.37  Aligned_cols=49  Identities=27%  Similarity=0.647  Sum_probs=43.0

Q ss_pred             CCCccccccccccccCCccEEec-cCCeeChhhHHHHHhcC--CCCCccceeccC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELA-CKHIYHSECIVPWLRLH--NSCPVCRHEVPV  292 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lp-C~H~FH~~CI~~WL~~~--~sCPvCR~~l~~  292 (358)
                      .++..|+||++.|.   .++.++ |+|.||..||..|++.+  .+||+||.++..
T Consensus        13 ~~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~   64 (74)
T 2yur_A           13 PDELLCLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVS   64 (74)
T ss_dssp             CGGGSCSSSCCCCT---TCEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCC
T ss_pred             CCCCCCcCCChHHh---CCeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCC
Confidence            45689999999998   678899 99999999999999876  589999997544

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

Probab=99.22  E-value=8.2e-12  Score=97.42  Aligned_cols=54  Identities=26%  Similarity=0.601  Sum_probs=46.1

Q ss_pred             cCCCccccccccccccCCc-cEEeccCCeeChhhHHHHHhcC---CCCCccceeccCC
Q 018299          240 LANDTTCPVCKEEFKVGGE-ARELACKHIYHSECIVPWLRLH---NSCPVCRHEVPVS  293 (358)
Q Consensus       240 ~~~~~~C~ICle~~~~~~~-~~~lpC~H~FH~~CI~~WL~~~---~sCPvCR~~l~~~  293 (358)
                      +.+...|+||++.|...+. ++.++|+|.||..||..|++.+   .+||+||..+...
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           12 LREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             CCSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             ccCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            4457899999999986543 8889999999999999999986   6899999988653

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

Probab=99.21  E-value=7e-12  Score=97.75  Aligned_cols=52  Identities=21%  Similarity=0.641  Sum_probs=44.4

Q ss_pred             CCccccccccccccCCccEEeccC-----CeeChhhHHHHHhcCC--CCCccceeccCCC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACK-----HIYHSECIVPWLRLHN--SCPVCRHEVPVSS  294 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~-----H~FH~~CI~~WL~~~~--sCPvCR~~l~~~~  294 (358)
                      ++..|.||+++|..++.+ ++||+     |.||..||.+||+.++  +||+||+++....
T Consensus        14 ~~~~C~IC~~~~~~~~~l-~~pC~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~   72 (80)
T 2d8s_A           14 SQDICRICHCEGDDESPL-ITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMET   72 (80)
T ss_dssp             TSCCCSSSCCCCCSSSCE-ECSSSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCC
T ss_pred             CCCCCeEcCccccCCCee-EeccccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCc
Confidence            467999999999876654 68996     9999999999999764  8999999987654

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

Probab=99.21  E-value=9e-12  Score=94.05  Aligned_cols=51  Identities=24%  Similarity=0.647  Sum_probs=43.7

Q ss_pred             cCCCccccccccccccCCccEEeccCCeeChhhHHHHHh---cCCCCCccceeccCC
Q 018299          240 LANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLR---LHNSCPVCRHEVPVS  293 (358)
Q Consensus       240 ~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~---~~~sCPvCR~~l~~~  293 (358)
                      +.++..|+||++.+.   .++.++|+|.||..||..|++   ....||+||..+..+
T Consensus        17 ~~~~~~C~IC~~~~~---~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   70 (73)
T 2ysl_A           17 LQEEVICPICLDILQ---KPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKN   70 (73)
T ss_dssp             CCCCCBCTTTCSBCS---SEEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCC
T ss_pred             CccCCEeccCCcccC---CeEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcc
Confidence            345789999999998   678889999999999999997   355799999988654

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

Probab=99.20  E-value=9.2e-12  Score=96.27  Aligned_cols=48  Identities=19%  Similarity=0.596  Sum_probs=43.4

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceecc
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVP  291 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~  291 (358)
                      .....|+||++.|.   .++.++|+|.||..||..|++...+||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQ---NPVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCC---SEEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhc---CeeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            34679999999997   6778999999999999999999999999999885

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

Probab=99.19  E-value=4.4e-12  Score=108.17  Aligned_cols=49  Identities=37%  Similarity=0.900  Sum_probs=44.3

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccCC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      ++..|+||++.|.   .++.++|+|.||..||..|+..+.+||+||..+...
T Consensus        52 ~~~~C~iC~~~~~---~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           52 NELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             HHSBCTTTCSBCS---SEEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             ccCCCcccCcccC---CceECCCCCCccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            4568999999998   688999999999999999999999999999988543

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

Probab=99.17  E-value=1e-11  Score=92.37  Aligned_cols=50  Identities=16%  Similarity=0.523  Sum_probs=42.6

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHh-cCCCCCccceeccCC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLR-LHNSCPVCRHEVPVS  293 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~-~~~sCPvCR~~l~~~  293 (358)
                      .++..|+||++.+.   .++.++|+|.||..||..|++ ...+||+||..+..+
T Consensus        13 ~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           13 EDKYKCEKCHLVLC---SPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             CCCEECTTTCCEES---SCCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             CcCCCCCCCChHhc---CeeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            45689999999998   556689999999999999995 556899999988654

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

Probab=99.17  E-value=1.8e-11  Score=93.79  Aligned_cols=51  Identities=22%  Similarity=0.505  Sum_probs=44.8

Q ss_pred             cCCCccccccccccccCCccEEeccCCeeChhhHHHHHhc-CCCCCccceeccCC
Q 018299          240 LANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL-HNSCPVCRHEVPVS  293 (358)
Q Consensus       240 ~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~-~~sCPvCR~~l~~~  293 (358)
                      +.++..|+||++.|.   .++.++|+|.||..||..|++. +.+||+||..+...
T Consensus         5 ~~~~~~C~IC~~~~~---~Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~   56 (78)
T 1t1h_A            5 FPEYFRCPISLELMK---DPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             CSSSSSCTTTSCCCS---SEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             CcccCCCCCcccccc---CCEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChh
Confidence            345789999999998   6788999999999999999987 77899999988643

>3lrq_A E3 ubiquitin-protein ligase TRIM37; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; HET: MSE; 2.29A {Homo sapiens}

Probab=99.14  E-value=4.9e-12  Score=102.11  Aligned_cols=49  Identities=31%  Similarity=0.729  Sum_probs=43.6

Q ss_pred             CCCccccccccccccCCccEE-eccCCeeChhhHHHHHhcC-CCCCccceeccC
Q 018299          241 ANDTTCPVCKEEFKVGGEARE-LACKHIYHSECIVPWLRLH-NSCPVCRHEVPV  292 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~-lpC~H~FH~~CI~~WL~~~-~sCPvCR~~l~~  292 (358)
                      .++..|+||++.|.   .++. ++|+|.||..||..|++.. .+||+||..+..
T Consensus        20 ~~~~~C~IC~~~~~---~p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (100)
T 3lrq_A           20 AEVFRCFICMEKLR---DARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQL   70 (100)
T ss_dssp             HHHTBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCCCCCccCCcccc---CccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCH
Confidence            45689999999998   6777 8999999999999999988 689999999854

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

Probab=99.14  E-value=4.8e-12  Score=105.58  Aligned_cols=51  Identities=24%  Similarity=0.569  Sum_probs=1.1

Q ss_pred             CCccccccccccccC-------------C--ccEEeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVG-------------G--EARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~-------------~--~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      .++.|+||++.|...             +  .+..++|+|.||..||.+||+.+++||+||.++..
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~~  112 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEF  112 (117)
T ss_dssp             CC----------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeeee
Confidence            468999999999742             1  23345899999999999999999999999998643

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

Probab=99.13  E-value=3.2e-11  Score=93.05  Aligned_cols=51  Identities=33%  Similarity=0.783  Sum_probs=44.2

Q ss_pred             cCCCccccccccccccCCccEEeccCCeeChhhHHHHHhc------CCCCCccceeccCC
Q 018299          240 LANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL------HNSCPVCRHEVPVS  293 (358)
Q Consensus       240 ~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~------~~sCPvCR~~l~~~  293 (358)
                      +.++..|+||++.|.   .++.++|+|.||..||..|++.      ...||+||..+...
T Consensus        16 ~~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecw_A           16 IKEEVTCPICLELLK---EPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG   72 (85)
T ss_dssp             CCTTTSCTTTCSCCS---SCEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTT
T ss_pred             CccCCCCcCCChhhC---cceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHH
Confidence            345789999999998   6778999999999999999998      66799999988653

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

Probab=99.12  E-value=4.8e-11  Score=87.72  Aligned_cols=44  Identities=25%  Similarity=0.741  Sum_probs=38.6

Q ss_pred             cCCCccccccccccccCCccEEeccCCeeChhhHHHHHhc---CCCCCcc
Q 018299          240 LANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL---HNSCPVC  286 (358)
Q Consensus       240 ~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~---~~sCPvC  286 (358)
                      +.++..|+||++.|.   .++.++|+|.||..||..|++.   ..+||+|
T Consensus        17 ~~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           17 LQEEVICPICLDILQ---KPVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCBCTTTCSBCS---SCEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             CccCCCCCcCCchhC---CeEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            345789999999998   6888999999999999999983   5579998

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

Probab=99.12  E-value=2.5e-11  Score=98.91  Aligned_cols=52  Identities=29%  Similarity=0.699  Sum_probs=45.4

Q ss_pred             ccCCCccccccccccccCCccEEe-ccCCeeChhhHHHHHhcCCCCCccceeccCC
Q 018299          239 HLANDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       239 ~~~~~~~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      .+.++..|+||++.|.   .++.+ +|+|.||..||..|++.+.+||+||..+...
T Consensus        11 ~~~~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           11 ELNPHLMCVLCGGYFI---DATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             HHGGGTBCTTTSSBCS---SEEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             ccCCcCCCccCChHHh---CcCEeCCCCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            3456789999999998   56776 9999999999999999999999999988653

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

Probab=99.12  E-value=5e-11  Score=91.94  Aligned_cols=50  Identities=30%  Similarity=0.730  Sum_probs=43.9

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHhc------CCCCCccceeccCC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL------HNSCPVCRHEVPVS  293 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~------~~sCPvCR~~l~~~  293 (358)
                      .++..|+||++.+.   .++.++|+|.||..||..|++.      ...||+||..+...
T Consensus        17 ~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecv_A           17 KEEVTCPICLELLT---QPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPE   72 (85)
T ss_dssp             CCCCCCTTTCSCCS---SCBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSS
T ss_pred             cCCCCCCCCCcccC---CceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHH
Confidence            45789999999998   5677899999999999999987      67899999988653

>3fl2_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA repair, ring finger domain, metal binding, DNA replication; 1.75A {Homo sapiens}

Probab=99.10  E-value=1.2e-11  Score=103.25  Aligned_cols=48  Identities=25%  Similarity=0.555  Sum_probs=43.0

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhcCC-CCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN-SCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~-sCPvCR~~l~~  292 (358)
                      ++..|+||++.|.   .++.++|+|.||..||..|+..+. +||+||..+..
T Consensus        51 ~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           51 ETFQCICCQELVF---RPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHTBCTTTSSBCS---SEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             cCCCCCcCChHHc---CcEEeeCCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            4679999999999   788899999999999999998655 89999999865

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

Probab=99.08  E-value=1.7e-11  Score=93.81  Aligned_cols=50  Identities=32%  Similarity=0.682  Sum_probs=43.4

Q ss_pred             cCCCccccccccccccCCccEEeccCCeeChhhHHHHHhc-------CCCCCccceeccC
Q 018299          240 LANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL-------HNSCPVCRHEVPV  292 (358)
Q Consensus       240 ~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~-------~~sCPvCR~~l~~  292 (358)
                      +.++..|+||++.|.   .++.++|+|.||..||..|++.       ...||+||..+..
T Consensus         9 ~~~~~~C~IC~~~~~---~p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~   65 (79)
T 2egp_A            9 VQEEVTCPICLELLT---EPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSF   65 (79)
T ss_dssp             CCCCCEETTTTEECS---SCCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCS
T ss_pred             cccCCCCcCCCcccC---CeeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCH
Confidence            345789999999998   5677899999999999999987       5679999998865

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

Probab=99.07  E-value=9.3e-11  Score=92.54  Aligned_cols=49  Identities=27%  Similarity=0.673  Sum_probs=42.8

Q ss_pred             cCCCccccccccccccCCccEEec-cCCeeChhhHHHHHhcC--CCCCccceecc
Q 018299          240 LANDTTCPVCKEEFKVGGEARELA-CKHIYHSECIVPWLRLH--NSCPVCRHEVP  291 (358)
Q Consensus       240 ~~~~~~C~ICle~~~~~~~~~~lp-C~H~FH~~CI~~WL~~~--~sCPvCR~~l~  291 (358)
                      +.++..|+||++.|.   .++.++ |+|.||..||..|+..+  .+||+||..+.
T Consensus        10 ~~~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           10 IPDELLCLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CCTTTEETTTTEECS---SCEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CCcCCCCCCCChhhc---CceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            345789999999998   788999 99999999999999754  48999999873

>1z6u_A NP95-like ring finger protein isoform B; structural genomics consortium, ligase, ubiquitin-protein ligase, cell cycle regulation, SGC; 2.10A {Homo sapiens}

Probab=99.07  E-value=1.9e-11  Score=105.97  Aligned_cols=50  Identities=24%  Similarity=0.582  Sum_probs=44.1

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCC-CCCccceeccCC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN-SCPVCRHEVPVS  293 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~-sCPvCR~~l~~~  293 (358)
                      .+...|+||++.|.   .++.++|+|.||..||..|+.... +||+||..+...
T Consensus        76 ~~~~~C~IC~~~~~---~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           76 EQSFMCVCCQELVY---QPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHHTBCTTTSSBCS---SEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             ccCCEeecCChhhc---CCEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            34679999999998   778899999999999999999765 799999998664

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

Probab=99.07  E-value=6.3e-11  Score=98.70  Aligned_cols=54  Identities=24%  Similarity=0.654  Sum_probs=46.2

Q ss_pred             CCccccccccccccC----CccEEeccCCeeChhhHHHHHhcCCCCCccceeccCCCC
Q 018299          242 NDTTCPVCKEEFKVG----GEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSA  295 (358)
Q Consensus       242 ~~~~C~ICle~~~~~----~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~~  295 (358)
                      ++..|+||++.|...    ..++.++|+|.||..||..||+.+.+||+||+.+.....
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l   63 (133)
T 4ap4_A            6 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   63 (133)
T ss_dssp             CSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCE
T ss_pred             CCCCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCccccc
Confidence            467999999999742    344899999999999999999999999999999876543

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

Probab=99.07  E-value=3.6e-11  Score=96.40  Aligned_cols=48  Identities=33%  Similarity=0.658  Sum_probs=42.8

Q ss_pred             CCccccccccccccCCccEEe-ccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      ++..|+||++.|.   .++.+ +|+|.||..||..|++.+.+||+||..+..
T Consensus        21 ~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           21 DLLRCGICFEYFN---IAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             HHTBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCCCcccCChhhC---CcCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            4679999999998   56677 899999999999999999999999998854

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

Probab=99.04  E-value=1.7e-10  Score=88.55  Aligned_cols=52  Identities=19%  Similarity=0.507  Sum_probs=42.9

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhcC--CCCCccceeccCCCC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLH--NSCPVCRHEVPVSSA  295 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~--~sCPvCR~~l~~~~~  295 (358)
                      ....|+||++.+..+...  ..|+|.||..||.+||+.+  .+||+||.++..+..
T Consensus        14 ~i~~C~IC~~~i~~g~~C--~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~~   67 (74)
T 2ct0_A           14 AVKICNICHSLLIQGQSC--ETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIP   67 (74)
T ss_dssp             SSCBCSSSCCBCSSSEEC--SSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCCC
T ss_pred             CCCcCcchhhHcccCCcc--CCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCCC
Confidence            357999999999855422  2799999999999999987  789999999875543

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

Probab=99.04  E-value=7.7e-11  Score=84.78  Aligned_cols=43  Identities=35%  Similarity=0.858  Sum_probs=37.0

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHh---cCCCCCcc
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLR---LHNSCPVC  286 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~---~~~sCPvC  286 (358)
                      .++..|+||++.+.   .++.++|+|.||..||..|++   ...+||+|
T Consensus        13 ~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLK---EPVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCS---SCCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccCCCCccCCcccC---ccEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            45689999999998   567789999999999999954   45689998

>2ckl_B Ubiquitin ligase protein RING2; BMI1, RING1B, polycomb, E3-ligase, nuclear protein, chromosomal protein, transcription regulation; 2.0A {Mus musculus} PDB: 3rpg_C 2h0d_B

Probab=99.02  E-value=5.2e-11  Score=104.20  Aligned_cols=49  Identities=29%  Similarity=0.798  Sum_probs=42.4

Q ss_pred             CCCccccccccccccCCccEEe-ccCCeeChhhHHHHHhc-CCCCCccceeccC
Q 018299          241 ANDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRL-HNSCPVCRHEVPV  292 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~~-~~sCPvCR~~l~~  292 (358)
                      .++..|+||++.|.   .++.+ +|+|.||..||..|++. +.+||+||..+..
T Consensus        52 ~~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           52 HSELMCPICLDMLK---NTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHHHBCTTTSSBCS---SEEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCCcccChHhh---CcCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            34679999999998   46666 99999999999999997 6789999999854

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

Probab=98.98  E-value=2.5e-10  Score=84.42  Aligned_cols=51  Identities=24%  Similarity=0.524  Sum_probs=40.7

Q ss_pred             Ccccccccc-ccccCCc-cEEeccCCeeChhhHHHHHhcC-CCCCccceeccCC
Q 018299          243 DTTCPVCKE-EFKVGGE-ARELACKHIYHSECIVPWLRLH-NSCPVCRHEVPVS  293 (358)
Q Consensus       243 ~~~C~ICle-~~~~~~~-~~~lpC~H~FH~~CI~~WL~~~-~sCPvCR~~l~~~  293 (358)
                      +..|+||++ .+..... .+.++|+|.||..||..|+... .+||+||..+...
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   56 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccc
Confidence            578999999 7764332 2567999999999999997654 5799999988653

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

Probab=98.96  E-value=1.9e-10  Score=95.78  Aligned_cols=52  Identities=25%  Similarity=0.694  Sum_probs=44.5

Q ss_pred             CCccccccccccccC----CccEEeccCCeeChhhHHHHHhcCCCCCccceeccCC
Q 018299          242 NDTTCPVCKEEFKVG----GEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       242 ~~~~C~ICle~~~~~----~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      +...|+||++.|...    ...+.++|+|.||..||.+||+.+++||+||..+..+
T Consensus        71 ~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  126 (133)
T 4ap4_A           71 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK  126 (133)
T ss_dssp             SSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChh
Confidence            467899999999742    2348889999999999999999999999999988543

>1jm7_A BRCA1, breast cancer type 1 susceptibility protein; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=98.95  E-value=2.4e-10  Score=93.05  Aligned_cols=49  Identities=29%  Similarity=0.773  Sum_probs=42.5

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhcCC---CCCccceeccCC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN---SCPVCRHEVPVS  293 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~---sCPvCR~~l~~~  293 (358)
                      +...|+||++.+.   .++.++|+|.||..||..|+..+.   +||+||..+...
T Consensus        20 ~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (112)
T 1jm7_A           20 KILECPICLELIK---EPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (112)
T ss_dssp             HHTSCSSSCCCCS---SCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             CCCCCcccChhhc---CeEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHh
Confidence            3579999999998   566789999999999999998764   799999988654

>3hct_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha, coiled coil, cytoplasm, metal- binding, UBL conjugation, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 3hcu_A 2eci_A 2jmd_A

Probab=98.95  E-value=2.6e-10  Score=94.44  Aligned_cols=50  Identities=28%  Similarity=0.621  Sum_probs=44.0

Q ss_pred             cCCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCC-CCCccceeccC
Q 018299          240 LANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN-SCPVCRHEVPV  292 (358)
Q Consensus       240 ~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~-sCPvCR~~l~~  292 (358)
                      +.++..|+||++.+.   .++.++|+|.||..||..|++... +||+||..+..
T Consensus        15 ~~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   65 (118)
T 3hct_A           15 LESKYECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLE   65 (118)
T ss_dssp             CCGGGBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCCCcCChhhc---CeEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCH
Confidence            345789999999998   678899999999999999998876 89999998854

>3l11_A E3 ubiquitin-protein ligase RNF168; E3 ligase, ring domain, DNA damage, chromatin regulator, CHR protein, DNA repair, metal-binding, nucleus; 2.12A {Homo sapiens}

Probab=98.95  E-value=7.5e-11  Score=97.08  Aligned_cols=48  Identities=27%  Similarity=0.650  Sum_probs=42.8

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhc-CCCCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL-HNSCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~-~~sCPvCR~~l~~  292 (358)
                      ++..|+||++.|.   .++.++|+|.||..||..|++. ..+||+||..+..
T Consensus        14 ~~~~C~iC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           14 SECQCGICMEILV---EPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHBCTTTCSBCS---SCEECTTSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCccCCcccC---ceeEcCCCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            4679999999998   7888999999999999999987 5689999998853

>3knv_A TNF receptor-associated factor 2; cross-brace, alternative splicing, apoptosis, cytoplasm, metal-binding, UBL conjugation, zinc, zinc-finger; 1.90A {Homo sapiens}

Probab=98.95  E-value=1.5e-10  Score=99.33  Aligned_cols=51  Identities=25%  Similarity=0.559  Sum_probs=44.3

Q ss_pred             ccCCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCC-CCCccceeccC
Q 018299          239 HLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN-SCPVCRHEVPV  292 (358)
Q Consensus       239 ~~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~-sCPvCR~~l~~  292 (358)
                      .+.++..|+||++.|.   .++.++|+|.||..||..|++... +||+||.++..
T Consensus        27 ~l~~~~~C~IC~~~~~---~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   78 (141)
T 3knv_A           27 KLEAKYLCSACRNVLR---RPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIY   78 (141)
T ss_dssp             GCCGGGBCTTTCSBCS---SEEECTTSCEEEHHHHHHHGGGSCEECHHHHHTTCC
T ss_pred             cCCcCcCCCCCChhhc---CcEECCCCCccCHHHHHHHHhcCCCCCCCCCCcccc
Confidence            3456789999999998   678899999999999999998765 79999998744

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

Probab=98.92  E-value=6.1e-10  Score=87.39  Aligned_cols=49  Identities=12%  Similarity=0.165  Sum_probs=44.8

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      .+...|+||++.|.   .++.++|||.|+..||..||..+.+||+|+..+..
T Consensus        12 p~~~~CpI~~~~m~---dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   60 (85)
T 2kr4_A           12 PDEFRDPLMDTLMT---DPVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTE   60 (85)
T ss_dssp             CTTTBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             chheECcccCchhc---CCeECCCCCEECHHHHHHHHhcCCCCCCCcCCCCh
Confidence            34789999999999   88999999999999999999998999999998854

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

Probab=98.91  E-value=3.7e-10  Score=111.66  Aligned_cols=47  Identities=28%  Similarity=0.735  Sum_probs=42.6

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHh-cCCCCCccceeccC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLR-LHNSCPVCRHEVPV  292 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~-~~~sCPvCR~~l~~  292 (358)
                      ...|+||++.+.   .++.+||+|.||..||..|+. .+.+||+||..+..
T Consensus       332 ~~~C~ICle~~~---~pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~  379 (389)
T 2y1n_A          332 FQLCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKG  379 (389)
T ss_dssp             SSBCTTTSSSBC---CEEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCE
T ss_pred             CCCCCccCcCCC---CeEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCC
Confidence            469999999997   788999999999999999999 67889999998854

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B

Probab=98.90  E-value=8.1e-10  Score=89.46  Aligned_cols=49  Identities=14%  Similarity=0.184  Sum_probs=44.9

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      .+...|+||++.|.   .++.++|||.|+..||..||..+.+||+|+.++..
T Consensus        27 p~~~~CpI~~~~m~---dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   75 (100)
T 2kre_A           27 PDEFRDPLMDTLMT---DPVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTE   75 (100)
T ss_dssp             STTTBCTTTCSBCS---SEEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCT
T ss_pred             cHhhCCcCccCccc---CCeECCCCCEEchHHHHHHHHcCCCCCCCCCCCCh
Confidence            34689999999999   88999999999999999999988899999998864

>1rmd_A RAG1; V(D)J recombination, antibody, MAD, ring finger, zinc binuclear cluster, zinc finger, DNA-binding protein; 2.10A {Mus musculus} SCOP: g.37.1.1 g.44.1.1

Probab=98.89  E-value=5.5e-10  Score=91.99  Aligned_cols=48  Identities=27%  Similarity=0.728  Sum_probs=43.0

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhc-CCCCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL-HNSCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~-~~sCPvCR~~l~~  292 (358)
                      ++..|+||++.+.   .++.++|+|.||..||..|++. ..+||+||..+..
T Consensus        22 ~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (116)
T 1rmd_A           22 KSISCQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFP   70 (116)
T ss_dssp             HHTBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCCCCCCCCcHhc---CcEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCH
Confidence            3679999999998   6778999999999999999997 6789999998854

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2

Probab=98.89  E-value=1e-09  Score=88.53  Aligned_cols=49  Identities=12%  Similarity=0.133  Sum_probs=44.9

Q ss_pred             CCCccccccccccccCCccEEeccC-CeeChhhHHHHHhcCCCCCccceeccC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACK-HIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~-H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      .++..|+||++.|+   .++.++|+ |.|+..||..||..+.+||+||.+|..
T Consensus        20 p~~~~CpI~~~~m~---dPV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~   69 (98)
T 1wgm_A           20 CDEFLDPIMSTLMC---DPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             CTTTBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             cHhcCCcCcccccc---CCeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCCh
Confidence            34789999999999   88999999 999999999999998899999998864

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

Probab=98.85  E-value=2e-09  Score=83.35  Aligned_cols=55  Identities=22%  Similarity=0.483  Sum_probs=42.7

Q ss_pred             cCCCccccccccccccCCccEEec--cCCeeChhhHHHHHhc-CCCCCccceeccCCCC
Q 018299          240 LANDTTCPVCKEEFKVGGEARELA--CKHIYHSECIVPWLRL-HNSCPVCRHEVPVSSA  295 (358)
Q Consensus       240 ~~~~~~C~ICle~~~~~~~~~~lp--C~H~FH~~CI~~WL~~-~~sCPvCR~~l~~~~~  295 (358)
                      +.++..|+||++.+...+ ++.+|  |||.||..||..|++. ...||+||+.+.....
T Consensus         8 ~~~~~~CpICle~~~~~d-~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~   65 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEIDD-INFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPA   65 (78)
T ss_dssp             CCCCCBCTTTCCBCCTTT-TTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSS
T ss_pred             cccCCcCCccCccCcccc-ccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCch
Confidence            345789999999886433 33444  9999999999999854 4679999999876544

>2vje_A E3 ubiquitin-protein ligase MDM2; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_A* 2hdp_A

Probab=98.82  E-value=1.6e-09  Score=80.46  Aligned_cols=47  Identities=21%  Similarity=0.499  Sum_probs=41.2

Q ss_pred             CCccccccccccccCCccEEe--ccCCe-eChhhHHHHHhcCCCCCccceecc
Q 018299          242 NDTTCPVCKEEFKVGGEAREL--ACKHI-YHSECIVPWLRLHNSCPVCRHEVP  291 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~l--pC~H~-FH~~CI~~WL~~~~sCPvCR~~l~  291 (358)
                      ++..|.||++.+.   .++.+  ||+|. ||..|+..|++.+..||+||.++.
T Consensus         7 ~~~~C~IC~~~~~---~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            7 AIEPCVICQGRPK---NGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             GGSCCTTTSSSCS---CEEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CcCCCCcCCCCCC---CEEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            4679999999987   55665  99999 899999999999999999999874

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

Probab=98.78  E-value=1.1e-09  Score=79.08  Aligned_cols=47  Identities=28%  Similarity=0.615  Sum_probs=40.3

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccCCC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSS  294 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~  294 (358)
                      +...|+||++.|.   .++.|+|+|.||..||..|   ...||+||+.+....
T Consensus         5 ~~~~C~IC~~~~~---~p~~l~CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T 1bor_A            5 QFLRCQQCQAEAK---CPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CCSSCSSSCSSCB---CCSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             cCCCceEeCCccC---CeEEcCCCCcccHHHHccC---CCCCCcCCcEeecCC
Confidence            4678999999998   6788999999999999884   668999999886543

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

Probab=98.77  E-value=6e-10  Score=85.01  Aligned_cols=44  Identities=18%  Similarity=0.591  Sum_probs=39.4

Q ss_pred             CCccccccccccccCCccEEeccCCe-eChhhHHHHHhcCCCCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHI-YHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~-FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      ++..|+||++.+.   .++.+||+|. ||..|+..|    ..||+||..+..
T Consensus        23 ~~~~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           23 EEKLCKICMDRNI---AIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HHTBCTTTSSSBC---CEEEETTCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             cCCCCCCCCCCCC---CEEEcCCCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            4679999999988   7889999999 999999999    889999998753

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

Probab=98.76  E-value=1e-09  Score=90.68  Aligned_cols=46  Identities=28%  Similarity=0.702  Sum_probs=41.0

Q ss_pred             CCccccccccccccCCccEEe-ccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      +...|+||++.|.   .++.+ +|+|.||..||..|+.  ..||+||..+..
T Consensus        21 ~~~~C~IC~~~~~---~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~   67 (117)
T 1jm7_B           21 KLLRCSRCTNILR---EPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWI   67 (117)
T ss_dssp             HTTSCSSSCSCCS---SCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSC
T ss_pred             hCCCCCCCChHhh---CccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCcc
Confidence            4679999999998   67777 9999999999999998  789999998843

>2vje_B MDM4 protein; proto-oncogene, phosphorylation, alternative splicing, HOST-virus interaction, UBL conjugation pathway, zinc-finger, polymorphism; HET: FLC; 2.20A {Homo sapiens} PDB: 2vjf_B*

Probab=98.75  E-value=4e-09  Score=78.05  Aligned_cols=47  Identities=19%  Similarity=0.534  Sum_probs=40.7

Q ss_pred             CCccccccccccccCCccEEe--ccCCe-eChhhHHHHHhcCCCCCccceecc
Q 018299          242 NDTTCPVCKEEFKVGGEAREL--ACKHI-YHSECIVPWLRLHNSCPVCRHEVP  291 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~l--pC~H~-FH~~CI~~WL~~~~sCPvCR~~l~  291 (358)
                      .+..|.||++.+.   ....+  ||+|. ||..|+..|.+....||+||.++.
T Consensus         6 ~~~~C~IC~~~~~---~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            6 LLKPCSLCEKRPR---DGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GGSBCTTTSSSBS---CEEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             cCCCCcccCCcCC---CeEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            3579999999877   45555  99998 999999999998889999999874

>2yu4_A E3 SUMO-protein ligase NSE2; SP-ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.68  E-value=8.3e-09  Score=82.25  Aligned_cols=48  Identities=33%  Similarity=0.736  Sum_probs=41.2

Q ss_pred             CCCccccccccccccCCccEEec-cCCeeChhhHHHHHhcC------CCCCc--ccee-cc
Q 018299          241 ANDTTCPVCKEEFKVGGEARELA-CKHIYHSECIVPWLRLH------NSCPV--CRHE-VP  291 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lp-C~H~FH~~CI~~WL~~~------~sCPv--CR~~-l~  291 (358)
                      ..+..|+||++.|.   .++.++ |+|.|+..||..||..+      .+||+  |+.. +.
T Consensus         5 ~~~~~CPI~~~~~~---dPV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~   62 (94)
T 2yu4_A            5 SSGFTCPITKEEMK---KPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIR   62 (94)
T ss_dssp             SSCCBCTTTCSBCS---SEEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBC
T ss_pred             CcEeECcCcCchhc---CCEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccC
Confidence            35689999999999   788896 99999999999999864      48999  9866 53

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

Probab=98.65  E-value=9.5e-09  Score=90.04  Aligned_cols=50  Identities=28%  Similarity=0.621  Sum_probs=43.7

Q ss_pred             cCCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCC-CCCccceeccC
Q 018299          240 LANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN-SCPVCRHEVPV  292 (358)
Q Consensus       240 ~~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~-sCPvCR~~l~~  292 (358)
                      +.++..|+||++.|.   .++.++|+|.||..||..|++... +||+||..+..
T Consensus        15 ~~~~~~C~IC~~~~~---~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   65 (170)
T 3hcs_A           15 LESKYECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLE   65 (170)
T ss_dssp             CCGGGBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCCCCCCChhhc---CcEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcch
Confidence            445789999999998   678899999999999999998754 89999998854

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

Probab=98.64  E-value=1.4e-08  Score=94.66  Aligned_cols=48  Identities=17%  Similarity=0.098  Sum_probs=42.8

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhcC-CCCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLH-NSCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~-~sCPvCR~~l~~  292 (358)
                      ....|+||++.|.   .+++++|||.||..||..||..+ .+||+||.++..
T Consensus       207 ~~~~c~i~~~~~~---dPv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~  255 (281)
T 2c2l_A          207 DYLCGKISFELMR---EPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQ  255 (281)
T ss_dssp             STTBCTTTCSBCS---SEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             cccCCcCcCCHhc---CCeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCch
Confidence            4689999999999   88999999999999999999874 459999998853

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

Probab=98.52  E-value=1.5e-08  Score=98.12  Aligned_cols=54  Identities=22%  Similarity=0.562  Sum_probs=41.5

Q ss_pred             CCcccccccccccc-CCccE----EeccCCeeChhhHHHHHhcC-----------CCCCccceeccCCCC
Q 018299          242 NDTTCPVCKEEFKV-GGEAR----ELACKHIYHSECIVPWLRLH-----------NSCPVCRHEVPVSSA  295 (358)
Q Consensus       242 ~~~~C~ICle~~~~-~~~~~----~lpC~H~FH~~CI~~WL~~~-----------~sCPvCR~~l~~~~~  295 (358)
                      ...+|+||++.+.. ++.+.    ...|+|.||..||.+||+..           .+||+||.++....+
T Consensus       307 ~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~sf~  376 (381)
T 3k1l_B          307 EELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTSFA  376 (381)
T ss_dssp             SCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGGGG
T ss_pred             CCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCccHH
Confidence            45799999999886 32221    23699999999999999863           359999999976543

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

Probab=98.49  E-value=6.7e-08  Score=86.13  Aligned_cols=49  Identities=16%  Similarity=0.089  Sum_probs=43.3

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHhcC-CCCCccceeccC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLH-NSCPVCRHEVPV  292 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~-~sCPvCR~~l~~  292 (358)
                      .+...|+||++.|.   .++.++|||.|+..||..||..+ .+||+|+.++..
T Consensus       104 p~~f~CPI~~elm~---DPV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~  153 (179)
T 2f42_A          104 PDYLCGKISFELMR---EPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQ  153 (179)
T ss_dssp             CGGGBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             cHhhcccCccccCC---CCeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCCh
Confidence            34689999999999   78999999999999999999874 469999998854

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

Probab=98.47  E-value=4.8e-08  Score=74.38  Aligned_cols=44  Identities=18%  Similarity=0.589  Sum_probs=37.8

Q ss_pred             CccccccccccccCCccEEeccCCe-eChhhHHHHHhcCCCCCccceeccCC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHI-YHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~-FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      +..|+||++.+.   .++.+||+|. ||..|+..    ...||+||..+...
T Consensus        25 ~~~C~IC~~~~~---~~~~~pCgH~~~C~~C~~~----~~~CP~Cr~~i~~~   69 (75)
T 2ecg_A           25 EKLCKICMDRNI---AIVFVPCGHLVTCKQCAEA----VDKCPMCYTVITFK   69 (75)
T ss_dssp             HHSCSSSCSSCC---CBCCSSSCCCCBCHHHHHH----CSBCTTTCCBCCCC
T ss_pred             CCCCCcCCCCCC---CEEEecCCCHHHHHHHhhC----CCCCccCCceecCc
Confidence            568999999988   7788999999 99999964    37899999988553

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

Probab=98.45  E-value=7.4e-08  Score=70.77  Aligned_cols=48  Identities=31%  Similarity=0.758  Sum_probs=37.8

Q ss_pred             CCccccccccccccCCccEEeccC--C---eeChhhHHHHHhc--CCCCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACK--H---IYHSECIVPWLRL--HNSCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~--H---~FH~~CI~~WL~~--~~sCPvCR~~l~~  292 (358)
                      +...|.||+++.  ++. ..+||.  +   .||..||..|+..  +.+||+|++++..
T Consensus         5 ~~~~CrIC~~~~--~~~-l~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            5 DVPVCWICNEEL--GNE-RFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             SCCEETTTTEEC--SCC-CCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCEeEEeecCC--CCc-eecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            467999999974  333 368855  4   9999999999975  5679999998754

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

Probab=98.45  E-value=9.8e-08  Score=71.69  Aligned_cols=45  Identities=31%  Similarity=0.665  Sum_probs=39.0

Q ss_pred             CCccccccccccccCCccEEeccCCe-eChhhHHHHHhcCCCCCccceeccCC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHI-YHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~-FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      ++..|.||++.+.   .++.+||+|. ||..|+..    ...||+||..+...
T Consensus        14 ~~~~C~IC~~~~~---~~v~~pCgH~~~C~~C~~~----~~~CP~CR~~i~~~   59 (68)
T 2ea5_A           14 NSKDCVVCQNGTV---NWVLLPCRHTCLCDGCVKY----FQQCPMCRQFVQES   59 (68)
T ss_dssp             CSSCCSSSSSSCC---CCEETTTTBCCSCTTHHHH----CSSCTTTCCCCCCE
T ss_pred             CCCCCCCcCcCCC---CEEEECCCChhhhHHHHhc----CCCCCCCCcchhce
Confidence            4679999999987   7899999999 99999984    47899999988553

>2yho_A E3 ubiquitin-protein ligase mylip; ligase, E2 ligase-E3 ligase complex, ring zinc-finger, UBL conjugation pathway; 2.10A {Homo sapiens} PDB: 2yhn_A

Probab=98.38  E-value=4e-08  Score=75.98  Aligned_cols=44  Identities=34%  Similarity=0.643  Sum_probs=38.6

Q ss_pred             CCccccccccccccCCccEEeccCCe-eChhhHHHHHhcCCCCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHI-YHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~-FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      ++..|.||++.+.   .++.+||+|. ||..|+..|    ..||+||..+..
T Consensus        17 ~~~~C~IC~~~~~---~~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~   61 (79)
T 2yho_A           17 EAMLCMVCCEEEI---NSTFCPCGHTVCCESCAAQL----QSCPVCRSRVEH   61 (79)
T ss_dssp             HHTBCTTTSSSBC---CEEEETTCBCCBCHHHHTTC----SBCTTTCCBCCE
T ss_pred             CCCEeEEeCcccC---cEEEECCCCHHHHHHHHHhc----CcCCCCCchhhC
Confidence            3568999999988   7889999999 999999987    499999998854

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A

Probab=98.32  E-value=1.6e-07  Score=69.17  Aligned_cols=49  Identities=6%  Similarity=0.233  Sum_probs=43.0

Q ss_pred             CccccccccccccCCccEEe-ccCCeeChhhHHHHHhcCCCCCccceeccCCC
Q 018299          243 DTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHNSCPVCRHEVPVSS  294 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~  294 (358)
                      ...|+||++.++   .++.+ +|||.|...||.+||+.+.+||+++.+|..+.
T Consensus         3 ~~~CpIs~~~m~---dPV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~   52 (61)
T 2bay_A            3 HMLCAISGKVPR---RPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEE   52 (61)
T ss_dssp             -CCCTTTCSCCS---SEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGG
T ss_pred             eEEecCCCCCCC---CCEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhh
Confidence            368999999999   67788 89999999999999999889999999886543

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

Probab=98.31  E-value=2.3e-07  Score=73.55  Aligned_cols=48  Identities=25%  Similarity=0.654  Sum_probs=38.1

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhcC--------CCCCc--ccee
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLH--------NSCPV--CRHE  289 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~--------~sCPv--CR~~  289 (358)
                      +..+|+||++++...+....++|+|.||..||..+++..        .+||.  |+..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            357899999998754444444799999999999999742        25999  9987

>3htk_C E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-ring, ring, ATP-binding, chromosomal protein, coiled coil, DNA damage; 2.31A {Saccharomyces cerevisiae}

Probab=98.24  E-value=4.6e-07  Score=85.00  Aligned_cols=49  Identities=22%  Similarity=0.584  Sum_probs=41.3

Q ss_pred             CCCccccccccccccCCccEE-eccCCeeChhhHHHHHhcC--CCCCc--cceeccC
Q 018299          241 ANDTTCPVCKEEFKVGGEARE-LACKHIYHSECIVPWLRLH--NSCPV--CRHEVPV  292 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~-lpC~H~FH~~CI~~WL~~~--~sCPv--CR~~l~~  292 (358)
                      .....|+||++.|.   .++. +.|||.|+..||..|++.+  .+||+  |+..+..
T Consensus       179 ~~el~CPIcl~~f~---DPVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~  232 (267)
T 3htk_C          179 KIELTCPITCKPYE---APLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSM  232 (267)
T ss_dssp             BCCSBCTTTSSBCS---SEEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECG
T ss_pred             ceeeECcCccCccc---CCeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCch
Confidence            34789999999998   5665 5899999999999999875  36999  9998754

>3t6p_A Baculoviral IAP repeat-containing protein 2; ring, BIR, CARD, UBA, apoptosis, ubiquitin ligase, SMAC/ ubiquitin, caspase, IAP family, SMAC mimetic; 1.90A {Homo sapiens} PDB: 1qbh_A 2l9m_A 3eb5_A 3eb6_A 4auq_B

Probab=98.23  E-value=2.2e-07  Score=90.83  Aligned_cols=45  Identities=27%  Similarity=0.660  Sum_probs=40.0

Q ss_pred             CCCccccccccccccCCccEEeccCCe-eChhhHHHHHhcCCCCCccceeccC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHI-YHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~-FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      .++..|+||++.+.   .++.+||+|. ||..|+..|    ..||+||..+..
T Consensus       293 ~~~~~C~IC~~~~~---~~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          293 QEERTCKVCMDKEV---SVVFIPCGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             HTTCBCTTTSSSBC---CEEEETTCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             cCCCCCCccCCcCC---ceEEcCCCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            34689999999998   7889999999 999999988    789999998753

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

Probab=97.86  E-value=8.8e-06  Score=65.35  Aligned_cols=45  Identities=27%  Similarity=0.633  Sum_probs=37.5

Q ss_pred             cccccccccccCCccEEeccCCeeChhhHHHHHhc-CCCCCccceecc
Q 018299          245 TCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL-HNSCPVCRHEVP  291 (358)
Q Consensus       245 ~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~-~~sCPvCR~~l~  291 (358)
                      .|.+|--.+.  ...+.+||+|+||.+|+..|.+. .++||.|+.++.
T Consensus         3 fC~~C~~Pi~--iygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~   48 (101)
T 3vk6_A            3 FCDKCGLPIK--VYGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQ   48 (101)
T ss_dssp             BCTTTCSBCS--EEEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCS
T ss_pred             ecCccCCCeE--EEeeeccccccHHHHHHHHHHhccCCCCcCcCCeee
Confidence            5888877766  36788899999999999999865 578999999873

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

Probab=97.62  E-value=2.5e-05  Score=72.42  Aligned_cols=50  Identities=20%  Similarity=0.551  Sum_probs=41.4

Q ss_pred             CccccccccccccCCccEEec-cCCeeChhhHHHHHhcCC--CCCccceeccCCCC
Q 018299          243 DTTCPVCKEEFKVGGEARELA-CKHIYHSECIVPWLRLHN--SCPVCRHEVPVSSA  295 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lp-C~H~FH~~CI~~WL~~~~--sCPvCR~~l~~~~~  295 (358)
                      ...|.||.+.+..|   ...+ |+|.||..|+..|++.+.  .||.|+..++....
T Consensus       180 i~~C~iC~~iv~~g---~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~~~  232 (238)
T 3nw0_A          180 VKICNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIP  232 (238)
T ss_dssp             CCBCTTTCSBCSSC---EECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSCCC
T ss_pred             CCcCcchhhHHhCC---cccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCCCC
Confidence            56899999998854   3443 999999999999998765  79999999877643

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

Probab=92.26  E-value=0.086  Score=41.34  Aligned_cols=33  Identities=21%  Similarity=0.584  Sum_probs=25.6

Q ss_pred             CCccccccccccccCCccEE--eccCCeeChhhHHHH
Q 018299          242 NDTTCPVCKEEFKVGGEARE--LACKHIYHSECIVPW  276 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~--lpC~H~FH~~CI~~W  276 (358)
                      ++..|.||++.+..  .++.  +.|+|.||..|+..+
T Consensus         2 ee~~C~~C~~~~~~--~av~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            2 EKVLCQFCDQDPAQ--DAVKTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CCCBCTTCCSSSCC--BCCEEETTTTEEECHHHHHHH
T ss_pred             CCCCCcCCCCCCCC--CceEECCcCChHHhHHHCHHH
Confidence            35789999986432  3344  889999999999983

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=91.70  E-value=0.087  Score=38.91  Aligned_cols=45  Identities=22%  Similarity=0.536  Sum_probs=32.8

Q ss_pred             CCccccccccccccCCccEEe-ccCCeeChhhHHHHHhcCC----CCCccceec
Q 018299          242 NDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHN----SCPVCRHEV  290 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~~~~----sCPvCR~~l  290 (358)
                      ....|.||.+.   + +++.- .|...||..|+.+.|..-.    .||.|....
T Consensus        11 ~~~~C~vC~~~---~-~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           11 PGARCGVCGDG---T-DVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             TTCCCTTTSCC---T-TCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCcCCCCCC---C-eEEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            45789999753   2 33333 4999999999999887543    499997643

>4ayb_P DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2pmz_P 2wb1_P 2y0s_P 3hkz_P 2waq_P 4b1o_P 4b1p_X

Probab=88.93  E-value=0.2  Score=34.46  Aligned_cols=36  Identities=17%  Similarity=0.489  Sum_probs=25.6

Q ss_pred             CeeeeeccCcceeecCC-CCCCccCCCCCCCceEEEc
Q 018299           30 PLYWCYQCHRAVRISST-NPSEIACPRCSGHFVSEIE   65 (358)
Q Consensus        30 ~~YwCh~C~r~V~i~~~-~~~ei~CP~C~~gFvEEi~   65 (358)
                      ..|=|-.|.+++.-+-. ...+|.||+|+=..+..+-
T Consensus         2 ~iY~C~rCg~~fs~~el~~lP~IrCpyCGyrii~KvR   38 (48)
T 4ayb_P            2 AVYRCGKCWKTFTDEQLKVLPGVRCPYCGYKIIFMVR   38 (48)
T ss_dssp             ---CCCCTTTTCCCCCSCCCSSSCCTTTCCSCEECCC
T ss_pred             cEEEeeccCCCccHHHHhhCCCcccCccCcEEEEEec
Confidence            46899999999885543 3458999999987776654

>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}

Probab=88.48  E-value=0.31  Score=39.79  Aligned_cols=35  Identities=14%  Similarity=0.349  Sum_probs=26.9

Q ss_pred             CCCeeeeeccCcceeecCCCCCCc-cCCCCCCCceEEEc
Q 018299           28 NYPLYWCYQCHRAVRISSTNPSEI-ACPRCSGHFVSEIE   65 (358)
Q Consensus        28 t~~~YwCh~C~r~V~i~~~~~~ei-~CP~C~~gFvEEi~   65 (358)
                      ....|||..|...+.+.   .... .||.|++..++-+.
T Consensus        70 ~p~~~~C~~CG~~~e~~---~~~~~~CP~Cgs~~~~i~~  105 (119)
T 2kdx_A           70 EKVELECKDCSHVFKPN---ALDYGVCEKCHSKNVIITQ  105 (119)
T ss_dssp             ECCEEECSSSSCEECSC---CSTTCCCSSSSSCCCEEEE
T ss_pred             ccceEEcCCCCCEEeCC---CCCCCcCccccCCCcEEec
Confidence            46799999999988753   2246 89999999776543

>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=88.25  E-value=0.27  Score=36.06  Aligned_cols=35  Identities=20%  Similarity=0.535  Sum_probs=29.0

Q ss_pred             CCeeeeeccCcceeecCCCCCCccCCCCCCCceEEEc
Q 018299           29 YPLYWCYQCHRAVRISSTNPSEIACPRCSGHFVSEIE   65 (358)
Q Consensus        29 ~~~YwCh~C~r~V~i~~~~~~ei~CP~C~~gFvEEi~   65 (358)
                      .-.|-|-.|...|.+...+  .|.||+|+...+...-
T Consensus        19 ~v~Y~C~~Cg~~~~l~~~~--~iRC~~CG~RILyK~R   53 (63)
T 3h0g_L           19 TMIYLCADCGARNTIQAKE--VIRCRECGHRVMYKMR   53 (63)
T ss_dssp             CCCCBCSSSCCBCCCCSSS--CCCCSSSCCCCCBCCC
T ss_pred             CeEEECCCCCCeeecCCCC--ceECCCCCcEEEEEec
Confidence            5679999999999987544  4999999999887654

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=87.75  E-value=0.11  Score=37.58  Aligned_cols=49  Identities=18%  Similarity=0.472  Sum_probs=33.6

Q ss_pred             CCCccccccccccccCCccEEe-ccCCeeChhhHHHHHh-----cCCCCCcccee
Q 018299          241 ANDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLR-----LHNSCPVCRHE  289 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~-----~~~sCPvCR~~  289 (358)
                      .+...|+||...+..+...+.- .|...||..|+.--..     ..-.||.|+..
T Consensus         4 ~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~k   58 (64)
T 1we9_A            4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcCc
Confidence            3467899999887544433333 4999999999875432     23459999753

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=85.83  E-value=0.29  Score=35.31  Aligned_cols=45  Identities=33%  Similarity=0.750  Sum_probs=31.4

Q ss_pred             CCCccccccccccccCCccEEe-ccCCeeChhhHHHHHhcCC----CCCcccee
Q 018299          241 ANDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHN----SCPVCRHE  289 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~~~~----sCPvCR~~  289 (358)
                      ..+..|.||...   + .++.- .|...||..|+.+-|....    .||.|..+
T Consensus         9 ~~~~~C~vC~~~---g-~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A            9 DHQDYCEVCQQG---G-EIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             CCCSSCTTTSCC---S-SEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCCccCCCC---C-cEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            346799999873   2 23232 4999999999998654322    49999753

>1wil_A KIAA1045 protein; ring finger domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: g.50.1.3

Probab=84.87  E-value=0.49  Score=36.61  Aligned_cols=32  Identities=25%  Similarity=0.747  Sum_probs=23.3

Q ss_pred             CCCccccccccccccCCccEEec---cCCeeChhhHHHH
Q 018299          241 ANDTTCPVCKEEFKVGGEARELA---CKHIYHSECIVPW  276 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lp---C~H~FH~~CI~~W  276 (358)
                      ..+..|.||.- +..+   ..+|   |+-+||..|+.+-
T Consensus        13 ~~D~~C~VC~~-~t~~---~l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           13 VNDEMCDVCEV-WTAE---SLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTTCC-CCSS---CCSSCSSSSSCCCHHHHHHH
T ss_pred             CCCcccCcccc-cccc---ceeccccccccccHhhcccc
Confidence            35889999963 2322   2344   8999999999996

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=83.69  E-value=0.3  Score=36.41  Aligned_cols=49  Identities=22%  Similarity=0.481  Sum_probs=33.6

Q ss_pred             CCccccccccccccCCccEEe-ccCCeeChhhHHHHHhc----CCCCCccceecc
Q 018299          242 NDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRL----HNSCPVCRHEVP  291 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~~----~~sCPvCR~~l~  291 (358)
                      +...|.||..... ++..+.- .|...||..|+..-+..    .-.||.|+..+.
T Consensus        17 ~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~   70 (75)
T 2k16_A           17 QIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIK   70 (75)
T ss_dssp             EEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHC
T ss_pred             CCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchh
Confidence            3567999987643 3333333 49999999999876543    234999987764

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=82.69  E-value=0.44  Score=32.75  Aligned_cols=43  Identities=26%  Similarity=0.609  Sum_probs=28.4

Q ss_pred             cccccccccccCCccEEe-ccCCeeChhhHHHHHhcCC----CCCccce
Q 018299          245 TCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHN----SCPVCRH  288 (358)
Q Consensus       245 ~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~~~~----sCPvCR~  288 (358)
                      .|.||...-..+ ..+.- .|...||..|+.+=|....    .||.|+.
T Consensus         2 ~C~vC~~~~~~~-~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCC-CEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            588998754322 23333 4999999999987554322    3999964

>3a43_A HYPD, hydrogenase nickel incorporation protein HYPA; [NIFE] hydrogenase maturation, zinc-finger, nickel binding, metal-binding; HET: FME; 2.30A {Pyrococcus kodakaraensis} PDB: 3a44_A*

Probab=82.23  E-value=0.72  Score=38.82  Aligned_cols=36  Identities=19%  Similarity=0.546  Sum_probs=26.4

Q ss_pred             CCCeeeeeccCcceeecC-----------CC-------CCCccCCCCCCCceEE
Q 018299           28 NYPLYWCYQCHRAVRISS-----------TN-------PSEIACPRCSGHFVSE   63 (358)
Q Consensus        28 t~~~YwCh~C~r~V~i~~-----------~~-------~~ei~CP~C~~gFvEE   63 (358)
                      ....+||..|...+.+..           ..       ....+||.|++.-++-
T Consensus        67 ~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~h~~p~~~~~~~~CP~Cgs~~~~i  120 (139)
T 3a43_A           67 EEAVFKCRNCNYEWKLKEVKDKFDERIKEDIHFIPEVVHAFLACPKCGSHDFEV  120 (139)
T ss_dssp             ECCEEEETTTCCEEEGGGCTTCCSCCCGGGCCCCGGGCGGGCSCSSSSCCCEEE
T ss_pred             cCCcEECCCCCCEEecccccccccccccccccccccccccCCcCccccCCccEE
Confidence            467999999999887644           10       0036899999998763

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A

Probab=82.20  E-value=0.84  Score=49.72  Aligned_cols=49  Identities=14%  Similarity=0.124  Sum_probs=43.6

Q ss_pred             CCccccccccccccCCccEEeccC-CeeChhhHHHHHhcCCCCCccceeccCC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACK-HIYHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~-H~FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      +...|+|-++.+.   .++++|.| +.|-..+|..||..+.+||+=|.+|...
T Consensus       890 ~~F~cPIs~~lM~---DPVilpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~  939 (968)
T 3m62_A          890 DEFLDPLMYTIMK---DPVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLE  939 (968)
T ss_dssp             GGGBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGG
T ss_pred             HHhCCcchhhHHh---CCeEcCCCCEEECHHHHHHHHhcCCCCCCCCCCCCcc
Confidence            3578999999999   89999987 6999999999999999999999988643

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=82.09  E-value=0.53  Score=41.59  Aligned_cols=48  Identities=21%  Similarity=0.485  Sum_probs=33.8

Q ss_pred             CccccccccccccCCc---cEEe-ccCCeeChhhHHHH------Hh-----cCCCCCccceec
Q 018299          243 DTTCPVCKEEFKVGGE---AREL-ACKHIYHSECIVPW------LR-----LHNSCPVCRHEV  290 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~---~~~l-pC~H~FH~~CI~~W------L~-----~~~sCPvCR~~l  290 (358)
                      +..|+||...+..++.   .+.. -|..+||..|+.--      +.     ..-.||.|+..-
T Consensus         2 G~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~   64 (183)
T 3lqh_A            2 GNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERH   64 (183)
T ss_dssp             CCBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSS
T ss_pred             cCcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCC
Confidence            4579999998887652   3444 39999999998531      11     145799998743

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=81.23  E-value=0.22  Score=35.23  Aligned_cols=45  Identities=29%  Similarity=0.750  Sum_probs=30.4

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHhcCC----CCCccce
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN----SCPVCRH  288 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~----sCPvCR~  288 (358)
                      ..+..|.||...   ++-+.--.|...||..|+.+-|....    .||.|..
T Consensus         7 ~~~~~C~vC~~~---g~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            7 GHEDFCSVCRKS---GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SSCCSCSSSCCS---SCCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCccCCCC---CeEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            346789999874   22222224999999999997654322    3888854

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=80.35  E-value=0.9  Score=35.41  Aligned_cols=46  Identities=28%  Similarity=0.657  Sum_probs=32.7

Q ss_pred             CCCccccccccccccCCccEEe-ccCCeeChhhHHHHHhcCC----CCCccceec
Q 018299          241 ANDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHN----SCPVCRHEV  290 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~~~~----sCPvCR~~l  290 (358)
                      ..+..|.||.+.   + .+..- .|.-.||..|+.+=|..-.    .||.|....
T Consensus        23 ~n~~~C~vC~~~---g-~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~   73 (88)
T 1fp0_A           23 DSATICRVCQKP---G-DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   73 (88)
T ss_dssp             SSSSCCSSSCSS---S-CCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCcCcCcCCC---C-CEEECCCCCCceecccCCCCCCCCcCCCcCCccccCCC
Confidence            346799999864   2 23333 4999999999988665422    499998653

>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=80.10  E-value=1  Score=34.57  Aligned_cols=34  Identities=26%  Similarity=0.685  Sum_probs=25.9

Q ss_pred             CCCeeeeeccCcceeecCCCCCCccCCCCCCCceE
Q 018299           28 NYPLYWCYQCHRAVRISSTNPSEIACPRCSGHFVS   62 (358)
Q Consensus        28 t~~~YwCh~C~r~V~i~~~~~~ei~CP~C~~gFvE   62 (358)
                      ....+||-.|...|..... ...+.||.|+..|--
T Consensus        22 ~~~~~wCP~C~~~~~~~~~-~~~v~C~~C~~~FC~   55 (86)
T 2ct7_A           22 DPKFLWCAQCSFGFIYERE-QLEATCPQCHQTFCV   55 (86)
T ss_dssp             CCCEECCSSSCCCEECCCS-CSCEECTTTCCEECS
T ss_pred             CCCEeECcCCCchheecCC-CCceEeCCCCCcccc
Confidence            4568899999998865443 345899999988864

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=80.05  E-value=0.39  Score=41.96  Aligned_cols=46  Identities=30%  Similarity=0.662  Sum_probs=33.0

Q ss_pred             CCccccccccccccCCccEEe-ccCCeeChhhHHHHHhcCC----CCCccceecc
Q 018299          242 NDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHN----SCPVCRHEVP  291 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~~~~----sCPvCR~~l~  291 (358)
                      .+..|.||.+.   |+ +... .|...||..|+.+-|....    .||.|+....
T Consensus         3 ~~~~C~~C~~~---g~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   53 (184)
T 3o36_A            3 NEDWCAVCQNG---GE-LLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSK   53 (184)
T ss_dssp             SCSSCTTTCCC---SS-CEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSSS
T ss_pred             CCCccccCCCC---Ce-eeecCCCCcccCccccCCCCCCCCCCCEECccccCccc
Confidence            46789999854   33 3333 4999999999988776432    4999987543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	358
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	6e-17
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	5e-15
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	1e-10
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-10
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	1e-09
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	3e-09
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	4e-08
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	5e-07
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	5e-07
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	1e-06
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	1e-05
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	6e-05
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	2e-04
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	5e-04

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 71.8 bits (176), Expect = 6e-17
 Identities = 23/52 (44%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 242 NDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHNSCPVCRHEVPV 292
           +   C VC  E + G EAR L  C H +H+EC+  WL  H++CP+CR  V V
Sbjct: 4   DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV 55

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 66.9 bits (163), Expect = 5e-15
 Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 6/64 (9%)

Query: 246 CPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSSASSSHDVDSDD 305
           CP+C E+      +  L C H +   CI  W+R + +CP+C+  V     S  H ++SD 
Sbjct: 8   CPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE----SVVHTIESDS 61

Query: 306 EHGD 309
           E GD
Sbjct: 62  EFGD 65

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 1e-10
 Identities = 12/69 (17%), Positives = 19/69 (27%), Gaps = 15/69 (21%)

Query: 236 MESHLANDTTCPVCKEEF---------------KVGGEARELACKHIYHSECIVPWLRLH 280
           + +       C +C+                            C H +H  CI  WL+  
Sbjct: 14  LWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTR 73

Query: 281 NSCPVCRHE 289
             CP+   E
Sbjct: 74  QVCPLDNRE 82

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]} Length = 79

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

 Score = 54.6 bits (131), Expect = 1e-10
 Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 4/47 (8%)

Query: 245 TCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL-HNSCPVCRHEV 290
            C +C E  K   + +   C H+  + C+  W       CP CR E+
Sbjct: 25  LCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEI 68

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.4 bits (123), Expect = 1e-09
 Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 6/49 (12%)

Query: 245 TCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVS 293
            C  C+ E K     + L C H   S C+         CP+C+   P+ 
Sbjct: 8   RCQQCQAEAK---CPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLG 50

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 3e-09
 Identities = 11/51 (21%), Positives = 16/51 (31%), Gaps = 3/51 (5%)

Query: 243 DTTCPVCKEEFKVGGEARELA--CKHIYHSECIVPWLRL-HNSCPVCRHEV 290
           D  CP CK         + +   C H     C+         +CP C   +
Sbjct: 3   DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 53

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.5 bits (115), Expect = 4e-08
 Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 6/78 (7%)

Query: 229 AIPTVKIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN---SCPV 285
            +  V+ + + +     CP+C E  K   E     C HI+   C++  L        CP+
Sbjct: 7   RVEEVQNVINAMQKILECPICLELIK---EPVSTKCDHIFCKFCMLKLLNQKKGPSQCPL 63

Query: 286 CRHEVPVSSASSSHDVDS 303
           C++++   S   S     
Sbjct: 64  CKNDITKRSLQESTRFSQ 81

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]} Length = 52

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 5e-07
 Identities = 12/48 (25%), Positives = 16/48 (33%), Gaps = 2/48 (4%)

Query: 246 CPVCKEEFKVGGEA-RELACKHIYHSECIVPWLRLHN-SCPVCRHEVP 291
           CP+C E  ++         C +     C        N  CP CR   P
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYP 50

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.9 bits (106), Expect = 5e-07
 Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 4/61 (6%)

Query: 238 SHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNS-CPVCRHEVPVSSAS 296
           +H     +C +C+       +  E +CKH++   CI+  L++  S CP CR+    +   
Sbjct: 18  AHFVKSISCQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLE 74

Query: 297 S 297
           S
Sbjct: 75  S 75

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

 Score = 42.9 bits (100), Expect = 1e-06
 Identities = 10/52 (19%), Positives = 15/52 (28%), Gaps = 4/52 (7%)

Query: 245 TCPVCKEEFKVGGE--ARELACKHIYHSECIVPWLRLH--NSCPVCRHEVPV 292
            C +C EE                  H  C+  WL +    +C +C      
Sbjct: 8   VCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT 59

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]} Length = 97

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.3 bits (96), Expect = 1e-05
 Identities = 15/75 (20%), Positives = 24/75 (32%), Gaps = 4/75 (5%)

Query: 229 AIPTVKIMESHLANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRH 288
           A    +     L     C  C    +         C+HI+ S C+     +   CPVC  
Sbjct: 8   AWAHSRAALDRLEKLLRCSRCTNILRE--PVCLGGCEHIFCSNCVSDC--IGTGCPVCYT 63

Query: 289 EVPVSSASSSHDVDS 303
              +     +  +DS
Sbjct: 64  PAWIQDLKINRQLDS 78

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.0 bits (92), Expect = 6e-05
 Identities = 18/95 (18%), Positives = 27/95 (28%), Gaps = 24/95 (25%)

Query: 218 GPPPVPEAAIQAIPTVKIMESHLANDTTCPVCKEEFKVGGEA---------------REL 262
           G    PE  I+        E  +A +  C +C E+  V                   R  
Sbjct: 4   GSSGEPEQVIRKY----TEELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLT 59

Query: 263 ACKHIYHSECIVPWLR-----LHNSCPVCRHEVPV 292
            C H +H  C++             CP C+     
Sbjct: 60  KCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGE 94

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 36.7 bits (84), Expect = 2e-04
 Identities = 3/50 (6%), Positives = 18/50 (36%), Gaps = 2/50 (4%)

Query: 245 TCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSS 294
            C +  +  +    + +   + I+    +  +++   + P+    + +  
Sbjct: 2   LCAISGKVPRRPVLSPK--SRTIFEKSLLEQYVKDTGNDPITNEPLSIEE 49

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 5e-04
 Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 8/55 (14%)

Query: 241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN--------SCPVCR 287
           +  + C +C  E+ V        C+ I+ + C+  ++ L          SCP   
Sbjct: 3   SGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA 57

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	358
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.59
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.45
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.31
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.3
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.29
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.27
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.25
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.15
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.08
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.06
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.05
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.92
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	98.9
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	98.89
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.86
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.63
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.26
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	90.63
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	87.52
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	84.75

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

Probab=99.59  E-value=2.7e-16  Score=112.59  Aligned_cols=51  Identities=43%  Similarity=0.944  Sum_probs=46.8

Q ss_pred             CCCccccccccccccCCccEEec-cCCeeChhhHHHHHhcCCCCCccceecc
Q 018299          241 ANDTTCPVCKEEFKVGGEARELA-CKHIYHSECIVPWLRLHNSCPVCRHEVP  291 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lp-C~H~FH~~CI~~WL~~~~sCPvCR~~l~  291 (358)
                      +++.+|+||+++|..++.++.++ |+|.||..||..||+.+++||+||++|.
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            45678999999999999998886 9999999999999999999999999874

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

Probab=99.45  E-value=2.1e-14  Score=106.78  Aligned_cols=48  Identities=31%  Similarity=0.837  Sum_probs=42.8

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      .+.|+||++.|.  +.++.++|+|.||..||..||+.+.+||+||+++..
T Consensus         5 ~d~C~IC~~~~~--~~~~~~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~   52 (68)
T d1chca_           5 AERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCSSCCSCCC--SCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCccCCcCcc--CCcEEeCCCCcCcHHHHHHHHHhCCcCCCCCcchHh
Confidence            568999999986  356778999999999999999999999999998754

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.31  E-value=5.1e-13  Score=108.38  Aligned_cols=72  Identities=25%  Similarity=0.506  Sum_probs=49.6

Q ss_pred             CCCCCCHHHHHhCCceeeeccccCCCccccccccccccC---------------CccEEeccCCeeChhhHHHHHhcC--
Q 018299          218 GPPPVPEAAIQAIPTVKIMESHLANDTTCPVCKEEFKVG---------------GEARELACKHIYHSECIVPWLRLH--  280 (358)
Q Consensus       218 ~~ppas~~~i~~lp~~~~~~~~~~~~~~C~ICle~~~~~---------------~~~~~lpC~H~FH~~CI~~WL~~~--  280 (358)
                      +..+.++.+++.+..    ......+..|+||++.|...               ..+..++|+|+||..||..||+..  
T Consensus         4 ~ss~~pe~v~~~~~e----~~~~~~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~   79 (114)
T d1v87a_           4 GSSGEPEQVIRKYTE----ELKVAPEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNK   79 (114)
T ss_dssp             CSSCCHHHHHHHHEE----ECSSCCSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCC
T ss_pred             CCCCCCHHHHHHHHH----HhcccccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCc
Confidence            334455556554321    11222367899999988532               235677899999999999999854  


Q ss_pred             ---CCCCccceeccCC
Q 018299          281 ---NSCPVCRHEVPVS  293 (358)
Q Consensus       281 ---~sCPvCR~~l~~~  293 (358)
                         .+||+||..+..+
T Consensus        80 ~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          80 DGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             SSCCBCTTTCCBSSSC
T ss_pred             CCCCccccccchhccC
Confidence               3799999987554

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.30  E-value=5.4e-13  Score=103.85  Aligned_cols=50  Identities=24%  Similarity=0.572  Sum_probs=42.4

Q ss_pred             CCccccccccccccCC---------------ccEEeccCCeeChhhHHHHHhcCCCCCccceecc
Q 018299          242 NDTTCPVCKEEFKVGG---------------EARELACKHIYHSECIVPWLRLHNSCPVCRHEVP  291 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~---------------~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~  291 (358)
                      .++.|+||++.+....               .+..++|+|+||..||.+||+.+++||+||+++.
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~   84 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE   84 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEETTSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEccccCcccHHHHHHHHHHCCcCCCCCCccc
Confidence            3567999999885422               3577889999999999999999999999999874

>d1ur6b_ g.44.1.1 (B:) Not-4 N-terminal RING finger domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Not-4 N-terminal RING finger domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=3.6e-13  Score=94.87  Aligned_cols=49  Identities=22%  Similarity=0.467  Sum_probs=40.9

Q ss_pred             ccccccccccccCCc-cEEeccCCeeChhhHHHHHhcC-CCCCccceeccC
Q 018299          244 TTCPVCKEEFKVGGE-ARELACKHIYHSECIVPWLRLH-NSCPVCRHEVPV  292 (358)
Q Consensus       244 ~~C~ICle~~~~~~~-~~~lpC~H~FH~~CI~~WL~~~-~sCPvCR~~l~~  292 (358)
                      .+|+||+++|..++. ++.++|+|.||..||..|++.+ ++||+||+++..
T Consensus         1 leCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           1 VECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             CEETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            379999999986654 4456899999999999999865 469999998854

>d1fbva4 g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=99.27  E-value=1.4e-12  Score=99.53  Aligned_cols=49  Identities=27%  Similarity=0.722  Sum_probs=42.7

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhc-CCCCCccceeccCCC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL-HNSCPVCRHEVPVSS  294 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~-~~sCPvCR~~l~~~~  294 (358)
                      ...|+||++.+.   .++.++|+|.||..||..||+. +++||+||..|....
T Consensus        23 ~~~C~IC~~~~~---~~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~   72 (79)
T d1fbva4          23 FQLCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE   72 (79)
T ss_dssp             TTBCTTTSSSBC---CEECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCC
T ss_pred             CCCCccCCCcCC---CeEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCc
Confidence            357999999988   7889999999999999999985 567999999996543

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.25  E-value=1.4e-12  Score=95.87  Aligned_cols=51  Identities=22%  Similarity=0.460  Sum_probs=41.1

Q ss_pred             CCccccccccccccCC--ccEEeccCCeeChhhHHHHHhc-CCCCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVGG--EARELACKHIYHSECIVPWLRL-HNSCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~--~~~~lpC~H~FH~~CI~~WL~~-~~sCPvCR~~l~~  292 (358)
                      ++..|+||++.+....  ....++|+|.||..||..||+. +.+||+||+.|..
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~   55 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRK   55 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSS
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCccc
Confidence            4689999999865432  3456689999999999999965 4579999998854

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.15  E-value=3.8e-12  Score=90.81  Aligned_cols=46  Identities=7%  Similarity=0.253  Sum_probs=41.5

Q ss_pred             cccccccccccCCccEEec-cCCeeChhhHHHHHhcCCCCCccceeccCC
Q 018299          245 TCPVCKEEFKVGGEARELA-CKHIYHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       245 ~C~ICle~~~~~~~~~~lp-C~H~FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      .|+||++.++   .++.++ |||+||..||.+||+.+.+||+||.++..+
T Consensus         2 ~C~Ic~~~~~---~Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~   48 (56)
T d2baya1           2 LCAISGKVPR---RPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   48 (56)
T ss_dssp             CCTTTCSCCS---SEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             CCccCCchHH---hcCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHH
Confidence            6999999998   677775 999999999999999999999999988654

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.08  E-value=1.1e-11  Score=96.05  Aligned_cols=48  Identities=27%  Similarity=0.729  Sum_probs=42.0

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhcC-CCCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLH-NSCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~-~sCPvCR~~l~~  292 (358)
                      +...|+||++.+.   .++.++|+|.||..||..|++.+ .+||+||.++..
T Consensus        22 ~~l~C~IC~~~~~---~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~   70 (86)
T d1rmda2          22 KSISCQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFP   70 (86)
T ss_dssp             HHTBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             cCcCCccCCcchh---cceecCCCChhhHHHHHHHHhhCCCcCcccCCCCCh
Confidence            3568999999998   78899999999999999999865 579999998743

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.06  E-value=2.3e-11  Score=96.96  Aligned_cols=48  Identities=29%  Similarity=0.784  Sum_probs=41.8

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhcCC---CCCccceeccCC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHN---SCPVCRHEVPVS  293 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~---sCPvCR~~l~~~  293 (358)
                      ...|+||++.|.   .++.++|+|.||..||..|++...   .||+||.++...
T Consensus        21 ~l~CpIC~~~~~---~pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (103)
T d1jm7a_          21 ILECPICLELIK---EPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (103)
T ss_dssp             HTSCSSSCCCCS---SCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             CcCCCccCchhC---CeEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChh
Confidence            568999999998   677899999999999999998754   799999988543

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.05  E-value=1.2e-11  Score=88.37  Aligned_cols=46  Identities=28%  Similarity=0.623  Sum_probs=39.8

Q ss_pred             CccccccccccccCCccEEeccCCeeChhhHHHHHhcCCCCCccceeccCCC
Q 018299          243 DTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLHNSCPVCRHEVPVSS  294 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~~~  294 (358)
                      ...|+||++.|.   .++.++|+|.||..||..|   +.+||+||.++....
T Consensus         6 ~l~C~IC~~~~~---~p~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T d1bora_           6 FLRCQQCQAEAK---CPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CSSCSSSCSSCB---CCSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             CCCCcccCcccC---CCEEecCCCHHhHHHHHcC---CCcCcCCCCcccCCC
Confidence            469999999998   6788999999999999765   668999999997543

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.92  E-value=4.2e-10  Score=84.94  Aligned_cols=50  Identities=20%  Similarity=0.452  Sum_probs=43.9

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHhcC-CCCCccceeccCC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLH-NSCPVCRHEVPVS  293 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~-~sCPvCR~~l~~~  293 (358)
                      .++..|+||++.|.   .++.++|+|.||..||..|++.+ ..||+|+..+...
T Consensus         6 P~~l~CpIc~~~m~---dPV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~   56 (78)
T d1t1ha_           6 PEYFRCPISLELMK---DPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHA   56 (78)
T ss_dssp             SSSSSCTTTSCCCS---SEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSC
T ss_pred             CccCCCcCcCchhh---CceEccCCCcchHHHHHHHHHHCCCCCCcccccCCcc
Confidence            35789999999999   78899999999999999999875 5699999988653

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.90  E-value=4.9e-10  Score=85.04  Aligned_cols=49  Identities=16%  Similarity=0.102  Sum_probs=42.9

Q ss_pred             CCCccccccccccccCCccEEeccCCeeChhhHHHHHhc-CCCCCccceeccC
Q 018299          241 ANDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRL-HNSCPVCRHEVPV  292 (358)
Q Consensus       241 ~~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~-~~sCPvCR~~l~~  292 (358)
                      .++..|+||++.|.   .++.++|||.|+..||..||.. +.+||+||.++..
T Consensus         5 P~~l~CpIc~~l~~---dPv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~   54 (80)
T d2c2la2           5 PDYLCGKISFELMR---EPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQ   54 (80)
T ss_dssp             CSTTBCTTTCSBCS---SEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CccccCcCcCchhh---hhcccCCcCeecHHHHHHHHhcCCccCCCccccccc
Confidence            35789999999999   7889999999999999999976 4579999998743

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

Probab=98.89  E-value=3.1e-10  Score=81.56  Aligned_cols=48  Identities=25%  Similarity=0.562  Sum_probs=37.5

Q ss_pred             CCccccccccccccCCccEEec-----cCCeeChhhHHHHHhc--CCCCCccceeccC
Q 018299          242 NDTTCPVCKEEFKVGGEARELA-----CKHIYHSECIVPWLRL--HNSCPVCRHEVPV  292 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lp-----C~H~FH~~CI~~WL~~--~~sCPvCR~~l~~  292 (358)
                      +...|.||++.+...   ...+     |+|.||..||..|++.  +.+||+||+++..
T Consensus         5 d~~~C~IC~~~~~~~---~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           5 DVPVCWICNEELGNE---RFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             SCCEETTTTEECSCC---CCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCccCCccCCCc---eeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            467899999988632   3334     4599999999999964  4579999998754

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.86  E-value=1.6e-10  Score=90.98  Aligned_cols=45  Identities=27%  Similarity=0.650  Sum_probs=38.0

Q ss_pred             CccccccccccccCCccEE-eccCCeeChhhHHHHHhcCCCCCccceeccC
Q 018299          243 DTTCPVCKEEFKVGGEARE-LACKHIYHSECIVPWLRLHNSCPVCRHEVPV  292 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~-lpC~H~FH~~CI~~WL~~~~sCPvCR~~l~~  292 (358)
                      ...|+||++.|.   .++. .+|+|.||..||..|+.  +.||+||..+..
T Consensus        22 ~l~C~IC~~~~~---~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~   67 (97)
T d1jm7b_          22 LLRCSRCTNILR---EPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWI   67 (97)
T ss_dssp             TTSCSSSCSCCS---SCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSC
T ss_pred             cCCCccCCchhh---cCceeCCCCCchhHHHHHHHHh--ccccccCCcCch
Confidence            569999999998   4555 47999999999999984  469999988754

>d1wgma_ g.44.1.2 (A:) Ubiquitin conjugation factor E4A {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Ubiquitin conjugation factor E4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.63  E-value=8.3e-09  Score=81.29  Aligned_cols=49  Identities=12%  Similarity=0.133  Sum_probs=43.6

Q ss_pred             CCccccccccccccCCccEEeccC-CeeChhhHHHHHhcCCCCCccceeccCC
Q 018299          242 NDTTCPVCKEEFKVGGEARELACK-HIYHSECIVPWLRLHNSCPVCRHEVPVS  293 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~-H~FH~~CI~~WL~~~~sCPvCR~~l~~~  293 (358)
                      ++..|+||++.|.   .+++++|+ |.|+..||..||+.+.+||+|+.+|...
T Consensus        21 ~~f~CPI~~~lm~---dPV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~   70 (98)
T d1wgma_          21 DEFLDPIMSTLMC---DPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMD   70 (98)
T ss_dssp             TTTBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTT
T ss_pred             HHhCCcCchhHHH---HHHhcccccchhhHHHHHHHHHhcCCcccccccccch
Confidence            4689999999999   88999965 5899999999999999999999988543

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.26  E-value=8.7e-08  Score=74.11  Aligned_cols=47  Identities=23%  Similarity=0.565  Sum_probs=37.9

Q ss_pred             CCccccccccccccCCccEEeccCCeeChhhHHHHHhcC----C----CCCccce
Q 018299          242 NDTTCPVCKEEFKVGGEARELACKHIYHSECIVPWLRLH----N----SCPVCRH  288 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~lpC~H~FH~~CI~~WL~~~----~----sCPvCR~  288 (358)
                      ....|+||++++...+.+..++|+|.||..||..|++..    .    +||.|..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            357999999999876666777899999999999999642    1    4998654

>d1f62a_ g.50.1.2 (A:) Williams-Beuren syndrome transcription factor, WSTF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Williams-Beuren syndrome transcription factor, WSTF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.63  E-value=0.04  Score=36.56  Aligned_cols=43  Identities=26%  Similarity=0.609  Sum_probs=29.7

Q ss_pred             cccccccccccCCccEEe-ccCCeeChhhHHHHHhcCC----CCCccce
Q 018299          245 TCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHN----SCPVCRH  288 (358)
Q Consensus       245 ~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~~~~----sCPvCR~  288 (358)
                      .|.||...-..+ ..+.- .|...||..|+.+-+....    .||.|+.
T Consensus         2 ~C~vC~~~~~~~-~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCC-CEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            588997654322 33333 4999999999998765432    3999974

>d1we9a_ g.50.1.2 (A:) PHD finger protein At5g26210 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At5g26210
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=87.52  E-value=0.045  Score=38.05  Aligned_cols=47  Identities=19%  Similarity=0.480  Sum_probs=32.9

Q ss_pred             CCccccccccccccCCccEEe-ccCCeeChhhHHHHHh-----cCCCCCccce
Q 018299          242 NDTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLR-----LHNSCPVCRH  288 (358)
Q Consensus       242 ~~~~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~-----~~~sCPvCR~  288 (358)
                      ....|.||......++..+.- .|+..||..|+..-..     .+-.||.|+.
T Consensus         5 ~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~   57 (64)
T d1we9a_           5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcC
Confidence            467999999877655544444 4999999999964221     1235999975

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.75  E-value=0.21  Score=35.14  Aligned_cols=44  Identities=30%  Similarity=0.662  Sum_probs=29.6

Q ss_pred             CccccccccccccCCccEEe-ccCCeeChhhHHHHHhcCC----CCCccceec
Q 018299          243 DTTCPVCKEEFKVGGEAREL-ACKHIYHSECIVPWLRLHN----SCPVCRHEV  290 (358)
Q Consensus       243 ~~~C~ICle~~~~~~~~~~l-pC~H~FH~~CI~~WL~~~~----sCPvCR~~l  290 (358)
                      ...|.||.+.   ++ ++.- .|...||..|+.+.|....    .||.|+...
T Consensus         7 c~~C~~C~~~---~~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   55 (70)
T d1fp0a1           7 ATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   55 (70)
T ss_dssp             SSCCSSSCSS---SC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCCCCCc---CE-EEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcC
Confidence            3467777543   33 3333 4999999999998875533    399996543