Citrus Sinensis ID: 017955

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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-------360---
Protein Sequence
MAESPSQAPTPTTPTASDTDPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIPVTLTPPFSPPSLTPDHVDDPSFGSQFLQVLRLIAQAARDEDAPQQLTQDPQYGHDFLRIELDGWENDAREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENEDEEDLRRRWRDVLPLRIRDFATRSRSGRNRILDWAEILNNSIEFRLEAPESDRYIGNPADYMDAAGYEALLQNLAESDGGRRGAPRAAKSAVLELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEERKKRVSAGASVGGASGSAGGNLSLG
Secondary Structure (PSIPRED)
cccccccccccccccccccccccEEEcccccccccccccccccccccccccccEEcccccccccccccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHcccccccccccHHHHHccccEEEccccccccccccccccccccEEEEccccccccHHcHHHHHHccccccccccccccccHHHHHHHHHHHcccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccEEEEcccccEccccccccccccccccccccEEEccccccccccccccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccccccccHEEccccccccccccccccccccccHccccccHHHHHHHHHHccccccccccccHHHHHcccEEEEEccccccEccccHcccccccHHcccccccccccccEcHHHHHccccccEEEEcccccccHHHccccccccccccccccccEEEccccc
Coil and Loop (DISEMBL)
maespsqaptpttptasdtdptqywchhcekrvsietlanlpdvicheckngfvesipvtltppfsppsltpdhvddpsfgsQFLQVLRLIAQAardedapqqltqdpqyghDFLRIEldgwendaredendeneenrnvdeegdeneneneddeeneggedrsdneneenienedeEDLRRRWRDVLPLRIRDFatrsrsgrnRILDWAEILNNSIEfrleapesdryignpadyMDAAGYEALLQNLaesdggrrgapraaksavlelptveilseQETIVCAICKdtvnvgetatklpcghvyhgdcivpwldsrntcpvcrfelptddpeyEEERKKRVSAgasvggasgsaggnlslg
Flexible Loop (DISEMBL)
maespsqaptpttptasdtdpTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIPVTLTPPFSPPSLTPDHVDDPSFGSQFLQVLRLIAQAARDEDAPQQLTQDPQYGHDFLRIELDGWendaredendeneenrnvdeegdeneneneddeeneggedrsdneneenienedeedlrrrwrdvlplrirdfatrsrsgrnrilDWAEILNNSIEFRLEAPESDRYIGNPADYMDAAGYEALLQNLAESDGGRRGAPRAAKSAVlelptveilseqETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFElptddpeyeEERKKRVsagasvggasgsaggnlslg
Low Complexity Region (SEG)
MAESpsqaptpttptasdtdptqYWCHHCEKRVSIETLANLPDVICHECKNGFVESIpvtltppfsppsltpDHVDDPSFGSQFLQVLRLIAQAARDEDAPQQLTQDPQYGHDFLRIELDGWendaredendeneenrnvdeegdeneneneddeeneggedrsdneneenienedeedLRRRWRDVLPLRIRDFATRSRSGRNRILDWAEILNNSIEFRLEAPESDRYIGNPADYMDAAGYEALLQNLAESDGGRRGAPRAAKSAVLELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEERKKRvsagasvggasgsaggNLSLG
Disordered region (IsUnstruct)
**********************QYWCHHCEKRVSIETLANLPDVICHECKNGFVESIPVTLT******************GSQFLQVLRLIAQ****************YGHDFLRIELDGW************************************************************RWRDVLPLRIRDFATRSRSGRNRILDWAEILNNSIEFRLEAPESDRYIGNPADYMDAAGYEALLQN*****************AVLELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFEL***********************************
Disordered Region (DISOPRED)
***********************YWCHHCEKRVSIETLANLPDVICHECKNG*************************PSFGSQFLQVLRLIAQAA**********QDPQYGHDFLRIELDGWEN********************************************************************************************************YIGNPADYMDAAGYEALLQ*****************SAVLELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP**********************************
Disordered Region (DISEMBL)
********************PTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIPVTLTPPFSPPSLTPDHVDDPSFGSQFLQVLRLIAQAARDEDAPQQLTQDPQYGHDFLRIELDGWEND*******************************************************RRRWRDVLPLRIRDFATRSRSGRNRILDWAEILNNSIEFRLEAPESDRYIGNPADYMDAAGYEALLQNLAE************KSAVLELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD*********************GSAGGNLSLG
Disordered Region (DISPRO)
*******************DPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIP**********************GSQFLQVLRLIAQAARDEDAPQQLTQDPQYGHDFLRIEL**************************************************ENIENEDEEDLRRRWRDVLPLRIRDFATRSRSGRNRILDWAEILNNSIEFRLEAPESDRYIGNPADYMDAAGYEALLQNLAESDGGRRGAPRAAKSAVLELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD************AGA****************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAESPSQAPTPTTPTASDTDPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIPVTLTPPFSPPSLTPDHVDDPSFGSQFLQVLRLIAQAARDEDAPQQLTQDPQYGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxEGGEDRSDNENEENIENEDEEDLRRRWRDVLPLRIRDFATRSRSGRNRILDWAEILNNSIEFRLEAPESDRYIGNPADYMDAAGYEALLQNLAESDGGRRGAPRAAKSAVLELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEERKKRVSAGASVGGASGSAGGNLSLG
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	363	2.2.26 [Sep-21-2011]
Q9SPL2	334	E3 ubiquitin-protein liga	yes	no	0.829	0.901	0.491	6e-69
Q8LPN7	328	E3 ubiquitin-protein liga	no	no	0.330	0.365	0.484	4e-28
P0CH30	338	E3 ubiquitin-protein liga	N/A	no	0.366	0.393	0.449	2e-27
Q0II22	313	RING finger protein 126 O	yes	no	0.683	0.792	0.273	2e-17
Q9BV68	326	RING finger protein 126 O	yes	no	0.696	0.776	0.277	2e-17
Q9VE61	147	E3 ubiquitin-protein liga	yes	no	0.231	0.571	0.465	1e-16
Q9CY62	165	E3 ubiquitin-protein liga	yes	no	0.269	0.593	0.397	1e-16
Q9P0P0	153	E3 ubiquitin-protein liga	no	no	0.247	0.588	0.433	2e-16
Q7ZW78	156	E3 ubiquitin-protein liga	no	no	0.250	0.583	0.430	3e-16
Q8RXD3	310	E3 ubiquitin-protein liga	no	no	0.352	0.412	0.352	4e-16

>sp|Q9SPL2|CIP8_ARATH E3 ubiquitin-protein ligase CIP8 OS=Arabidopsis thaliana GN=CIP8 PE=1 SV=1

 Score =  261 bits (667), Expect = 6e-69,   Method: Compositional matrix adjust.
 Identities = 176/358 (49%), Positives = 224/358 (62%), Gaps = 57/358 (15%)

Query: 1   MAESPSQAPTPTTPTASDTDPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESI--- 57
           M+++PS +P  T           +WC+HC KRV +ETL +   V+C EC  GFVESI   
Sbjct: 1   MSDAPSSSPDATA---------SHWCYHCNKRVVVETLDDF--VVCCECNKGFVESIQPT 49

Query: 58  PVTLTPPFSPPSLTPD-HVDDPSFGSQFLQVLRLIAQAARDEDAPQQLTQDPQYGHDFLR 116
           P   + P  P  L+PD +V+D S GS FLQ+LRL+A A      P+ L     Y  DF R
Sbjct: 50  PAAYSSPAPPQPLSPDLNVEDSSIGSHFLQMLRLLAHAPSQRSPPRHLDV-LSYEDDFFR 108

Query: 117 IELDGWENDAREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENED 176
           +EL+                +RN  ++ ++ + ++ D+EE +  E+ + N+ E+      
Sbjct: 109 LELN----------------SRNEIDDDEDEDEDDGDEEEEDEEENLTVNDEEDE----- 147

Query: 177 EEDLRRRWRDVLPLRIRDFATRSRSGRNRILDWAEIL----NNSIEFRLEAPESDRYIGN 232
           E+DLRRR R   PL      T+SR+GRNRILDWAEIL    +NSIEFR+E   SDRY GN
Sbjct: 148 EDDLRRRNR--FPLT----TTQSRTGRNRILDWAEILMGIEDNSIEFRME---SDRYAGN 198

Query: 233 PADYMD-AAGYEALLQNLAESDGGRRG----APRAAKSAVLELPTVEILSEQ--ETIVCA 285
           PADY+D AAGYEALLQNLAE DGG  G    AP AAKSA+  L T E+ S +    +VCA
Sbjct: 199 PADYIDDAAGYEALLQNLAEGDGGGGGGRRGAPPAAKSAIEALETFEVSSSEGEMVMVCA 258

Query: 286 ICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEERKKRV 343
           +CKD + +GET  KLPCGH YHGDCIVPWL +RN+CPVCRF+L TDD EYEEERKKR 
Sbjct: 259 VCKDGMVMGETGKKLPCGHCYHGDCIVPWLGTRNSCPVCRFQLETDDAEYEEERKKRT 316

E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins. Probably forms a minimal ubiquitin ligase complex in cooperation with the E2 enzyme UBC8. Its interaction with COP1 suggests that it may participate in proteasome-mediated degradation of HY5 in vivo.
Arabidopsis thaliana (taxid: 3702)
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 =  125 bits (315), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 61/126 (48%), Positives = 79/126 (62%), Gaps = 6/126 (4%)

Query: 217 IEFRLEAPESD---RYIGNPADYMDAAGYEALLQNLAESDGGRRGAPRAAKSAVLELPTV 273
            EF +E   SD   R  GN  DY    G E L+Q LAE+D  R G P A+KSA+  LPTV
Sbjct: 143 FEFVIENHPSDPGNRMPGNFGDYFFGPGLEQLIQQLAENDPNRYGTPPASKSAIDALPTV 202

Query: 274 EI---LSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPT 330
           ++   + + E   CA+C D    G    ++PC HV+H DC++PWL+  N+CPVCRFELPT
Sbjct: 203 KVTKDMLKSEMNQCAVCMDEFEDGSDVKQMPCKHVFHQDCLLPWLELHNSCPVCRFELPT 262

Query: 331 DDPEYE 336
           DDP+YE
Sbjct: 263 DDPDYE 268

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

 Score =  123 bits (309), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 67/149 (44%), Positives = 84/149 (56%), Gaps = 16/149 (10%)

Query: 217 IEFRLEAPESD---RYIGNPADYMDAAGYEALLQNLAESDGGRRGAPRAAKSAVLELPTV 273
           IEF ++   SD   R   N  DY    G E L+Q LAE+D  R G P A+KSA+  LP V
Sbjct: 151 IEFVIQNNPSDQGFRLPANIGDYFIGPGLEQLIQQLAENDPNRYGTPPASKSAIEALPLV 210

Query: 274 EILSE---QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPT 330
            I       E   CA+C D    G  A ++PC H+YH DC++PWL+  N+CPVCR ELPT
Sbjct: 211 NITKSNLNSEFNQCAVCMDDFEEGTEAKQMPCKHLYHKDCLLPWLELHNSCPVCRHELPT 270

Query: 331 DDPEYEEERKKRVSAGASVGGASGSAGGN 359
           DDP+YE            V GA G++GGN
Sbjct: 271 DDPDYERR----------VRGAQGTSGGN 289

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: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

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

 Score = 90.9 bits (224), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 90/329 (27%), Positives = 136/329 (41%), Gaps = 81/329 (24%)

Query: 21  PTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIPVTLTPPFSPPSLTPDHVDDPSF 80
           P +Y+CH C    S+E +  LPD IC  C++GF+E +P          + + ++   PS 
Sbjct: 8   PGRYFCHCC----SVEIVPRLPDYICPRCESGFIEELPEE--------TRSAENGSAPST 55

Query: 81  GSQFLQVLRLIAQAARD---EDAPQQLTQDPQ-YGHDFLRI-----ELDGWENDAREDEN 131
            S         A  +R    E+  Q L   PQ YGH    I     E+  +   A+ D++
Sbjct: 56  AS---------ADQSRQQPFENVDQPLFTLPQGYGHFAFGIFDDSFEIPTFPPGAQADDS 106

Query: 132 DENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENEDEEDLRRRWRDVLPLR 191
            + E  R                                    E E+  R R+    P R
Sbjct: 107 RDPESRR------------------------------------EREQHSRHRYGARQP-R 129

Query: 192 IRDFATRSRSGRNRILDWAEILNNSIEFRLEAPESDRYIG---------NPADYM-DAAG 241
            R  A R+ +GR+  +   E +   +   +  P +   +G         NP DY   A G
Sbjct: 130 ARLTARRA-TGRHEGVPTLEGIIQQLVNGIITPATIPNLGLGPWGVLHSNPMDYAWGANG 188

Query: 242 YEALLQNLAESDGGRRGAPRAAKSAVLELPTVEILSEQ--ETIVCAICKDTVNVGETATK 299
            +A++  L  +     G P A K  +  LPTV +  E     + C +CKD   +GE   +
Sbjct: 189 LDAIITQLL-NQFENTGPPPADKEKIQALPTVPVTEEHVGSGLECPVCKDDYGLGEHVRQ 247

Query: 300 LPCGHVYHGDCIVPWLDSRNTCPVCRFEL 328
           LPC H++H  CIVPWL+  ++CPVCR  L
Sbjct: 248 LPCNHLFHDGCIVPWLEQHDSCPVCRKSL 276

Bos taurus (taxid: 9913)

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

 Score = 90.1 bits (222), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 89/321 (27%), Positives = 127/321 (39%), Gaps = 68/321 (21%)

Query: 21  PTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIP--VTLTPPFSPPSLTPDHVDDP 78
           P +Y+CH C    S+E +  LPD IC  C++GF+E +P     T   S PS  P     P
Sbjct: 8   PGRYFCHCC----SVEIVPRLPDYICPRCESGFIEELPEETRSTENGSAPSTAPTDQSRP 63

Query: 79  SFGSQFLQVLRLIAQAARDEDAPQQLTQDPQ-YGHDFLRIELDGWENDAREDENDENEEN 137
                              E   Q L   PQ YG     I  D +E              
Sbjct: 64  PL-----------------EHVDQHLFTLPQGYGQFAFGIFDDSFEIPTFPPGAQA---- 102

Query: 138 RNVDEEGDENENENEDDEENEGGEDRSDNENEENIENEDEEDLRRRWRDVLPLRIRDFAT 197
               ++G + E+  E D  +                       R R+    P R R   T
Sbjct: 103 ----DDGRDPESRRERDHPS-----------------------RHRYGARQP-RAR-LTT 133

Query: 198 RSRSGRNRILDWAEILNNSIEFRLEAPESDRYIG-------NPADYM-DAAGYEALLQNL 249
           R  +GR+  +   E +   +   +  P +   +G       NP DY   A G +A++  L
Sbjct: 134 RRATGRHEGVPTLEGIIQQLVNGIITPATIPSLGPWGVLHSNPMDYAWGANGLDAIITQL 193

Query: 250 AESDGGRRGAPRAAKSAVLELPTVEILSEQ--ETIVCAICKDTVNVGETATKLPCGHVYH 307
             +     G P A K  +  LPTV +  E     + C +CKD   +GE   +LPC H++H
Sbjct: 194 L-NQFENTGPPPADKEKIQALPTVPVTEEHVGSGLECPVCKDDYALGERVRQLPCNHLFH 252

Query: 308 GDCIVPWLDSRNTCPVCRFEL 328
             CIVPWL+  ++CPVCR  L
Sbjct: 253 DGCIVPWLEQHDSCPVCRKSL 273

Homo sapiens (taxid: 9606)

>sp|Q9VE61|RN181_DROME E3 ubiquitin-protein ligase RNF181 homolog OS=Drosophila melanogaster GN=CG7694 PE=2 SV=1

 Score = 87.8 bits (216), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 40/86 (46%), Positives = 55/86 (63%), Gaps = 2/86 (2%)

Query: 259 APRAAKSAVLELPTVEILSEQET--IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLD 316
            P A+K A+LELP  EI+   E   + C++CK+    G+    LPC H +H +CI+ WL 
Sbjct: 43  VPEASKRAILELPVHEIVKSDEGGDLECSVCKEPAEEGQKYRILPCKHEFHEECILLWLK 102

Query: 317 SRNTCPVCRFELPTDDPEYEEERKKR 342
             N+CP+CR+EL TDDP YEE R+ R
Sbjct: 103 KTNSCPLCRYELETDDPVYEELRRFR 128

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.

Drosophila melanogaster (taxid: 7227)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9CY62|RN181_MOUSE E3 ubiquitin-protein ligase RNF181 OS=Mus musculus GN=Rnf181 PE=2 SV=1

 Score = 87.4 bits (215), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 39/98 (39%), Positives = 55/98 (56%)

Query: 246 LQNLAESDGGRRGAPRAAKSAVLELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHV 305
            ++L   D      P AAK+ V  LP   I S +  + C +C       ET  ++PC H+
Sbjct: 50  FEDLGLVDWEHHLPPPAAKAVVESLPRTVISSAKADLKCPVCLLEFEAEETVIEMPCHHL 109

Query: 306 YHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEERKKRV 343
           +H +CI+PWL   N+CP+CR ELPTDD  YEE +K + 
Sbjct: 110 FHSNCILPWLSKTNSCPLCRHELPTDDDSYEEHKKDKA 147

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.

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q9P0P0|RN181_HUMAN E3 ubiquitin-protein ligase RNF181 OS=Homo sapiens GN=RNF181 PE=1 SV=1

 Score = 87.4 bits (215), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 39/90 (43%), Positives = 52/90 (57%)

Query: 253 DGGRRGAPRAAKSAVLELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIV 312
           D      P AAK+ V  LP   I   Q  + C +C       ETA ++PC H++H  CI+
Sbjct: 45  DWDHHLPPPAAKTVVENLPRTVIRGSQAELKCPVCLLEFEEEETAIEMPCHHLFHSSCIL 104

Query: 313 PWLDSRNTCPVCRFELPTDDPEYEEERKKR 342
           PWL   N+CP+CR+ELPTDD  YEE R+ +
Sbjct: 105 PWLSKTNSCPLCRYELPTDDDTYEEHRRDK 134

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.

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q7ZW78|RN181_DANRE E3 ubiquitin-protein ligase RNF181 OS=Danio rerio GN=rnf181 PE=2 SV=2

 Score = 86.3 bits (212), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 40/93 (43%), Positives = 58/93 (62%), Gaps = 2/93 (2%)

Query: 252 SDGGRRGAPRAAKSAVLELPTVEILSEQ--ETIVCAICKDTVNVGETATKLPCGHVYHGD 309
           SD  +R  P AAK+ V  LP V I  EQ  + + C +C       E+  ++PC H++H  
Sbjct: 45  SDWDQRLPPPAAKAVVQSLPVVIISPEQADKGVKCPVCLLEFEEQESVREMPCKHLFHTG 104

Query: 310 CIVPWLDSRNTCPVCRFELPTDDPEYEEERKKR 342
           CI+PWL+  N+CP+CR ELPTD+ +YEE +K +
Sbjct: 105 CILPWLNKTNSCPLCRLELPTDNADYEEFKKDK 137

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.

Danio rerio (taxid: 7955)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|Q8RXD3|AIP2_ARATH E3 ubiquitin-protein ligase AIP2 OS=Arabidopsis thaliana GN=AIP2 PE=1 SV=1

 Score = 86.3 bits (212), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 48/136 (35%), Positives = 72/136 (52%), Gaps = 8/136 (5%)

Query: 230 IGNPADYMDAA--GYEALLQNLAESDGGRRGAPRAAKSAVLELPTVEILSEQETIV---- 283
           IG  A+ M     G + ++ ++ + DGG   AP A+K  V +LP +    E         
Sbjct: 170 IGETANLMQELINGLDMIIPDILD-DGGPPRAPPASKEVVEKLPVIIFTEELLKKFGAEA 228

Query: 284 -CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEERKKR 342
            C ICK+ + +G+   +LPC H +H  C+ PWLD  N+CP+CR ELPTDD +YE  +++ 
Sbjct: 229 ECCICKENLVIGDKMQELPCKHTFHPPCLKPWLDEHNSCPICRHELPTDDQKYENWKERE 288

Query: 343 VSAGASVGGASGSAGG 358
             A     GA  +  G
Sbjct: 289 KEAEEERKGAENAVRG 304

E3 ubiquitin-protein ligase that acts as a negative regulator of abscisic acid (ABA) signaling. Mediates ubiquitination and subsequent proteasomal degradation of the transcription factor ABI3.

Arabidopsis thaliana (taxid: 3702)

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	363
255538976	358	zinc finger protein, putative [Ricinus c	0.911	0.924	0.664	1e-106
356575409	337	PREDICTED: E3 ubiquitin-protein ligase C	0.848	0.913	0.569	4e-89
225457933	334	PREDICTED: E3 ubiquitin-protein ligase C	0.848	0.922	0.532	7e-78
15238295	334	E3 ubiquitin-protein ligase CIP8 [Arabid	0.829	0.901	0.491	4e-67
297797513	330	hypothetical protein ARALYDRAFT_496711 [	0.829	0.912	0.491	1e-66
356536435	333	PREDICTED: E3 ubiquitin-protein ligase C	0.396	0.432	0.738	5e-56
302142685	285	unnamed protein product [Vitis vinifera]	0.677	0.863	0.417	4e-49
302774280	614	hypothetical protein SELMODRAFT_451325 [	0.842	0.498	0.351	4e-46
302769950	613	hypothetical protein SELMODRAFT_451322 [	0.341	0.202	0.611	1e-40
383171379	138	Pinus taeda anonymous locus 0_10618_01 g	0.366	0.963	0.558	5e-36

>gi|255538976|ref|XP_002510553.1| zinc finger protein, putative [Ricinus communis] gi|223551254|gb|EEF52740.1| zinc finger protein, putative [Ricinus communis]

 Score =  392 bits (1007), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 230/346 (66%), Positives = 263/346 (76%), Gaps = 15/346 (4%)

Query: 1   MAESPSQAPTPTTPTASDTDPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIPVT 60
           MAESPSQ P P +    +TD  QYWC+ C KRVS ETLAN  DVIC ECKNGFVE I   
Sbjct: 1   MAESPSQPPIPAS--ILETDTRQYWCYRCIKRVSTETLANESDVICLECKNGFVELITAA 58

Query: 61  LTPPFSPPSLTPDHVDDPSFGSQFLQVLRLIAQAARDEDAPQQLTQDPQYGHDFLRIELD 120
            TPP + PSLT D  DD +FGSQFLQ+LR+IAQAAR+ED P  L QDP    DFLRIEL+
Sbjct: 59  ATPPSNTPSLTSDQADDSTFGSQFLQMLRIIAQAAREEDTPPPLPQDPYSEDDFLRIELN 118

Query: 121 GWENDAREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENEDEEDL 180
           GW+ND  E+++ ++ +N N          EN D+ E++ GED SDNE EE    ++EED+
Sbjct: 119 GWDNDEDEEDDKDSNKNEN---------EENRDEGEHDDGEDISDNETEEENREDEEEDM 169

Query: 181 RRRWRDVLPLRIRDFATRSRSGRNRILDWAEIL----NNSIEFRLEAPESDRYIGNPADY 236
           RRR RD L LRIR+FATR+RSGRNRILDWAEIL    +NSIEF LE PE+DRYIGNP DY
Sbjct: 170 RRRRRDFLRLRIREFATRARSGRNRILDWAEILMGLEDNSIEFLLEVPETDRYIGNPEDY 229

Query: 237 MDAAGYEALLQNLAESDGGRRGAPRAAKSAVLELPTVEILSEQETIVCAICKDTVNVGET 296
           +DAAGYEALLQNLAESD GRRGAP A+KS+V  LPT  I  E++T VCAICKD VNVGET
Sbjct: 230 VDAAGYEALLQNLAESDDGRRGAPPASKSSVSALPTAVITLEEQTRVCAICKDMVNVGET 289

Query: 297 ATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEERKKR 342
            TKLPC H YHGDCIVPWL SRN+CPVCRFELPTDD EYEEERKK+
Sbjct: 290 ETKLPCDHGYHGDCIVPWLGSRNSCPVCRFELPTDDTEYEEERKKK 335

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356575409|ref|XP_003555834.1| PREDICTED: E3 ubiquitin-protein ligase CIP8-like [Glycine max]

 Score =  334 bits (857), Expect = 4e-89,   Method: Compositional matrix adjust.
 Identities = 193/339 (56%), Positives = 226/339 (66%), Gaps = 31/339 (9%)

Query: 6   SQAPTPTTPTASDTDPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIPVTLTPPF 65
           S+AP P T   +D  P  YWC+HCEKRVS+ETLANLPDV+C ECKNGFVES+P       
Sbjct: 2   SEAPPPPT---ADASPPPYWCYHCEKRVSVETLANLPDVVCGECKNGFVESMPTPSRS-- 56

Query: 66  SPPSLTPDHVDDPSFGSQFLQVLRLIAQAARDEDAPQQLTQDPQYGHDFLRIELDGWEND 125
                     DDP FGSQFLQVLRLIAQ+ARD+DA           +DFLRIEL GW+ND
Sbjct: 57  ---RSPSASSDDPYFGSQFLQVLRLIAQSARDDDASPPPPPSRSPENDFLRIELGGWDND 113

Query: 126 AREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENEDEEDLRRRWR 185
              + +D+N +    + E  E+ + NED     GG+D         +      DL     
Sbjct: 114 EENENDDDNGDEEFEEHEEAEDRSGNEDPH---GGDDEDLRRRRRELLRLRIRDL----- 165

Query: 186 DVLPLRIRDFATRSRSGRNRILDWAEIL----NNSIEFRLEAPESDRYIGNPADYMDAAG 241
                     ATR+RS RNRILDWAEIL    +NSIEFRL+ PESDRY+GNP DY+DAA 
Sbjct: 166 ----------ATRTRSMRNRILDWAEILMGLEDNSIEFRLQLPESDRYVGNPEDYVDAAE 215

Query: 242 YEALLQNLAESDGG-RRGAPRAAKSAVLELPTVEILSEQETIVCAICKDTVNVGETATKL 300
           YEALLQ LAESDGG RRGAP A+K+A+  LPTV+I SE E + CAICKD + VG+ A +L
Sbjct: 216 YEALLQTLAESDGGGRRGAPPASKAALEALPTVKIASESEAVACAICKDLLGVGDAAKRL 275

Query: 301 PCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEER 339
           PCGH YHGDCIVPWL SRN+CPVCRFELPTDD EYEEER
Sbjct: 276 PCGHRYHGDCIVPWLSSRNSCPVCRFELPTDDKEYEEER 314

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225457933|ref|XP_002273623.1| PREDICTED: E3 ubiquitin-protein ligase CIP8 isoform 1 [Vitis vinifera] gi|359492263|ref|XP_003634390.1| PREDICTED: E3 ubiquitin-protein ligase CIP8 isoform 2 [Vitis vinifera] gi|147826680|emb|CAN66109.1| hypothetical protein VITISV_007725 [Vitis vinifera]

 Score =  297 bits (760), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 179/336 (53%), Positives = 221/336 (65%), Gaps = 28/336 (8%)

Query: 13  TPTASDTDPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIPVTLTPPFSPPSLTP 72
           +P  SDT    YWC+ C+K VSIETL +LPDVIC+ECK GFVE+I V    P +P     
Sbjct: 4   SPIQSDT--LHYWCYQCDKHVSIETLPDLPDVICNECKTGFVETIGVA---PTAPEPRNA 58

Query: 73  DHVDDPSFGSQFLQVLRLIAQAARDEDAPQQLTQDPQYGHDFLRIELDGWENDAREDEND 132
           D +D+ S    F + LR IAQ   D++ P  L  D     DFLRI+LDGW+ND  ED ++
Sbjct: 59  DQIDERSLVYAFTRRLRHIAQPPSDDEDPPSLPPDHASEDDFLRIDLDGWDNDEDEDVSE 118

Query: 133 ENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIEN-EDEEDLRRRWRDVLPLR 191
            + E                  EE E  EDRSDNENE N+   E + D  RR R++L  R
Sbjct: 119 NDGEG-----------------EEQEEEEDRSDNENEGNVYRPEIDRDHLRRRREMLRRR 161

Query: 192 IRDFATRSRSGRNRILDWAEIL---NNSIEFRLEAPESDRYIGNPADYMDAAGYEALLQN 248
           I + A  S    N +LDWA ++   +++IEF  + PE + Y GNP DY+DAAGYE LLQN
Sbjct: 162 IHNLAAAS-GNPNAVLDWAILMASEDSTIEFHFQMPEPEGYTGNPEDYVDAAGYEELLQN 220

Query: 249 LAESDGG-RRGAPRAAKSAVLELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYH 307
           LAESDG  RRGAP A+KSA+  LP+VEI SE++ + CAICKD V++ E A KLPCGH YH
Sbjct: 221 LAESDGAARRGAPPASKSAISALPSVEIKSEEQVLACAICKDVVSICEIARKLPCGHGYH 280

Query: 308 GDCIVPWLDSRNTCPVCRFELPTDDPEYEEERKKRV 343
           GDCIVPWL+SRN+CPVCRFELPTDD EYEEERKKR+
Sbjct: 281 GDCIVPWLNSRNSCPVCRFELPTDDSEYEEERKKRL 316

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15238295|ref|NP_201297.1| E3 ubiquitin-protein ligase CIP8 [Arabidopsis thaliana] gi|61211690|sp|Q9SPL2.1|CIP8_ARATH RecName: Full=E3 ubiquitin-protein ligase CIP8; AltName: Full=COP1-interacting protein 8 gi|5929906|gb|AAD56636.1|AF162150_1 COP1-interacting protein CIP8 [Arabidopsis thaliana] gi|8843756|dbj|BAA97304.1| COP1-interacting protein CIP8 [Arabidopsis thaliana] gi|19698865|gb|AAL91168.1| COP1-interacting protein CIP8 [Arabidopsis thaliana] gi|30984560|gb|AAP42743.1| At5g64920 [Arabidopsis thaliana] gi|111146876|gb|ABH07378.1| COP1-interacting protein 8 [Arabidopsis thaliana] gi|332010587|gb|AED97970.1| E3 ubiquitin-protein ligase CIP8 [Arabidopsis thaliana]

 Score =  261 bits (667), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 176/358 (49%), Positives = 224/358 (62%), Gaps = 57/358 (15%)

Query: 1   MAESPSQAPTPTTPTASDTDPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESI--- 57
           M+++PS +P  T           +WC+HC KRV +ETL +   V+C EC  GFVESI   
Sbjct: 1   MSDAPSSSPDATA---------SHWCYHCNKRVVVETLDDF--VVCCECNKGFVESIQPT 49

Query: 58  PVTLTPPFSPPSLTPD-HVDDPSFGSQFLQVLRLIAQAARDEDAPQQLTQDPQYGHDFLR 116
           P   + P  P  L+PD +V+D S GS FLQ+LRL+A A      P+ L     Y  DF R
Sbjct: 50  PAAYSSPAPPQPLSPDLNVEDSSIGSHFLQMLRLLAHAPSQRSPPRHLDV-LSYEDDFFR 108

Query: 117 IELDGWENDAREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENED 176
           +EL+                +RN  ++ ++ + ++ D+EE +  E+ + N+ E+      
Sbjct: 109 LELN----------------SRNEIDDDEDEDEDDGDEEEEDEEENLTVNDEEDE----- 147

Query: 177 EEDLRRRWRDVLPLRIRDFATRSRSGRNRILDWAEIL----NNSIEFRLEAPESDRYIGN 232
           E+DLRRR R   PL      T+SR+GRNRILDWAEIL    +NSIEFR+E   SDRY GN
Sbjct: 148 EDDLRRRNR--FPLT----TTQSRTGRNRILDWAEILMGIEDNSIEFRME---SDRYAGN 198

Query: 233 PADYMD-AAGYEALLQNLAESDGGRRG----APRAAKSAVLELPTVEILSEQ--ETIVCA 285
           PADY+D AAGYEALLQNLAE DGG  G    AP AAKSA+  L T E+ S +    +VCA
Sbjct: 199 PADYIDDAAGYEALLQNLAEGDGGGGGGRRGAPPAAKSAIEALETFEVSSSEGEMVMVCA 258

Query: 286 ICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEERKKRV 343
           +CKD + +GET  KLPCGH YHGDCIVPWL +RN+CPVCRF+L TDD EYEEERKKR 
Sbjct: 259 VCKDGMVMGETGKKLPCGHCYHGDCIVPWLGTRNSCPVCRFQLETDDAEYEEERKKRT 316

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297797513|ref|XP_002866641.1| hypothetical protein ARALYDRAFT_496711 [Arabidopsis lyrata subsp. lyrata] gi|297312476|gb|EFH42900.1| hypothetical protein ARALYDRAFT_496711 [Arabidopsis lyrata subsp. lyrata]

 Score =  259 bits (662), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 176/358 (49%), Positives = 219/358 (61%), Gaps = 57/358 (15%)

Query: 1   MAESPSQAPTPTTPTASDTDPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESI--- 57
           M+++PS +P  T           +WC+HC KRV +ETL +   V+C EC  GFVESI   
Sbjct: 1   MSDAPSSSPGATA---------SHWCYHCNKRVVVETLDDF--VVCCECNKGFVESIQPI 49

Query: 58  PVTLTPPFSPPSLTPD-HVDDPSFGSQFLQVLRLIAQAARDEDAPQQLTQDPQYGHDFLR 116
           P   + P  P  L+PD  V+D S GS FLQ+LRL+A A      P+ L     Y  DF R
Sbjct: 50  PAAYSSPAPPQPLSPDLTVEDSSIGSHFLQMLRLLAHAPSQRSPPRHL-DVLSYEDDFFR 108

Query: 117 IELDGWENDAREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENED 176
           +EL+        ++ ++ +E    DEE +   N+ E                      E+
Sbjct: 109 LELNSRTEIDEVEDEEDGDEEEEEDEEENLTVNDEE----------------------EE 146

Query: 177 EEDLRRRWRDVLPLRIRDFATRSRSGRNRILDWAEIL----NNSIEFRLEAPESDRYIGN 232
           E+DLRRR R   PL      TRSR+GRNRILDWAEIL    +NSIEFR+E   S+RY GN
Sbjct: 147 EDDLRRRNR--FPLT----TTRSRTGRNRILDWAEILMGIEDNSIEFRME---SERYTGN 197

Query: 233 PADYMD-AAGYEALLQNLAESDGGRRG---APRAAKSAVLELPTVEILS-EQETI-VCAI 286
           PADY+D +AGYEALLQNLAE DGG  G   AP AAKSA+  L T ++ S E ET+ VCA+
Sbjct: 198 PADYIDDSAGYEALLQNLAEGDGGGGGRRGAPPAAKSAIEALETFQVTSSEGETVMVCAV 257

Query: 287 CKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEERKKRVS 344
           CKD + +GET  KLPCGH YHGDCI+PWL +RN+CPVCRF+L TDD EYEEERKKR S
Sbjct: 258 CKDGMVMGETGKKLPCGHCYHGDCIMPWLGTRNSCPVCRFQLQTDDAEYEEERKKRTS 315

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356536435|ref|XP_003536743.1| PREDICTED: E3 ubiquitin-protein ligase CIP8-like isoform 1 [Glycine max] gi|356536437|ref|XP_003536744.1| PREDICTED: E3 ubiquitin-protein ligase CIP8-like isoform 2 [Glycine max]

 Score =  224 bits (571), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 110/149 (73%), Positives = 124/149 (83%), Gaps = 5/149 (3%)

Query: 196 ATRSRSGRNRILDWAEIL----NNSIEFRLEAPESDRYIGNPADYMDAAGYEALLQNLAE 251
           ATR+RS RNRILDWAEIL    +NSIEFRL+ PESDRY+GNP DY+DAA YEALL  LAE
Sbjct: 169 ATRTRSMRNRILDWAEILMGLEDNSIEFRLQLPESDRYVGNPEDYVDAAEYEALLHTLAE 228

Query: 252 SDGG-RRGAPRAAKSAVLELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDC 310
           SDGG RRGAP A+K+AV  LPTV+I SE E + CAICKD + VG+ A +LPCGH YHGDC
Sbjct: 229 SDGGGRRGAPPASKAAVEALPTVKIASESEAVACAICKDLLGVGDLAKRLPCGHGYHGDC 288

Query: 311 IVPWLDSRNTCPVCRFELPTDDPEYEEER 339
           IVPWL SRN+CPVCR+ELPTDD EYEEER
Sbjct: 289 IVPWLSSRNSCPVCRYELPTDDKEYEEER 317

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302142685|emb|CBI19888.3| unnamed protein product [Vitis vinifera]

 Score =  201 bits (512), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 140/335 (41%), Positives = 175/335 (52%), Gaps = 89/335 (26%)

Query: 13  TPTASDTDPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIPVTLTPPFSPPSLTP 72
           +P  SDT    YWC+ C+K VSIETL +LPDVIC+ECK GFVE+I V    P +P     
Sbjct: 18  SPIQSDT--LHYWCYQCDKHVSIETLPDLPDVICNECKTGFVETIGVA---PTAPEPRNA 72

Query: 73  DHVDDPSFGSQFLQVLRLIAQAARDEDAPQQLTQDPQYGHDFLRIELDGWENDAREDEND 132
           D +D+ S    F + LR IAQ   D++ P  L  D     DFLRI+LDGW+ND       
Sbjct: 73  DQIDERSLVYAFTRRLRHIAQPPSDDEDPPSLPPDHASEDDFLRIDLDGWDND------- 125

Query: 133 ENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENEDEEDLRRRWRDVLPLRI 192
                               +DE+NEG   R           E + D  RR R++L  RI
Sbjct: 126 --------------------EDEDNEGNVYRP----------EIDRDHLRRRREMLRRRI 155

Query: 193 RDFATRSRSGRNRILDWAEIL---NNSIEFRLEAPESDRYIGNPADYMDAAGYEALLQNL 249
            + A  S    N +LDWA ++   +++IEF  + PE + Y GNP DY+DAAGYE LLQNL
Sbjct: 156 HNLAAAS-GNPNAVLDWAILMASEDSTIEFHFQMPEPEGYTGNPEDYVDAAGYEELLQNL 214

Query: 250 AESDG-GRRGAPRAAKSAVLELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHG 308
           AESDG  RRGAP A+KSA+  LP+VEI                                 
Sbjct: 215 AESDGAARRGAPPASKSAISALPSVEI--------------------------------- 241

Query: 309 DCIVPWLDSRNTCPVCRFELPTDDPEYEEERKKRV 343
                    +N+CPVCRFELPTDD EYEEERKKR+
Sbjct: 242 ---------KNSCPVCRFELPTDDSEYEEERKKRL 267

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302774280|ref|XP_002970557.1| hypothetical protein SELMODRAFT_451325 [Selaginella moellendorffii] gi|300162073|gb|EFJ28687.1| hypothetical protein SELMODRAFT_451325 [Selaginella moellendorffii]

 Score =  191 bits (486), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 143/407 (35%), Positives = 196/407 (48%), Gaps = 101/407 (24%)

Query: 24  YWCHHCEKRVSIETLANLPD-VICHECKNGFVESI----PVT------------------ 60
           YWC+ C K V++E   + P  +IC EC+NGFVE +    P T                  
Sbjct: 31  YWCYQCRKEVTVEAQEDGPSAMICSECRNGFVEPLGSPPPRTGEEAPGRSLNISSSNNNG 90

Query: 61  ----------------------LTPPFSPPSLTPDHVDDPSFGS----QFLQVLRLIAQA 94
                                  T P +P +      D  +FG     Q + VL+L+ QA
Sbjct: 91  SSGDTHGYPGNTLRRRRRRGNAPTVPRAPQAQAVSLTD--AFGQLYPQQLVHVLQLLGQA 148

Query: 95  ARDEDAPQQLTQDPQYGHDFLRIELDGWENDAREDENDENEENRNVDEEGDENENENEDD 154
           AR  +       D          + +  +  A+E EN  + +     + GD + +E+E +
Sbjct: 149 ARANNENNSGRSDDSRNEQHGEAQQESADATAQERENSSSLQRSEAHDGGDGDHDESESE 208

Query: 155 EE--------------------------NEGGEDRSDNENEENIENEDEEDLRRRWRDVL 188
            E                            G     DN ++E   NE E+   R+  + L
Sbjct: 209 VEAALLERWESEDEDDEDEWEEVGDEEGAAGQGGGDDNADDEGAHNEQEQ---RQPPEEL 265

Query: 189 PLRIRDFATRSRSGRN-----RILDW-AEILNN----SIEFRLEAPESDRYIGNPADYMD 238
           P R R+   R   G N      +  +  E+L N    +IE R+E P+   Y+GNP DY+D
Sbjct: 266 PPR-RNARVRREQGHNARRPTHLHHYLQELLQNLVGQNIEVRVEVPQ---YVGNPGDYVD 321

Query: 239 AAGYEALLQNLAESDGGRRGAPRAAKSAVLELPTVEILSEQETI-----VCAICKDTVNV 293
           A G+E LLQ LAE+D  RRGAP AAKSAV  LPT  IL EQ  +     VCA+CKDTV V
Sbjct: 322 ARGFELLLQQLAENDNSRRGAPPAAKSAVDTLPT--ILIEQAHLDDGSAVCAVCKDTVCV 379

Query: 294 GETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEERK 340
           GE A ++PC H+YH DCI+PWLDSRN+CPVCRFELPTDDP+YE++++
Sbjct: 380 GEPAKQMPCLHLYHADCILPWLDSRNSCPVCRFELPTDDPDYEDQKR 426

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302769950|ref|XP_002968394.1| hypothetical protein SELMODRAFT_451322 [Selaginella moellendorffii] gi|300164038|gb|EFJ30648.1| hypothetical protein SELMODRAFT_451322 [Selaginella moellendorffii]

 Score =  173 bits (438), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 82/134 (61%), Positives = 103/134 (76%), Gaps = 10/134 (7%)

Query: 212 ILNNSIEFRLEAPESDRYIGNPADYMDAAGYEALLQNLAESDGGRRGAPRAAKSAVLELP 271
           ++  +IE R+E P+   Y+GNP DY+DA G+E LLQ LAE+D  RRGAP AAKSAV  LP
Sbjct: 301 LVGQNIEVRVEVPQ---YVGNPGDYVDARGFELLLQQLAENDNSRRGAPPAAKSAVDTLP 357

Query: 272 TVEILSEQETI-----VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRF 326
           T  IL EQ  +     VCA+CKDTV VGE A ++PC H+YH DCI+PWLDSRN+CPVCRF
Sbjct: 358 T--ILIEQAHLDDGSAVCAVCKDTVCVGEPAKQMPCLHLYHADCILPWLDSRNSCPVCRF 415

Query: 327 ELPTDDPEYEEERK 340
           ELPTDDP+YE++++
Sbjct: 416 ELPTDDPDYEDQKR 429

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|383171379|gb|AFG68993.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence gi|383171380|gb|AFG68994.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence gi|383171381|gb|AFG68995.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence gi|383171382|gb|AFG68996.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence gi|383171383|gb|AFG68997.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence gi|383171384|gb|AFG68998.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence gi|383171385|gb|AFG68999.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence gi|383171386|gb|AFG69000.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence gi|383171387|gb|AFG69001.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence gi|383171388|gb|AFG69002.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence gi|383171389|gb|AFG69003.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence gi|383171390|gb|AFG69004.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence gi|383171391|gb|AFG69005.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence gi|383171392|gb|AFG69006.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence gi|383171393|gb|AFG69007.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence gi|383171394|gb|AFG69008.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence gi|383171395|gb|AFG69009.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence gi|383171396|gb|AFG69010.1| Pinus taeda anonymous locus 0_10618_01 genomic sequence

 Score =  157 bits (398), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 76/136 (55%), Positives = 98/136 (72%), Gaps = 3/136 (2%)

Query: 212 ILNNSIEFRLEAPESDRYIGNPADYMDAAGYEALLQNLAESDGGRRGAPRAAKSAVLELP 271
           I  NS E  LE  +   Y GNP DY+DA G+E LLQ+LAE+D  RRGAP AA+S + +LP
Sbjct: 3   IGGNSRESSLELHDRPFYAGNPGDYLDARGFEQLLQHLAETDNSRRGAPPAAQSVIEQLP 62

Query: 272 TVEILSEQE---TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFEL 328
            + I    E   + VCAICKD++ +G+ A +LPC H+YH +CI+PWL +RN+CPVCR+EL
Sbjct: 63  LIIIRQAHEEDGSSVCAICKDSLALGDQAKQLPCMHLYHPNCILPWLGARNSCPVCRYEL 122

Query: 329 PTDDPEYEEERKKRVS 344
           PTDDPEYEEE+   VS
Sbjct: 123 PTDDPEYEEEKCNAVS 138

Source: Pinus taeda

Species: Pinus taeda

Genus: Pinus

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	363
TAIR|locus:2177684	334	CIP8 "COP1-interacting protein	0.424	0.461	0.678	2.6e-69
TAIR|locus:2092231	328	AT3G19950 [Arabidopsis thalian	0.327	0.362	0.488	1e-32
TAIR|locus:2185108	493	AT5G01980 [Arabidopsis thalian	0.388	0.286	0.482	1.4e-32
TAIR|locus:1005716857	376	AT5G08139 [Arabidopsis thalian	0.415	0.401	0.401	3e-30
TAIR|locus:2193874	351	AT1G55530 [Arabidopsis thalian	0.319	0.330	0.420	1.6e-28
DICTYBASE|DDB_G0280089	457	DDB_G0280089 "RING zinc finger	0.311	0.247	0.393	4.3e-28
TAIR|locus:2075175	395	RDUF1 "RING and Domain of Unkn	0.292	0.268	0.443	2.1e-27
TAIR|locus:2092895	315	AT3G13430 [Arabidopsis thalian	0.300	0.346	0.417	3.6e-27
TAIR|locus:2161058	396	ATCRT1 [Arabidopsis thaliana (	0.347	0.318	0.413	4.5e-27
TAIR|locus:2058465	328	RHC1A "RING-H2 finger C1A" [Ar	0.297	0.329	0.424	2.5e-26

TAIR|locus:2177684 CIP8 "COP1-interacting protein 8" [Arabidopsis thaliana (taxid:3702)]

 Score = 544 (196.6 bits), Expect = 2.6e-69, Sum P(2) = 2.6e-69
 Identities = 118/174 (67%), Positives = 132/174 (75%)

Query:   180 LRRRWRDVLPLRIRDFATRSRSGRNRILDWAEIL----NNSIEFRLEAPESDRYIGNPAD 235
             LRRR R   PL      T+SR+GRNRILDWAEIL    +NSIEFR+E   SDRY GNPAD
Sbjct:   151 LRRRNR--FPLT----TTQSRTGRNRILDWAEILMGIEDNSIEFRME---SDRYAGNPAD 201

Query:   236 YMD-AAGYEALLQNLAESDGG----RRGAPRAAKSAVLELPTVEILS-EQETI-VCAICK 288
             Y+D AAGYEALLQNLAE DGG    RRGAP AAKSA+  L T E+ S E E + VCA+CK
Sbjct:   202 YIDDAAGYEALLQNLAEGDGGGGGGRRGAPPAAKSAIEALETFEVSSSEGEMVMVCAVCK 261

Query:   289 DTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEERKKR 342
             D + +GET  KLPCGH YHGDCIVPWL +RN+CPVCRF+L TDD EYEEERKKR
Sbjct:   262 DGMVMGETGKKLPCGHCYHGDCIVPWLGTRNSCPVCRFQLETDDAEYEEERKKR 315

GO:0005634 "nucleus" evidence=ISM

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

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

GO:0016567 "protein ubiquitination" evidence=IDA

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

 Score = 312 (114.9 bits), Expect = 1.0e-32, Sum P(2) = 1.0e-32
 Identities = 61/125 (48%), Positives = 78/125 (62%)

Query:   218 EFRLEAPESD---RYIGNPADYMDAAGYEALLQNLAESDGGRRGAPRAAKSAVLELPTVE 274
             EF +E   SD   R  GN  DY    G E L+Q LAE+D  R G P A+KSA+  LPTV+
Sbjct:   144 EFVIENHPSDPGNRMPGNFGDYFFGPGLEQLIQQLAENDPNRYGTPPASKSAIDALPTVK 203

Query:   275 ILSEQ---ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD 331
             +  +    E   CA+C D    G    ++PC HV+H DC++PWL+  N+CPVCRFELPTD
Sbjct:   204 VTKDMLKSEMNQCAVCMDEFEDGSDVKQMPCKHVFHQDCLLPWLELHNSCPVCRFELPTD 263

Query:   332 DPEYE 336
             DP+YE
Sbjct:   264 DPDYE 268

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

GO:0010200 "response to chitin" evidence=RCA

TAIR|locus:2185108 AT5G01980 [Arabidopsis thaliana (taxid:3702)]

 Score = 356 (130.4 bits), Expect = 1.4e-32, P = 1.4e-32
 Identities = 69/143 (48%), Positives = 93/143 (65%)

Query:   200 RSGRNRILDWAEILNNSIEFRLEAPESDRYIGNPADYMDAAGYEALLQNLAESDGGRRGA 259
             RS R RI++    L+ +I   LE  +   Y  N  DY+D  G++ LL+ LAESD  RRGA
Sbjct:   264 RSFRQRIIERRHSLSRNIFTGLEDLDFSPYAANVGDYLDERGFDELLEQLAESDNSRRGA 323

Query:   260 PRAAKSAVLELPTVEILSEQ--ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS 317
             P A+ S V  LP V I  E   + +VCAICK+  ++    T+LPC H+YH  CIVPWL +
Sbjct:   324 PPASVSCVRNLPRVIIAEEHVMKGLVCAICKELFSLRNETTQLPCLHLYHAHCIVPWLSA 383

Query:   318 RNTCPVCRFELPTDDPEYEEERK 340
             RN+CP+CR+ELPTDD +YEE ++
Sbjct:   384 RNSCPLCRYELPTDDKDYEEGKR 406

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

TAIR|locus:1005716857 AT5G08139 [Arabidopsis thaliana (taxid:3702)]

 Score = 334 (122.6 bits), Expect = 3.0e-30, P = 3.0e-30
 Identities = 63/157 (40%), Positives = 93/157 (59%)

Query:   190 LRIRDFATRSRSGRNRILDWAEILNNSIEFRLEAPESDRYIGNPAD-YMDAAGYEALLQN 248
             + +    TR R+  +  L W  +LN+++E   +    + YIG   D Y+    Y+ L + 
Sbjct:   213 ISLEGLVTRERAEGSGNLGWEVLLNHTLEINFDVDNRELYIGGDHDDYVQ--DYDMLFEQ 270

Query:   249 LAESDGGRRGAPRAAKSAVLELPTVEILSEQET---IVCAICKDTVNVGETATKLPCGHV 305
              A+++    G P  +KS +  LP V +  E +    +VCA+CKD +N+G  A +LPC H 
Sbjct:   271 FADAEVSVIGLPPTSKSFLNNLPVVLLEGENDDDGGLVCAVCKDEMNIGNKAVQLPCNHK 330

Query:   306 YHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEERKKR 342
             YH +CIVPWL  RNTCPVCR+ELPTDD EYE+ + +R
Sbjct:   331 YHSECIVPWLKVRNTCPVCRYELPTDDAEYEQRKTQR 367

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

TAIR|locus:2193874 AT1G55530 [Arabidopsis thaliana (taxid:3702)]

 Score = 265 (98.3 bits), Expect = 1.6e-28, Sum P(2) = 1.6e-28
 Identities = 50/119 (42%), Positives = 71/119 (59%)

Query:   214 NNSIEFRLEAPESDRYIGNPADYMDAAGYEALLQNLAESDGGRRGAPRAAKSAVLELPTV 273
             N +I  +  A       G+  DY    G+E LLQ LAE+D  R G P A K AV  L TV
Sbjct:   156 NQTITVQNSADMDSVPAGSLGDYFIGPGFEMLLQRLAENDPNRYGTPPAKKEAVEALATV 215

Query:   274 EILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD 332
             +I   +ET+ C++C D   +G  A  +PC H +H DC++PWL+  ++CPVCR++LP D+
Sbjct:   216 KI---EETLQCSVCLDDFEIGTEAKLMPCTHKFHSDCLLPWLELHSSCPVCRYQLPADE 271

GO:0005737 "cytoplasm" evidence=ISM

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

DICTYBASE|DDB_G0280089 DDB_G0280089 "RING zinc finger-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 261 (96.9 bits), Expect = 4.3e-28, Sum P(2) = 4.3e-28
 Identities = 46/117 (39%), Positives = 72/117 (61%)

Query:   229 YIGNPADYMDAAGYEALLQNLAESDGGRRGAPRAAKSAV--LELPTVEILSEQETIVCAI 286
             Y+GNP DY     ++  L  + ++   ++G P A+K  +  L+   V+     + + CA+
Sbjct:   300 YVGNPNDYFQGGDWQGFLNRMFQASK-KKGTPPASKEEIEKLKRDRVDQTIVDQKVDCAV 358

Query:   287 CKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEERK-KR 342
             CKD    G+   +LPC H+YH +CI+PWL+  N+CPVCRFEL TDD  YE++++ KR
Sbjct:   359 CKDEFKWGDDYIELPCQHLYHPECILPWLEQHNSCPVCRFELKTDDDSYEKDKELKR 415

GO:0008270 "zinc ion binding" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

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

 Score = 252 (93.8 bits), Expect = 2.1e-27, Sum P(2) = 2.1e-27
 Identities = 51/115 (44%), Positives = 72/115 (62%)

Query:   234 ADYMDAAGYEALLQNLA--ESDG---GRRGAPRAAKSAVLELPTVEILSEQETIV---CA 285
             ++ +  +G+E LL+ L+  E+ G   GR G P A+KSA+  LP VEI S+  T     CA
Sbjct:   158 SEILMGSGFERLLEQLSQIEASGNGIGRSGNPPASKSAIESLPRVEI-SDCHTKAEANCA 216

Query:   286 ICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEERK 340
             +C +    G    ++PC H++HGDCIVPWL  RN+CPVCRFELP+D  +   E +
Sbjct:   217 VCTEVFEAGIEGREMPCKHIFHGDCIVPWLSIRNSCPVCRFELPSDPIQRSNEEE 271

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:2092895 AT3G13430 [Arabidopsis thaliana (taxid:3702)]

 Score = 249 (92.7 bits), Expect = 3.6e-27, Sum P(2) = 3.6e-27
 Identities = 48/115 (41%), Positives = 69/115 (60%)

Query:   231 GNPADYMDAAGYEALLQNLAESD-GGRRGAPRAAKSAVLELPTVEILSEQETIVCAICKD 289
             G+  DY    G+E LLQ LAE+D   R G P A K AV  L  V+I  E   + C++C D
Sbjct:   173 GSLGDYFIGPGFETLLQRLAENDLNNRYGTPPATKEAVEALAMVKI--EDSLLQCSVCLD 230

Query:   290 TVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPT---DDPEYEEERKK 341
                +G  A ++PC H +H DC++PWL+  ++CPVCR+ LPT   D+P+ + E  +
Sbjct:   231 DFEIGMEAKEMPCKHKFHSDCLLPWLELHSSCPVCRYLLPTGDDDEPKTDAETSR 285

GO:0005737 "cytoplasm" evidence=ISM

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

GO:0006944 "cellular membrane fusion" evidence=RCA

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

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

 Score = 256 (95.2 bits), Expect = 4.5e-27, Sum P(2) = 4.5e-27
 Identities = 57/138 (41%), Positives = 81/138 (58%)

Query:   212 ILNNSIEFRLEAPESDRYIGNPA-----DYMDAAGYEALLQNLAESDGGRRGAPRAAKSA 266
             I+ N     L  P SD+   +P+     DY    G + LLQ+LAE+D  R+G P A K A
Sbjct:   186 IMINPYNQSLVVP-SDQNQNHPSLTSLGDYFIGPGLDLLLQHLAENDPNRQGTPPARKEA 244

Query:   267 VLELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRF 326
             V  LPTV+I+   E + C++C D    G  A ++PC H +H  CIVPWL+  ++CPVCRF
Sbjct:   245 VEALPTVKIM---EPLQCSVCLDDFEKGTEAKEMPCKHKFHVRCIVPWLELHSSCPVCRF 301

Query:   327 ELPT---DDPEYEEERKK 341
             ELP+   DD E + + ++
Sbjct:   302 ELPSSADDDDETKTDSER 319

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

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

 Score = 244 (91.0 bits), Expect = 2.5e-26, Sum P(2) = 2.5e-26
 Identities = 48/113 (42%), Positives = 62/113 (54%)

Query:   231 GNPADYMDAAGYEALLQNLAESDGGRRGAPRAAKSAVLELPTVEILSEQ---ETIVCAIC 287
             GN  DY    G E L + L+     RRG P A +SA+  LPT++I           C +C
Sbjct:   135 GNTGDYFFGPGLEELFEQLSAGTT-RRGPPPAPRSAIDALPTIKIAQRHLRSSDSNCPVC 193

Query:   288 KDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPT-DDPEYEEER 339
             KD   +G  A ++PC H+YH DCIVPWL   N+CPVCR ELP+   P   + R
Sbjct:   194 KDEFELGSEAKQMPCNHIYHSDCIVPWLVQHNSCPVCRQELPSASGPSSSQNR 246

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

GO:0005618 "cell wall" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9SPL2	CIP8_ARATH	6, ., 3, ., 2, ., -	0.4916	0.8292	0.9011	yes	no

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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00014397001 SubName- Full=Putative uncharacterized protein (Chromosome chr18 scaffold_1, whole genome shotgun sequence); (334 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	363
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	3e-16
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	2e-12
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	2e-10
smart00184	40	smart00184, RING, Ring finger	6e-10
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	1e-09
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	4e-09
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	1e-08
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	4e-08
pfam14369	34	pfam14369, zf-RING_3, zinc-finger	1e-07
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	2e-05
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	2e-05
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	6e-05
pfam05285	317	pfam05285, SDA1, SDA1	8e-05
pfam05285	317	pfam05285, SDA1, SDA1	1e-04
pfam04147	809	pfam04147, Nop14, Nop14-like family	2e-04
TIGR00927	1096	TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger	3e-04
pfam02724	583	pfam02724, CDC45, CDC45-like protein	3e-04
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	3e-04
pfam04931	784	pfam04931, DNA_pol_phi, DNA polymerase phi	4e-04
PRK12678	672	PRK12678, PRK12678, transcription termination fact	5e-04
pfam13445	55	pfam13445, zf-RING_LisH, RING-type zinc-finger, Li	0.001
pfam05764	238	pfam05764, YL1, YL1 nuclear protein	0.001
pfam03985	431	pfam03985, Paf1, Paf1	0.002
PRK14160	211	PRK14160, PRK14160, heat shock protein GrpE; Provi	0.002
COG4547	620	COG4547, CobT, Cobalamin biosynthesis protein CobT	0.002
PTZ00482	844	PTZ00482, PTZ00482, membrane-attack complex/perfor	0.003
PRK12678	672	PRK12678, PRK12678, transcription termination fact	0.004
PTZ00415	2849	PTZ00415, PTZ00415, transmission-blocking target a	0.004
pfam04050	171	pfam04050, Upf2, Up-frameshift suppressor 2	0.004

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

 Score = 71.7 bits (176), Expect = 3e-16
 Identities = 23/45 (51%), Positives = 27/45 (60%)

Query: 283 VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFE 327
            C IC D    GE    LPCGHV+H +C+  WL S NTCP+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 = 60.9 bits (148), Expect = 2e-12
 Identities = 21/46 (45%), Positives = 25/46 (54%), Gaps = 3/46 (6%)

Query: 284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR-NTCPVCRFEL 328
           C IC +     E    LPCGHV+   CI  WL S  NTCP+CR  +
Sbjct: 2   CPICLE--EFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 54.8 bits (132), Expect = 2e-10
 Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 2/44 (4%)

Query: 282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCR 325
           + C IC D   + +     PCGHV+  +CI+ +L  ++ CP+CR
Sbjct: 3   LECPICLD--LLRDPVVLTPCGHVFCRECILRYLKKKSKCPICR 44

Length = 45

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

 Score = 53.7 bits (129), Expect = 6e-10
 Identities = 18/42 (42%), Positives = 23/42 (54%), Gaps = 3/42 (7%)

Query: 284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVC 324
           C IC +     +    LPCGH +   CI  WL+S N TCP+C
Sbjct: 1   CPICLE--EYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 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|221705 pfam12678, zf-rbx1, RING-H2 zinc finger

 Score = 53.6 bits (129), Expect = 1e-09
 Identities = 22/56 (39%), Positives = 29/56 (51%), Gaps = 10/56 (17%)

Query: 280 ETIVCAICK--------DTVNVGETAT--KLPCGHVYHGDCIVPWLDSRNTCPVCR 325
           E  VCAIC+        +  + G+        CGH +H  CI  WL +RNTCP+CR
Sbjct: 18  EDDVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 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|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

 Score = 57.3 bits (138), Expect = 4e-09
 Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 11/76 (14%)

Query: 266 AVLELPTVEILSEQETIVCAICKDTV----------NVGETATKLPCGHVYHGDCIVPWL 315
           A+    T E L+  +   C IC D +           +  T  +LPCGH+ H  C+  WL
Sbjct: 273 AMYPTATEEQLTNSDRT-CTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWL 331

Query: 316 DSRNTCPVCRFELPTD 331
           + + TCP+CR  +  D
Sbjct: 332 ERQQTCPICRRPVIFD 347

Length = 491

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

 Score = 49.8 bits (119), Expect = 1e-08
 Identities = 19/42 (45%), Positives = 26/42 (61%), Gaps = 3/42 (7%)

Query: 284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVC 324
           C IC +     +  T LPCGH++   CI+ WL+S N TCP+C
Sbjct: 1   CPICLEEPK--DPVTILPCGHLFCSKCILSWLESGNVTCPLC 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|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

 Score = 53.8 bits (129), Expect = 4e-08
 Identities = 19/47 (40%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWL-DSRNTCPVCRFELP 329
           CAIC       +    LPC H +H  C+  WL    N CPVCR  +P
Sbjct: 326 CAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIP 372

Length = 374

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

 Score = 47.2 bits (113), Expect = 1e-07
 Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 2/36 (5%)

Query: 22 TQYWCHHCEKRVSIETLANLPDVICHECKNGFVESI 57
          ++YWC+ C++ V I    +    +C  C  GFVE I
Sbjct: 1  SRYWCYQCDRFVRIA--PSGDSDVCPRCGGGFVEEI 34

Length = 34

>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 = 42.5 bits (100), Expect = 2e-05
 Identities = 18/67 (26%), Positives = 26/67 (38%), Gaps = 13/67 (19%)

Query: 283 VCAICKDTVN--------VGETATKLP-----CGHVYHGDCIVPWLDSRNTCPVCRFELP 329
           VCAIC++ +               + P     C H +H  CI  WLD++  CP+ R    
Sbjct: 22  VCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWV 81

Query: 330 TDDPEYE 336
             D    
Sbjct: 82  LADGGAI 88

Length = 88

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

 Score = 46.2 bits (109), Expect = 2e-05
 Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 10/54 (18%)

Query: 284  CAICKDTVNVGETATKLP------CGHVYHGDCIVPWLDS--RNTCPVCRFELP 329
            CAIC   +++ +    LP      C + +H  C+  W  S  R+ CP+CR E+ 
Sbjct: 1472 CAICYSVLDMVDR--SLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523

Length = 1525

>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional

 Score = 43.6 bits (103), Expect = 6e-05
 Identities = 24/63 (38%), Positives = 30/63 (47%), Gaps = 12/63 (19%)

Query: 275 ILSEQETIV-------CAICKDTVNVGETATK----LP-CGHVYHGDCIVPWLDSRNTCP 322
           +LSE E +        CAIC + V   E        L  C HV+  +CI  W   +NTCP
Sbjct: 161 VLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCP 220

Query: 323 VCR 325
           VCR
Sbjct: 221 VCR 223

Length = 238

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 43.5 bits (103), Expect = 8e-05
 Identities = 17/60 (28%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 120 DGWENDAREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENEDEED 179
           + WE +  ED +DE E   +V+ + +   +++ED+EE +    ++  +++E +  EDEE+
Sbjct: 102 EEWEVEEDEDSDDEGEW-IDVESDKEIESSDSEDEEEKDEAAKKAKEDSDEELSEEDEEE 160

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|218538 pfam05285, SDA1, SDA1

 Score = 43.1 bits (102), Expect = 1e-04
 Identities = 16/61 (26%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 119 LDGWENDAREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENEDEE 178
           L+ W+ + R+ +  E     + D++ +E     ED++ ++ GE     E+++ IE+ D E
Sbjct: 75  LEKWKEEERKKKEAEQGLESDDDDDEEEEWEVEEDEDSDDEGEWIDV-ESDKEIESSDSE 133

Query: 179 D 179
           D
Sbjct: 134 D 134

This family consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus. Length = 317

>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family

 Score = 43.1 bits (102), Expect = 2e-04
 Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 120 DGWENDARED-ENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENEDEE 178
           D +E D  ++    + EE+   +E+G ++E+E +DD++ E  E+  D  +EE  E +++ 
Sbjct: 304 DEFEPDDDDNFGLGQGEEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDS 363

Query: 179 DL 180
           D 
Sbjct: 364 DD 365

Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. Length = 809

>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger

 Score = 42.7 bits (100), Expect = 3e-04
 Identities = 18/57 (31%), Positives = 30/57 (52%)

Query: 128 EDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENEDEEDLRRRW 184
           + E  ++E+  +     D  ++E E++EE E  E+  + E EE  E E+EE L   W
Sbjct: 842 QGEAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEEPLSLEW 898

[Transport and binding proteins, Cations and iron carrying compounds]. Length = 1096

>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein

 Score = 42.3 bits (100), Expect = 3e-04
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 110 YGHDFLRIELDGWENDAREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENE 169
           +G D + I  DG   +  +DE   ++  R  D E D++++E  D+E+ E  +   D +++
Sbjct: 93  FGSDQVVIFDDGDIEEELQDEPRYDDAYR--DLEEDDDDDEESDEEDEESSKSEDDEDDD 150

Query: 170 ENIENEDEEDLRRRWRDVLPLRIR 193
           ++ +++D     R        R  
Sbjct: 151 DDDDDDDIATRERSLERRRRRREW 174

CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others. Length = 583

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

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 13/56 (23%)

Query: 283 VCAICKDTVNVGETATKLP----------CGHVYHGDCIVPWLD---SRNTCPVCR 325
           VC IC+ + +      K P          C H +H  CI+ WL    S+  CP+CR
Sbjct: 23  VCGICRVSFDGTCPQCKFPGDDCPLVWGKCKHNFHMHCILKWLATETSKGLCPMCR 78

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|218333 pfam04931, DNA_pol_phi, DNA polymerase phi

 Score = 42.2 bits (99), Expect = 4e-04
 Identities = 16/58 (27%), Positives = 30/58 (51%)

Query: 123 ENDAREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENEDEEDL 180
           + D  E+ +D+ +E   +++   E+E++ ED EE+E  +D   NE    I+      L
Sbjct: 651 DEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAEANEGVVPIDKAVRRAL 708

This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localised exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. Length = 784

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 41.8 bits (99), Expect = 5e-04
 Identities = 16/83 (19%), Positives = 29/83 (34%), Gaps = 4/83 (4%)

Query: 123 ENDAREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENEDEEDLRR 182
                   + ++ + R+  E+GD  E     D  +  G  R  +  +   ++  E+   R
Sbjct: 191 GRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDR 250

Query: 183 RWRDVLPLRIRDFATRSRSGRNR 205
              D      R    R R  R+R
Sbjct: 251 DGDDGEGRGGR----RGRRFRDR 269

Length = 672

>gnl|CDD|222135 pfam13445, zf-RING_LisH, RING-type zinc-finger, LisH dimerisation motif

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 14/48 (29%), Positives = 18/48 (37%), Gaps = 3/48 (6%)

Query: 279 QETIVCAICKDTVNVGETATK-LPCGHVYHGDCIVPWLDSRNT--CPV 323
               VC I K+ +   E     LPCGHVY    +     +     CP 
Sbjct: 8   HSIFVCPISKEVMTDEENPPVMLPCGHVYSRKALEKLAKNGGKFKCPY 55

This zinc-finger is the dimerisation motif for LisH proteins, and is also a typical RING-type of plant ubiquitin ligases. Length = 55

>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein

 Score = 39.3 bits (92), Expect = 0.001
 Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 123 ENDAREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENEDEEDLRR 182
           E +  EDE          +EE DE     E++EE E   D  D+E++E   +++EE  + 
Sbjct: 19  EEELEEDEFFWTYLLFE-EEEDDEEFEIEEEEEEEEVDSDFDDSEDDEPESDDEEEGEKE 77

Query: 183 RWRDVLPLR 191
             R+    +
Sbjct: 78  LQREERLKK 86

The proteins in this family are designated YL1. These proteins have been shown to be DNA-binding and may be a transcription factor. Length = 238

>gnl|CDD|217829 pfam03985, Paf1, Paf1

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 113 DFLRIELDGWENDAREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENI 172
           D  R  LD  + +  +++ DE EE R+ + E      E  +D E EG + R D  +E + 
Sbjct: 356 DKRRARLDPIDFEEVDEDEDEEEEQRSDEHEE-----EEGEDSEEEGSQSREDGSSESSS 410

Query: 173 ENEDEEDLRRR 183
           +   + + +  
Sbjct: 411 DVGSDSESKAD 421

Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. Length = 431

>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 14/61 (22%), Positives = 27/61 (44%)

Query: 123 ENDAREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENEDEEDLRR 182
           E + ++ +++  EE+   + E  E +   E+D E E  E     E+ E       E+L+ 
Sbjct: 2   EKECKDAKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEELKD 61

Query: 183 R 183
            
Sbjct: 62  E 62

Length = 211

>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]

 Score = 39.8 bits (93), Expect = 0.002
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 118 ELDGWENDAREDENDEN-EENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENED 176
           E DG ++    +E+ E   E     +E +E+E E  D E  EG  D ++   +   +  D
Sbjct: 233 EEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSESDESD 292

Query: 177 E 177
           E
Sbjct: 293 E 293

Length = 620

>gnl|CDD|240433 PTZ00482, PTZ00482, membrane-attack complex/perforin (MACPF) Superfamily; Provisional

 Score = 39.1 bits (91), Expect = 0.003
 Identities = 10/57 (17%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 123 ENDAREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENEDEED 179
           E D   ++++++  N    E   ++++  E  + +E   D   N ++ N  ++D+  
Sbjct: 93  EFDFLYEDDEDDAGNATSGESSTDDDSLLELPDRDEDA-DTQANNDQTNDFDQDDSS 148

Length = 844

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 38.7 bits (91), Expect = 0.004
 Identities = 12/83 (14%), Positives = 23/83 (27%), Gaps = 1/83 (1%)

Query: 123 ENDAREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEENIENEDEEDLRR 182
           E   R    +   +  + D      + +  ++     G DR       +  +   +D R 
Sbjct: 186 ERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNRE 245

Query: 183 RWRDVLPLRIRDFATRSRSGRNR 205
              D       +     R  R R
Sbjct: 246 DRGDR-DGDDGEGRGGRRGRRFR 267

Length = 672

>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230; Provisional

 Score = 38.9 bits (90), Expect = 0.004
 Identities = 19/54 (35%), Positives = 35/54 (64%), Gaps = 4/54 (7%)

Query: 120 DGWENDAREDENDENEENRNVDEEGDENENE----NEDDEENEGGEDRSDNENE 169
           D +  D  +++ DE++++   DEE +E E E    +++DEE+EGGED +  ++E
Sbjct: 149 DNFVIDDDDEDEDEDDDDEEDDEEEEEEEEEIKGFDDEDEEDEGGEDFTYEKSE 202

Length = 2849

>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2

 Score = 37.4 bits (87), Expect = 0.004
 Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 8/68 (11%)

Query: 123 ENDAREDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENE--------ENIEN 174
                E ++ E +E    ++E DE+ +E E D  ++  ++ SD+E E        E ++ 
Sbjct: 1   SGSESESDDGEEDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQEEEVDP 60

Query: 175 EDEEDLRR 182
           E E +  R
Sbjct: 61  EAEAEFDR 68

Transcripts harbouring premature signals for translation termination are recognised and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. Length = 171

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	363
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.5
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.49
PF14369	35	zf-RING_3: zinc-finger	99.41
PHA02929	238	N1R/p28-like protein; Provisional	99.23
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.21
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.18
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.14
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.06
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.02
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.01
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	98.96
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	98.95
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.91
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.88
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.85
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.84
PHA02926	242	zinc finger-like protein; Provisional	98.81
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.79
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	98.79
PF14634	44	zf-RING_5: zinc-RING finger domain	98.75
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.74
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.72
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.65
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.63
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.51
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.48
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.47
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.43
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.4
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.28
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.27
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.26
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.19
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.18
KOG4445	368	consensus Uncharacterized conserved protein, conta	98.12
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.11
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.09
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.06
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.05
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.05
KOG0825	1134	consensus PHD Zn-finger protein [General function	98.03
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.94
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.85
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.8
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.79
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.78
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.65
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	97.65
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	97.6
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.53
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.44
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.31
KOG2660	331	consensus Locus-specific chromosome binding protei	97.28
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.15
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.08
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.07
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.01
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	96.99
COG5152	259	Uncharacterized conserved protein, contains RING a	96.73
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.52
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	96.5
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.42
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	96.42
PF04641	260	Rtf2: Rtf2 RING-finger	96.27
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	96.2
KOG1002	791	consensus Nucleotide excision repair protein RAD16	96.16
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.14
PHA03096	284	p28-like protein; Provisional	96.04
COG5222	427	Uncharacterized conserved protein, contains RING Z	95.92
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	95.9
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	95.8
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	95.77
PF10446	458	DUF2457: Protein of unknown function (DUF2457); In	95.6
PHA02862	156	5L protein; Provisional	95.6
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	95.59
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	95.54
COG5236	493	Uncharacterized conserved protein, contains RING Z	95.48
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	95.46
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	95.28
PHA02825	162	LAP/PHD finger-like protein; Provisional	95.22
KOG3039	303	consensus Uncharacterized conserved protein [Funct	95.2
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	95.2
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	95.19
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	94.98
KOG1832	1516	consensus HIV-1 Vpr-binding protein [Cell cycle co	94.9
KOG1940	276	consensus Zn-finger protein [General function pred	94.78
KOG4739	233	consensus Uncharacterized protein involved in syna	94.72
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	94.68
PF04931	784	DNA_pol_phi: DNA polymerase phi; InterPro: IPR0070	94.67
COG0375	115	HybF Zn finger protein HypA/HybF (possibly regulat	94.54
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	94.54
COG5175	480	MOT2 Transcriptional repressor [Transcription]	94.51
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	94.34
PF10446	458	DUF2457: Protein of unknown function (DUF2457); In	94.26
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	93.71
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	93.3
KOG1001	674	consensus Helicase-like transcription factor HLTF/	93.23
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	92.8
KOG0298	1394	consensus DEAD box-containing helicase-like transc	92.11
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	92.07
TIGR00100	115	hypA hydrogenase nickel insertion protein HypA. In	91.93
PRK12380	113	hydrogenase nickel incorporation protein HybF; Pro	91.09
PRK00762	124	hypA hydrogenase nickel incorporation protein; Pro	90.88
PF01155	113	HypA: Hydrogenase expression/synthesis hypA family	90.86
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	90.69
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	90.56
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	90.48
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	90.45
KOG1832	1516	consensus HIV-1 Vpr-binding protein [Cell cycle co	90.4
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	90.36
PRK03681	114	hypA hydrogenase nickel incorporation protein; Val	90.31
PF09538	108	FYDLN_acid: Protein of unknown function (FYDLN_aci	89.48
KOG3002	299	consensus Zn finger protein [General function pred	89.2
PRK00564	117	hypA hydrogenase nickel incorporation protein; Pro	88.84
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	88.7
COG1996	49	RPC10 DNA-directed RNA polymerase, subunit RPC10 (	88.63
KOG4367	699	consensus Predicted Zn-finger protein [Function un	88.55
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	87.7
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	87.43
KOG3899	381	consensus Uncharacterized conserved protein [Funct	87.22
PRK03824	135	hypA hydrogenase nickel incorporation protein; Pro	85.97
PF06524	314	NOA36: NOA36 protein; InterPro: IPR010531 This fam	84.99
PF06524	314	NOA36: NOA36 protein; InterPro: IPR010531 This fam	84.69
KOG1609	323	consensus Protein involved in mRNA turnover and st	84.67
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	83.97
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	83.83
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	83.81
smart00834	41	CxxC_CXXC_SSSS Putative regulatory protein. CxxC_C	82.29
KOG3053	293	consensus Uncharacterized conserved protein [Funct	82.0
KOG0269	839	consensus WD40 repeat-containing protein [Function	81.48
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	81.28
COG4391	62	Uncharacterized protein conserved in bacteria [Fun	80.99
PF02724	622	CDC45: CDC45-like protein; InterPro: IPR003874 CDC	80.44
KOG1829	580	consensus Uncharacterized conserved protein, conta	80.15

>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=99.50  E-value=6.6e-15  Score=103.29  Aligned_cols=43  Identities=53%  Similarity=1.265  Sum_probs=40.3

Q ss_pred             cccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcC
Q 017955          283 VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCR  325 (363)
Q Consensus       283 ~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR  325 (363)
                      .|+||++.|..++.++.++|+|+||..||.+|++.+++||+||
T Consensus         2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence            6999999999888999999999999999999999999999997

...

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

Probab=99.49  E-value=2e-14  Score=141.01  Aligned_cols=77  Identities=32%  Similarity=0.709  Sum_probs=67.0

Q ss_pred             CCChhhHHHHHcCCceeeecccccc---cccccccccccCCceEEeCCCCcccHhhHHHHHhcCC-CCCCcCcCCCCCCh
Q 017955          258 GAPRAAKSAVLELPTVEILSEQETI---VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELPTDDP  333 (363)
Q Consensus       258 ~~~~~s~~~i~~lp~~~~~~~~~~~---~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~-sCPlCR~~l~~~d~  333 (363)
                      ......+..++.+|...++......   .|+|||+.|..|+.+++|||+|.||..||.+||.++. .||+|++.+.+...
T Consensus       203 ~~~r~~k~~l~~~p~~~f~~~~~~~~~~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~~~~  282 (348)
T KOG4628|consen  203 RRNRLIKRLLKKLPVRTFTKGDDEDATDTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRTDSG  282 (348)
T ss_pred             hhhhhHHHHHhhCCcEEeccccccCCCceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCCCCC
Confidence            5567789999999999988766544   8999999999999999999999999999999998775 59999999976654


Q ss_pred             h
Q 017955          334 E  334 (363)
Q Consensus       334 ~  334 (363)
                      .
T Consensus       283 ~  283 (348)
T KOG4628|consen  283 S  283 (348)
T ss_pred             C
Confidence            4

>PF14369 zf-RING_3: zinc-finger

Probab=99.41  E-value=7.7e-14  Score=93.44  Aligned_cols=34  Identities=47%  Similarity=1.079  Sum_probs=28.2

Q ss_pred             ceeeeecCCcceeeeccCCCceecccCCCCceeec
Q 017955           23 QYWCHHCEKRVSIETLANLPDVICHECKNGFVESI   57 (363)
Q Consensus        23 ~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~   57 (363)
                      +||||+|+++|++... ..++++||+|++||||||
T Consensus         2 ~ywCh~C~~~V~~~~~-~~~~~~CP~C~~gFvEei   35 (35)
T PF14369_consen    2 RYWCHQCNRFVRIAPS-PDSDVACPRCHGGFVEEI   35 (35)
T ss_pred             CEeCccCCCEeEeCcC-CCCCcCCcCCCCcEeEeC
Confidence            7999999988887655 333456999999999997

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.23  E-value=1.2e-11  Score=116.38  Aligned_cols=68  Identities=32%  Similarity=0.576  Sum_probs=53.1

Q ss_pred             hhHHHHHcCCceeeec-----ccccccccccccccccCC-----ceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955          262 AAKSAVLELPTVEILS-----EQETIVCAICKDTVNVGE-----TATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP  329 (363)
Q Consensus       262 ~s~~~i~~lp~~~~~~-----~~~~~~C~ICle~f~~~e-----~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~  329 (363)
                      ..+..+..+|.+....     ...+..|+||++.+....     .+..++|+|.||..||.+|++.+.+||+||..+.
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            3678888888776432     224678999999876433     1344569999999999999999999999999875

>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=99.21  E-value=8.7e-12  Score=97.10  Aligned_cols=46  Identities=41%  Similarity=0.972  Sum_probs=36.7

Q ss_pred             cccccccccccccc----------CCceEEeCCCCcccHhhHHHHHhcCCCCCCcC
Q 017955          280 ETIVCAICKDTVNV----------GETATKLPCGHVYHGDCIVPWLDSRNTCPVCR  325 (363)
Q Consensus       280 ~~~~C~ICle~f~~----------~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR  325 (363)
                      .+..|+||++.|..          .-.+...+|+|.||..||.+||+.+++||+||
T Consensus        18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            34569999999932          12455567999999999999999999999998

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 ....

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

Probab=99.18  E-value=1.3e-11  Score=120.43  Aligned_cols=68  Identities=34%  Similarity=0.731  Sum_probs=51.0

Q ss_pred             hhHHHHHcCCceeeec-ccccccccccccc-cccC---------CceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955          262 AAKSAVLELPTVEILS-EQETIVCAICKDT-VNVG---------ETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP  329 (363)
Q Consensus       262 ~s~~~i~~lp~~~~~~-~~~~~~C~ICle~-f~~~---------e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~  329 (363)
                      +.|..-+.++++...+ ...+..|.||++. |..+         -.+++|||||+||..|++.|+++.++||+||.++-
T Consensus       267 ~~kdl~~~~~t~t~eql~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~i  345 (491)
T COG5243         267 ATKDLNAMYPTATEEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVI  345 (491)
T ss_pred             HhhHHHhhcchhhhhhhcCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccc
Confidence            3344444444444333 3367889999998 4433         25799999999999999999999999999999954

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

Probab=99.14  E-value=2.3e-11  Score=116.10  Aligned_cols=51  Identities=37%  Similarity=0.881  Sum_probs=46.8

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHh-cCCCCCCcCcCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLD-SRNTCPVCRFELPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk-~~~sCPlCR~~l~~  330 (363)
                      ..-.|+|||+.|..++..+.|||+|.||..||.+|+. -++.||+||.++|+
T Consensus       322 ~GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         322 KGVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCceEEEEhhhhcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            4467999999999888999999999999999999998 57799999999986

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

Probab=99.06  E-value=5e-11  Score=113.38  Aligned_cols=51  Identities=27%  Similarity=0.843  Sum_probs=46.0

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCCh
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDP  333 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~  333 (363)
                      ...+|.|||+...   .+..+||||+||..||..|+..+..||+||..+++...
T Consensus       238 a~~kC~LCLe~~~---~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~pskv  288 (293)
T KOG0317|consen  238 ATRKCSLCLENRS---NPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPSKV  288 (293)
T ss_pred             CCCceEEEecCCC---CCCcCcCcchHHHHHHHHHHccccCCCcccccCCCcce
Confidence            4578999999876   78899999999999999999999999999999987654

>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=99.02  E-value=1.8e-10  Score=82.88  Aligned_cols=46  Identities=30%  Similarity=0.833  Sum_probs=40.1

Q ss_pred             cccccccccccccCCceEEeCCCCc-ccHhhHHHHHhcCCCCCCcCcCCC
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHV-YHGDCIVPWLDSRNTCPVCRFELP  329 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~-Fh~~CI~~WLk~~~sCPlCR~~l~  329 (363)
                      +..|.||++.+.   .+..+||+|. ||..|+..|++.+..||+||++|.
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            467999999876   6888999999 999999999999999999999875

...

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.01  E-value=2.4e-10  Score=103.94  Aligned_cols=55  Identities=27%  Similarity=0.597  Sum_probs=44.8

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc----------------CCCCCCcCcCCCCCChhHHH
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS----------------RNTCPVCRFELPTDDPEYEE  337 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~----------------~~sCPlCR~~l~~~d~~~~~  337 (363)
                      ....|+||++.+.   .++.++|+|.||..||.+|+..                ...||+||..|...+...-.
T Consensus        17 ~~~~CpICld~~~---dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiy   87 (193)
T PLN03208         17 GDFDCNICLDQVR---DPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIY   87 (193)
T ss_pred             CccCCccCCCcCC---CcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEee
Confidence            5678999999987   5677899999999999999853                24799999999876644433

>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=98.96  E-value=4.2e-10  Score=76.90  Aligned_cols=39  Identities=38%  Similarity=1.022  Sum_probs=33.4

Q ss_pred             ccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCc
Q 017955          284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVC  324 (363)
Q Consensus       284 C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlC  324 (363)
                      |+||++.+..  .++.++|||.||..||.+|++.+..||+|
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            8999999883  44788999999999999999998899998

>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=98.95  E-value=6.8e-10  Score=76.08  Aligned_cols=44  Identities=48%  Similarity=1.131  Sum_probs=36.6

Q ss_pred             cccccccccccCCceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCC
Q 017955          283 VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFEL  328 (363)
Q Consensus       283 ~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l  328 (363)
                      .|+||++.+.  .....++|+|.||..||..|++. +..||+||..+
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            4999999983  34555559999999999999998 67899999864

>smart00504 Ubox Modified RING finger domain

Probab=98.91  E-value=1.2e-09  Score=81.59  Aligned_cols=52  Identities=29%  Similarity=0.484  Sum_probs=44.9

Q ss_pred             ccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChhHH
Q 017955          282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYE  336 (363)
Q Consensus       282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~~~  336 (363)
                      ..|+||++.+.   .++.++|||+|++.||.+|++.+.+||+|+..+...+....
T Consensus         2 ~~Cpi~~~~~~---~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~   53 (63)
T smart00504        2 FLCPISLEVMK---DPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPN   53 (63)
T ss_pred             cCCcCCCCcCC---CCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeC
Confidence            46999999988   46788999999999999999998999999999976654443

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

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

Probab=98.88  E-value=1.4e-09  Score=75.84  Aligned_cols=38  Identities=34%  Similarity=0.955  Sum_probs=31.0

Q ss_pred             ccccccccccCCceEEeCCCCcccHhhHHHHHhcCC----CCCCc
Q 017955          284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN----TCPVC  324 (363)
Q Consensus       284 C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~----sCPlC  324 (363)
                      |+||++.|.   .++.|+|||.||..||..|++...    .||+|
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            899999998   789999999999999999997643    69988

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

Probab=98.85  E-value=7.7e-10  Score=102.55  Aligned_cols=50  Identities=34%  Similarity=0.848  Sum_probs=42.3

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcC---CCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR---NTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~---~sCPlCR~~l~~~d  332 (363)
                      ....|.|||+.-+   .++...|||.||+.||.+||+.+   +.||+|+..|..+.
T Consensus        46 ~~FdCNICLd~ak---dPVvTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~   98 (230)
T KOG0823|consen   46 GFFDCNICLDLAK---DPVVTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDT   98 (230)
T ss_pred             CceeeeeeccccC---CCEEeecccceehHHHHHHHhhcCCCeeCCccccccccce
Confidence            4567999999876   67778899999999999999864   47999999887665

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

Probab=98.84  E-value=1.3e-09  Score=97.20  Aligned_cols=51  Identities=35%  Similarity=0.771  Sum_probs=42.9

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD  331 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~  331 (363)
                      ....|+|||+.+... .+.-..|||+||..||+.-++....||+||+.|..+
T Consensus       130 ~~~~CPiCl~~~sek-~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k  180 (187)
T KOG0320|consen  130 GTYKCPICLDSVSEK-VPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHK  180 (187)
T ss_pred             cccCCCceecchhhc-cccccccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence            447799999998842 334567999999999999999999999999987654

>PHA02926 zinc finger-like protein; Provisional

Probab=98.81  E-value=2.2e-09  Score=99.10  Aligned_cols=52  Identities=29%  Similarity=0.698  Sum_probs=39.2

Q ss_pred             ccccccccccccccC-----CceEEe-CCCCcccHhhHHHHHhcC------CCCCCcCcCCCCC
Q 017955          280 ETIVCAICKDTVNVG-----ETATKL-PCGHVYHGDCIVPWLDSR------NTCPVCRFELPTD  331 (363)
Q Consensus       280 ~~~~C~ICle~f~~~-----e~~~~L-PC~H~Fh~~CI~~WLk~~------~sCPlCR~~l~~~  331 (363)
                      .+..|+|||+.....     .....| +|+|.||..||..|.+.+      .+||+||..+..-
T Consensus       169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~~I  232 (242)
T PHA02926        169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFRNI  232 (242)
T ss_pred             CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceeeee
Confidence            568899999976422     122344 599999999999999753      3699999987643

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

Probab=98.79  E-value=1.7e-09  Score=113.44  Aligned_cols=49  Identities=37%  Similarity=1.090  Sum_probs=43.6

Q ss_pred             ccccccccccccccCCc--eEEeCCCCcccHhhHHHHHhcCCCCCCcCcCC
Q 017955          280 ETIVCAICKDTVNVGET--ATKLPCGHVYHGDCIVPWLDSRNTCPVCRFEL  328 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~--~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l  328 (363)
                      ....|+||++.+..+..  +++|||+|+||..||+.|+++.++||+||..+
T Consensus       290 ~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~  340 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVL  340 (543)
T ss_pred             cCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhh
Confidence            46789999999985543  89999999999999999999999999999933

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

Probab=98.79  E-value=3.7e-09  Score=84.17  Aligned_cols=51  Identities=31%  Similarity=0.787  Sum_probs=39.2

Q ss_pred             cccccccccccccc--------CC--ceEEeCCCCcccHhhHHHHHhc---CCCCCCcCcCCCC
Q 017955          280 ETIVCAICKDTVNV--------GE--TATKLPCGHVYHGDCIVPWLDS---RNTCPVCRFELPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~--------~e--~~~~LPC~H~Fh~~CI~~WLk~---~~sCPlCR~~l~~  330 (363)
                      .+..|.||+..|..        ++  .++.-.|+|.||..||.+||.+   +..||+||+.+..
T Consensus        20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~   83 (85)
T PF12861_consen   20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKF   83 (85)
T ss_pred             CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeee
Confidence            47889999998873        11  1222349999999999999986   4589999998754

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.75  E-value=6.5e-09  Score=72.95  Aligned_cols=44  Identities=25%  Similarity=0.693  Sum_probs=38.7

Q ss_pred             cccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCc
Q 017955          283 VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRF  326 (363)
Q Consensus       283 ~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~  326 (363)
                      .|+||++.|.....+..++|+|+||..||..+......||+||+
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            49999999965567889999999999999999866779999985

>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=98.74  E-value=6.5e-09  Score=71.36  Aligned_cols=39  Identities=38%  Similarity=1.100  Sum_probs=33.2

Q ss_pred             ccccccccccCCceEEeCCCCcccHhhHHHHHh--cCCCCCCc
Q 017955          284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLD--SRNTCPVC  324 (363)
Q Consensus       284 C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk--~~~sCPlC  324 (363)
                      |+||++.+..  ....++|+|.||..||.+|++  ....||+|
T Consensus         1 C~iC~~~~~~--~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFED--PVILLPCGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSS--EEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccC--CCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence            8999999883  334889999999999999999  45589998

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=98.72  E-value=1.1e-08  Score=67.66  Aligned_cols=38  Identities=45%  Similarity=1.229  Sum_probs=33.3

Q ss_pred             ccccccccccCCceEEeCCCCcccHhhHHHHHh-cCCCCCCc
Q 017955          284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLD-SRNTCPVC  324 (363)
Q Consensus       284 C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk-~~~sCPlC  324 (363)
                      |+||++...   .+..++|+|.||..||..|++ .+..||+|
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            889999844   778899999999999999998 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)

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.65  E-value=1.6e-08  Score=101.70  Aligned_cols=50  Identities=30%  Similarity=0.700  Sum_probs=44.0

Q ss_pred             cccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955          279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD  331 (363)
Q Consensus       279 ~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~  331 (363)
                      .....|+||++.|.   .++.++|+|.||..||..|+.....||+||..+...
T Consensus        24 e~~l~C~IC~d~~~---~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~   73 (397)
T TIGR00599        24 DTSLRCHICKDFFD---VPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES   73 (397)
T ss_pred             ccccCCCcCchhhh---CccCCCCCCchhHHHHHHHHhCCCCCCCCCCccccc
Confidence            35678999999987   556789999999999999999988999999988764

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=98.63  E-value=1.7e-08  Score=78.78  Aligned_cols=51  Identities=33%  Similarity=0.760  Sum_probs=38.7

Q ss_pred             ccccccccccccc------------CCceEEeC-CCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955          281 TIVCAICKDTVNV------------GETATKLP-CGHVYHGDCIVPWLDSRNTCPVCRFELPTD  331 (363)
Q Consensus       281 ~~~C~ICle~f~~------------~e~~~~LP-C~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~  331 (363)
                      ...|.||...|..            ++.+...- |+|.||..||.+||..++.||+||+.+...
T Consensus        20 id~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~   83 (88)
T COG5194          20 IDVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLA   83 (88)
T ss_pred             cchhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEe
Confidence            4678888776642            22233333 999999999999999999999999987543

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

Probab=98.51  E-value=4.2e-08  Score=92.63  Aligned_cols=50  Identities=24%  Similarity=0.772  Sum_probs=43.6

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHH-HHhcCCC-CCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVP-WLDSRNT-CPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~-WLk~~~s-CPlCR~~l~~~d  332 (363)
                      .+..|+||++...   .+..+||||+||..||.. |-+++.- ||+||..+..+.
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            4678999999877   788999999999999999 9887775 999999886654

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

Probab=98.48  E-value=4.5e-08  Score=95.06  Aligned_cols=51  Identities=27%  Similarity=0.696  Sum_probs=46.5

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCCh
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDP  333 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~  333 (363)
                      .-+.|.||++.|.   .+.++||+|.||.-||..+|..+..||.|+..+...+.
T Consensus        22 ~lLRC~IC~eyf~---ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~L   72 (442)
T KOG0287|consen   22 DLLRCGICFEYFN---IPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESDL   72 (442)
T ss_pred             HHHHHhHHHHHhc---CceeccccchHHHHHHHHHhccCCCCCceecccchhhh
Confidence            4478999999998   78899999999999999999999999999999987664

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

Probab=98.47  E-value=1e-07  Score=74.11  Aligned_cols=54  Identities=28%  Similarity=0.516  Sum_probs=42.3

Q ss_pred             cccccccccccccCCceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCCCCCChhHHH
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFELPTDDPEYEE  337 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l~~~d~~~~~  337 (363)
                      ...|+||.+.|.   .++++||||.|.+.||..||+. +.+||+|+..+...+.....
T Consensus         4 ~f~CpIt~~lM~---dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn~   58 (73)
T PF04564_consen    4 EFLCPITGELMR---DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPNR   58 (73)
T ss_dssp             GGB-TTTSSB-S---SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-H
T ss_pred             ccCCcCcCcHhh---CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceECH
Confidence            467999999998   7889999999999999999998 78999999999887655533

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 ....

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

Probab=98.43  E-value=9e-08  Score=97.49  Aligned_cols=49  Identities=29%  Similarity=0.873  Sum_probs=42.0

Q ss_pred             cccccccccccccCCceEEeCCCCcccHhhHHHHHhcC-----CCCCCcCcCCCCCC
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR-----NTCPVCRFELPTDD  332 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~-----~sCPlCR~~l~~~d  332 (363)
                      +..|||||+...   .+..+.|||+||..||..+|...     ..||+||..|..++
T Consensus       186 ~~~CPICL~~~~---~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kd  239 (513)
T KOG2164|consen  186 DMQCPICLEPPS---VPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKD  239 (513)
T ss_pred             CCcCCcccCCCC---cccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccc
Confidence            678999999876   67777899999999999998764     48999999988755

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

Probab=98.40  E-value=2e-07  Score=65.37  Aligned_cols=38  Identities=37%  Similarity=0.965  Sum_probs=23.1

Q ss_pred             cccccccccc-CCceEEeCCCCcccHhhHHHHHhcCC----CCC
Q 017955          284 CAICKDTVNV-GETATKLPCGHVYHGDCIVPWLDSRN----TCP  322 (363)
Q Consensus       284 C~ICle~f~~-~e~~~~LPC~H~Fh~~CI~~WLk~~~----sCP  322 (363)
                      |+||++ |.. ...++.|+|||+||..||.+|++++.    .||
T Consensus         1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP   43 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP   43 (43)
T ss_dssp             -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred             CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence            899999 753 44688999999999999999998642    576

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

Probab=98.28  E-value=1.9e-07  Score=72.35  Aligned_cols=50  Identities=28%  Similarity=0.766  Sum_probs=38.3

Q ss_pred             ccccccccccccccC---------CceEEeC-CCCcccHhhHHHHHhcC---CCCCCcCcCCC
Q 017955          280 ETIVCAICKDTVNVG---------ETATKLP-CGHVYHGDCIVPWLDSR---NTCPVCRFELP  329 (363)
Q Consensus       280 ~~~~C~ICle~f~~~---------e~~~~LP-C~H~Fh~~CI~~WLk~~---~sCPlCR~~l~  329 (363)
                      .+..|.||.-.|..-         +.+..+- |.|.||..||.+|+...   ..||+||+.+.
T Consensus        19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            567899999988732         2233333 89999999999999754   37999999764

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

Probab=98.27  E-value=6.7e-07  Score=64.39  Aligned_cols=42  Identities=29%  Similarity=0.877  Sum_probs=33.3

Q ss_pred             cccccccccccCCceEEeCCC-----CcccHhhHHHHHhcC--CCCCCcC
Q 017955          283 VCAICKDTVNVGETATKLPCG-----HVYHGDCIVPWLDSR--NTCPVCR  325 (363)
Q Consensus       283 ~C~ICle~f~~~e~~~~LPC~-----H~Fh~~CI~~WLk~~--~sCPlCR  325 (363)
                      .|.||++ +...+.+.++||.     |++|..||.+|+..+  .+||+|+
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            4899998 3344566788975     899999999999654  4899995

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=98.26  E-value=3.4e-07  Score=87.45  Aligned_cols=47  Identities=30%  Similarity=0.704  Sum_probs=42.6

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP  329 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~  329 (363)
                      .-..|.||.+.|.   .+..++|+|.||.-||+..|..+.-||+||.+..
T Consensus        24 s~lrC~IC~~~i~---ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~~   70 (391)
T COG5432          24 SMLRCRICDCRIS---IPCETTCGHTFCSLCIRRHLGTQPFCPVCREDPC   70 (391)
T ss_pred             hHHHhhhhhheee---cceecccccchhHHHHHHHhcCCCCCccccccHH
Confidence            4478999999998   6788899999999999999999999999998764

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

Probab=98.19  E-value=5.1e-07  Score=91.41  Aligned_cols=50  Identities=36%  Similarity=0.980  Sum_probs=39.3

Q ss_pred             cccccccccccccCC---c-----------eEEeCCCCcccHhhHHHHHhcCC-CCCCcCcCCCC
Q 017955          281 TIVCAICKDTVNVGE---T-----------ATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELPT  330 (363)
Q Consensus       281 ~~~C~ICle~f~~~e---~-----------~~~LPC~H~Fh~~CI~~WLk~~~-sCPlCR~~l~~  330 (363)
                      ...|+|||..+..-.   .           -...||.|+||..|+..|...-+ .||+||.++++
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            457999999775311   1           22348999999999999999555 99999999985

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

Probab=98.18  E-value=7.5e-07  Score=95.74  Aligned_cols=52  Identities=27%  Similarity=0.758  Sum_probs=39.1

Q ss_pred             ccccccccccccccccCC---ceEEe-CCCCcccHhhHHHHHhcC--CCCCCcCcCCC
Q 017955          278 EQETIVCAICKDTVNVGE---TATKL-PCGHVYHGDCIVPWLDSR--NTCPVCRFELP  329 (363)
Q Consensus       278 ~~~~~~C~ICle~f~~~e---~~~~L-PC~H~Fh~~CI~~WLk~~--~sCPlCR~~l~  329 (363)
                      -.+...|+||+..+..-+   .-++. .|+|.||..||.+|++.+  ++||+||.+++
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            346788999998776211   11222 399999999999999874  58999998876

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

Probab=98.12  E-value=1.1e-06  Score=84.36  Aligned_cols=95  Identities=18%  Similarity=0.375  Sum_probs=68.3

Q ss_pred             cChhhHHHHHHHHHHhcCCCCCCChhhHHHHHcCCceeeecccccccccccccccccCCceEEeCCCCcccHhhHHHHHh
Q 017955          237 MDAAGYEALLQNLAESDGGRRGAPRAAKSAVLELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLD  316 (363)
Q Consensus       237 ~~~~~~e~Ll~~L~~~~~~~~~~~~~s~~~i~~lp~~~~~~~~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk  316 (363)
                      ++...+.+|.+++......+.+.+ ..-..|..-..+.-........|.|||.-|..+...++++|-|+||..|+-.+|.
T Consensus        72 l~d~~~~~i~~~~~~iikq~~g~p-ii~~lie~~~e~LT~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~  150 (368)
T KOG4445|consen   72 LGDPEFREIQRQIQEIIKQNSGMP-IICQLIEHCSEFLTENNHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLT  150 (368)
T ss_pred             CCcHHHHHHHHHHHHHHHhcCCCc-hhHHHHHHHHHHcccCCCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHH
Confidence            456788888888887776666643 3334444332232223336678999999999998899999999999999988764


Q ss_pred             ------------------c-----CCCCCCcCcCCCCCC
Q 017955          317 ------------------S-----RNTCPVCRFELPTDD  332 (363)
Q Consensus       317 ------------------~-----~~sCPlCR~~l~~~d  332 (363)
                                        .     ...||+||..|..+.
T Consensus       151 ~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~  189 (368)
T KOG4445|consen  151 ECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEE  189 (368)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccc
Confidence                              1     227999999886544

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.11  E-value=2e-06  Score=83.83  Aligned_cols=52  Identities=23%  Similarity=0.499  Sum_probs=37.4

Q ss_pred             cccccccccccccCCc--eEEeCCCCcccHhhHHHHH-hcCCCCCCcCcCCCCCC
Q 017955          281 TIVCAICKDTVNVGET--ATKLPCGHVYHGDCIVPWL-DSRNTCPVCRFELPTDD  332 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~--~~~LPC~H~Fh~~CI~~WL-k~~~sCPlCR~~l~~~d  332 (363)
                      +..||||+..-.....  ...-+|||.||..||...| .....||+|+..+...+
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            4579999995332222  2233799999999999966 44568999998776544

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).

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

Probab=98.09  E-value=8.1e-07  Score=84.11  Aligned_cols=50  Identities=36%  Similarity=0.883  Sum_probs=41.0

Q ss_pred             ccccccccccccccCC-------ceEEeCCCCcccHhhHHHHH--hcCCCCCCcCcCCC
Q 017955          280 ETIVCAICKDTVNVGE-------TATKLPCGHVYHGDCIVPWL--DSRNTCPVCRFELP  329 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e-------~~~~LPC~H~Fh~~CI~~WL--k~~~sCPlCR~~l~  329 (363)
                      .+..|+||-..+....       ...+|.|+|+||-.||+-|-  -++++||.|+..+-
T Consensus       223 ~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVd  281 (328)
T KOG1734|consen  223 SDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVD  281 (328)
T ss_pred             CcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhh
Confidence            5678999988776443       67889999999999999995  45779999987653

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

Probab=98.06  E-value=2.6e-06  Score=69.82  Aligned_cols=49  Identities=35%  Similarity=0.750  Sum_probs=36.9

Q ss_pred             ccccccccccccc-------------cCCceEEe-CCCCcccHhhHHHHHhcCCCCCCcCcCC
Q 017955          280 ETIVCAICKDTVN-------------VGETATKL-PCGHVYHGDCIVPWLDSRNTCPVCRFEL  328 (363)
Q Consensus       280 ~~~~C~ICle~f~-------------~~e~~~~L-PC~H~Fh~~CI~~WLk~~~sCPlCR~~l  328 (363)
                      ....|+||...+-             .++..+.. -|+|.||..||.+|||+++.||+|.++.
T Consensus        45 ~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW  107 (114)
T KOG2930|consen   45 VVDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEW  107 (114)
T ss_pred             eechhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcce
Confidence            5577999977542             11222222 3999999999999999999999998764

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

Probab=98.05  E-value=1.4e-06  Score=81.07  Aligned_cols=44  Identities=34%  Similarity=0.847  Sum_probs=38.7

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCc
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRF  326 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~  326 (363)
                      ....|+||++.|.   .++.+||+|.||..||..|+...-.||.||.
T Consensus        12 ~~~~C~iC~~~~~---~p~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   12 EELTCPICLEYFR---EPVLLPCGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             ccccChhhHHHhh---cCccccccchHhHHHHHHhcCCCcCCcccCC
Confidence            5678999999999   3488999999999999999995568999993

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

Probab=98.05  E-value=5.8e-07  Score=69.44  Aligned_cols=49  Identities=31%  Similarity=0.701  Sum_probs=23.2

Q ss_pred             cccccccccccc-cCCc--eEEe--CCCCcccHhhHHHHHhc----C-------CCCCCcCcCCC
Q 017955          281 TIVCAICKDTVN-VGET--ATKL--PCGHVYHGDCIVPWLDS----R-------NTCPVCRFELP  329 (363)
Q Consensus       281 ~~~C~ICle~f~-~~e~--~~~L--PC~H~Fh~~CI~~WLk~----~-------~sCPlCR~~l~  329 (363)
                      ...|.||+..+. .++.  +..-  .|+++||..||.+||..    +       ..||.|+.+|.
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~   66 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS   66 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence            357999999866 3332  2222  39999999999999973    1       15999998774

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

Probab=98.03  E-value=9.7e-07  Score=93.39  Aligned_cols=51  Identities=24%  Similarity=0.459  Sum_probs=46.4

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~  330 (363)
                      ....|+||+..|..+......+|+|+||..||..|.+..++||+||..|-.
T Consensus       122 ~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~  172 (1134)
T KOG0825|consen  122 VENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGE  172 (1134)
T ss_pred             hhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhhe
Confidence            456899999999988888888999999999999999999999999998753

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

Probab=97.94  E-value=3.2e-06  Score=81.29  Aligned_cols=49  Identities=33%  Similarity=0.573  Sum_probs=42.0

Q ss_pred             cccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC-CCCCcCcCCCCCC
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELPTDD  332 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~-sCPlCR~~l~~~d  332 (363)
                      ...|+||+....   .++.|+|+|.||.-||+--.++.+ +|++||.+|...-
T Consensus         7 ~~eC~IC~nt~n---~Pv~l~C~HkFCyiCiKGsy~ndk~~CavCR~pids~i   56 (324)
T KOG0824|consen    7 KKECLICYNTGN---CPVNLYCFHKFCYICIKGSYKNDKKTCAVCRFPIDSTI   56 (324)
T ss_pred             CCcceeeeccCC---cCccccccchhhhhhhcchhhcCCCCCceecCCCCcch
Confidence            356999999876   678999999999999999887755 6999999997654

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

Probab=97.85  E-value=6.9e-06  Score=81.43  Aligned_cols=54  Identities=30%  Similarity=0.701  Sum_probs=40.2

Q ss_pred             cccccccccccccccCC----ceEEeC-CCCcccHhhHHHHH--hc-----CCCCCCcCcCCCCCC
Q 017955          279 QETIVCAICKDTVNVGE----TATKLP-CGHVYHGDCIVPWL--DS-----RNTCPVCRFELPTDD  332 (363)
Q Consensus       279 ~~~~~C~ICle~f~~~e----~~~~LP-C~H~Fh~~CI~~WL--k~-----~~sCPlCR~~l~~~d  332 (363)
                      ..+..|.||++......    ...+|| |.|.||..||..|-  ++     .+.||.||.......
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~  224 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVN  224 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcccccc
Confidence            35678999999876322    123445 99999999999997  44     568999998765443

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

Probab=97.80  E-value=2.7e-06  Score=83.32  Aligned_cols=49  Identities=37%  Similarity=0.684  Sum_probs=38.8

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFELPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l~~  330 (363)
                      .+..|+|||..++.  ..+..-|.|.||..||.+-|+. ++.||.||+.+-.
T Consensus        42 ~~v~c~icl~llk~--tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~S   91 (381)
T KOG0311|consen   42 IQVICPICLSLLKK--TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVS   91 (381)
T ss_pred             hhhccHHHHHHHHh--hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccc
Confidence            45779999998872  3333349999999999998876 5699999997753

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

Probab=97.79  E-value=1.3e-05  Score=78.83  Aligned_cols=48  Identities=27%  Similarity=0.636  Sum_probs=41.6

Q ss_pred             ccccccccccccccCCceEEeCCCC-cccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGH-VYHGDCIVPWLDSRNTCPVCRFELPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H-~Fh~~CI~~WLk~~~sCPlCR~~l~~  330 (363)
                      ....|.|||...+   ...+|||.| -.|..|.+.---+++.||+||++|..
T Consensus       289 ~gkeCVIClse~r---dt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~  337 (349)
T KOG4265|consen  289 SGKECVICLSESR---DTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIEE  337 (349)
T ss_pred             CCCeeEEEecCCc---ceEEecchhhehhHhHHHHHHHhhcCCCccccchHh
Confidence            3578999999877   678999999 68999998877789999999998854

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

Probab=97.78  E-value=2.2e-05  Score=72.78  Aligned_cols=73  Identities=23%  Similarity=0.491  Sum_probs=60.8

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc--------CCCCCCcCcCCCCC----ChhHHHHHHhhhccCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS--------RNTCPVCRFELPTD----DPEYEEERKKRVSAGA  347 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~--------~~sCPlCR~~l~~~----d~~~~~~~~~~~~~~~  347 (363)
                      ....|..|--.+..++.+ +|.|-|+||..|+.+|-.+        ...||.|..+|.+.    .+..+..|.+...+.|
T Consensus        49 Y~pNC~LC~t~La~gdt~-RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~NlvsPva~aLre~L~qvNW  127 (299)
T KOG3970|consen   49 YNPNCRLCNTPLASGDTT-RLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLVSPVAEALREQLKQVNW  127 (299)
T ss_pred             CCCCCceeCCccccCcce-eehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccccchhHHHHHHHHHhhhH
Confidence            345699999988877655 6889999999999999764        22799999988654    4788999999999999


Q ss_pred             CCCCCC
Q 017955          348 SVGGAS  353 (363)
Q Consensus       348 ~~~g~~  353 (363)
                      +|+|+|
T Consensus       128 aRagLG  133 (299)
T KOG3970|consen  128 ARAGLG  133 (299)
T ss_pred             HhhccC
Confidence            999886

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

Probab=97.65  E-value=9.5e-06  Score=61.30  Aligned_cols=49  Identities=27%  Similarity=0.604  Sum_probs=24.2

Q ss_pred             cccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCCh
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDP  333 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~  333 (363)
                      -..|+||.+.++.  .+..-.|.|+||..||..-+.  ..||+|+.+.-..|.
T Consensus         7 lLrCs~C~~~l~~--pv~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD~   55 (65)
T PF14835_consen    7 LLRCSICFDILKE--PVCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQDI   55 (65)
T ss_dssp             TTS-SSS-S--SS---B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS-
T ss_pred             hcCCcHHHHHhcC--CceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHHH
Confidence            3679999999882  344456999999999988443  459999887655553

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

Probab=97.65  E-value=2.1e-05  Score=78.01  Aligned_cols=47  Identities=30%  Similarity=0.922  Sum_probs=35.5

Q ss_pred             cccccccccccCCceEEeC-CCCcccHhhHHHHHhcC---CCCCCcCcCCC
Q 017955          283 VCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSR---NTCPVCRFELP  329 (363)
Q Consensus       283 ~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~WLk~~---~sCPlCR~~l~  329 (363)
                      .|.||.+-+...+.+..+. |||+||..|+..|+..-   ..||+||..++
T Consensus         6 ~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~   56 (465)
T KOG0827|consen    6 ECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQ   56 (465)
T ss_pred             eeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeeccc
Confidence            5999955554444555555 99999999999999863   37999994443

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

Probab=97.60  E-value=2.2e-05  Score=79.16  Aligned_cols=48  Identities=27%  Similarity=0.861  Sum_probs=37.4

Q ss_pred             ccccccccccccccCC-ceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955          280 ETIVCAICKDTVNVGE-TATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP  329 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e-~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~  329 (363)
                      +--+|||||+-+...- .+....|.|.||..|+.+|.  ..+||+||.-..
T Consensus       174 ELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~  222 (493)
T KOG0804|consen  174 ELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS  222 (493)
T ss_pred             cCCCcchhHhhcCccccceeeeecccccchHHHhhcc--cCcChhhhhhcC
Confidence            3467999999987543 23444599999999999995  458999998665

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

Probab=97.53  E-value=2.4e-05  Score=77.75  Aligned_cols=51  Identities=35%  Similarity=0.893  Sum_probs=42.9

Q ss_pred             ccccccccccccCCceEEeCCCCcccHhhHHHHHhc--CCCCCCcCcCCCCCChhH
Q 017955          282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS--RNTCPVCRFELPTDDPEY  335 (363)
Q Consensus       282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~--~~sCPlCR~~l~~~d~~~  335 (363)
                      ..|-||-+.-+   .+++-||||..|..|+..|-..  .++||.||.+|....+..
T Consensus       370 eLCKICaendK---dvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~vi  422 (563)
T KOG1785|consen  370 ELCKICAENDK---DVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPVI  422 (563)
T ss_pred             HHHHHhhccCC---CcccccccchHHHHHHHhhcccCCCCCCCceeeEecccccee
Confidence            46999998755   7889999999999999999744  579999999998776543

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

Probab=97.44  E-value=8.4e-05  Score=74.25  Aligned_cols=49  Identities=31%  Similarity=0.812  Sum_probs=38.4

Q ss_pred             cccccccccccc--cCCceEEeCCCCcccHhhHHHHHhc--CCCCCCcCcCCC
Q 017955          281 TIVCAICKDTVN--VGETATKLPCGHVYHGDCIVPWLDS--RNTCPVCRFELP  329 (363)
Q Consensus       281 ~~~C~ICle~f~--~~e~~~~LPC~H~Fh~~CI~~WLk~--~~sCPlCR~~l~  329 (363)
                      ...|+|||+.+.  ....+..+.|+|.|...||.+||-+  +..||.|..+-.
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~kat   56 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGKAT   56 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCChhH
Confidence            467999999876  3345666779999999999999953  347999976543

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

Probab=97.31  E-value=6.7e-05  Score=80.04  Aligned_cols=50  Identities=28%  Similarity=0.778  Sum_probs=41.4

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcC-CCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR-NTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~-~sCPlCR~~l~~~d  332 (363)
                      .-..|++|-.-++   .+++..|+|.||..||..-+..+ ..||.|...|...|
T Consensus       642 ~~LkCs~Cn~R~K---d~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD  692 (698)
T KOG0978|consen  642 ELLKCSVCNTRWK---DAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND  692 (698)
T ss_pred             hceeCCCccCchh---hHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence            3478999998877   45667799999999999999765 58999999987655

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

Probab=97.28  E-value=5.8e-05  Score=73.63  Aligned_cols=53  Identities=25%  Similarity=0.598  Sum_probs=42.3

Q ss_pred             cccccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955          277 SEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD  331 (363)
Q Consensus       277 ~~~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~  331 (363)
                      .......|.+|...|..  .-++.-|-|.||++||.+.|...++||.|...|...
T Consensus        11 ~~n~~itC~LC~GYliD--ATTI~eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   11 ELNPHITCRLCGGYLID--ATTITECLHTFCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             hcccceehhhccceeec--chhHHHHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence            33456789999998873  233334999999999999999999999998877544

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

Probab=97.15  E-value=0.00028  Score=71.44  Aligned_cols=50  Identities=30%  Similarity=0.715  Sum_probs=44.0

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d  332 (363)
                      .+..|.||+..+.   .++.+||||.||..||.+-+-....||+||..+..-.
T Consensus        83 sef~c~vc~~~l~---~pv~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e~~  132 (398)
T KOG4159|consen   83 SEFECCVCSRALY---PPVVTPCGHSFCLECLDRSLDQETECPLCRDELVELP  132 (398)
T ss_pred             chhhhhhhHhhcC---CCccccccccccHHHHHHHhccCCCCcccccccccch
Confidence            4578999999887   6778899999999999998888889999999998733

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

Probab=97.08  E-value=0.0003  Score=52.25  Aligned_cols=42  Identities=21%  Similarity=0.665  Sum_probs=28.4

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcC--CCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR--NTCPV  323 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~--~sCPl  323 (363)
                      ....|||.+..|.  +.++-..|+|+|-+..|.+||+++  ..||+
T Consensus        10 ~~~~CPiT~~~~~--~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFE--DPVKSKKCGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-S--SEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhh--CCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence            4578999999988  355556799999999999999543  37998

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

Probab=97.07  E-value=0.00021  Score=72.41  Aligned_cols=52  Identities=31%  Similarity=0.809  Sum_probs=43.8

Q ss_pred             ccccccccccccccCCceEE-eCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChh
Q 017955          280 ETIVCAICKDTVNVGETATK-LPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPE  334 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~-LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~  334 (363)
                      ....|+||+..+.   .+.. ..|+|.||..||.+|+..+..||.||..+......
T Consensus        20 ~~l~C~~C~~vl~---~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~   72 (391)
T KOG0297|consen   20 ENLLCPICMSVLR---DPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEEL   72 (391)
T ss_pred             ccccCcccccccc---CCCCCCCCCCcccccccchhhccCcCCcccccccchhhcc
Confidence            5688999999988   4445 57999999999999999999999999887655443

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

Probab=97.01  E-value=0.0002  Score=71.26  Aligned_cols=47  Identities=30%  Similarity=0.893  Sum_probs=38.7

Q ss_pred             ccccccccccccccC-CceEEeCCCCcccHhhHHHHHhcCC--CCCCcCc
Q 017955          280 ETIVCAICKDTVNVG-ETATKLPCGHVYHGDCIVPWLDSRN--TCPVCRF  326 (363)
Q Consensus       280 ~~~~C~ICle~f~~~-e~~~~LPC~H~Fh~~CI~~WLk~~~--sCPlCR~  326 (363)
                      ....|..|-+.+... +..-.|||.||||..|+...|.++.  +||.||+
T Consensus       364 ~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  364 TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            457799998877643 4677899999999999999997754  8999993

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

Probab=96.99  E-value=0.00014  Score=53.14  Aligned_cols=46  Identities=24%  Similarity=0.561  Sum_probs=35.1

Q ss_pred             ccccccccccccCCceEEeCCCC-cccHhhHHHHHh-cCCCCCCcCcCCCC
Q 017955          282 IVCAICKDTVNVGETATKLPCGH-VYHGDCIVPWLD-SRNTCPVCRFELPT  330 (363)
Q Consensus       282 ~~C~ICle~f~~~e~~~~LPC~H-~Fh~~CI~~WLk-~~~sCPlCR~~l~~  330 (363)
                      ..|.||++.-.   .-+...||| -.|..|-.+-++ .+..||+||.++..
T Consensus         8 dECTICye~pv---dsVlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~d   55 (62)
T KOG4172|consen    8 DECTICYEHPV---DSVLYTCGHMCMCYACGLRLKKALHGCCPICRAPIKD   55 (62)
T ss_pred             cceeeeccCcc---hHHHHHcchHHhHHHHHHHHHHccCCcCcchhhHHHH
Confidence            67999999744   233456999 578999777666 78899999998753

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

Probab=96.73  E-value=0.00084  Score=61.42  Aligned_cols=51  Identities=22%  Similarity=0.460  Sum_probs=42.9

Q ss_pred             cccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChh
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPE  334 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~  334 (363)
                      -..|.||..+|.   .++...|||.||..|...-++....|-+|-+....--++
T Consensus       196 PF~C~iCKkdy~---spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~f~V  246 (259)
T COG5152         196 PFLCGICKKDYE---SPVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGRFWV  246 (259)
T ss_pred             ceeehhchhhcc---chhhhhcchhHHHHHHHHHhccCCcceecchhhccceeH
Confidence            357999999998   677788999999999999999999999998766554443

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

Probab=96.52  E-value=0.0012  Score=63.68  Aligned_cols=54  Identities=20%  Similarity=0.391  Sum_probs=45.4

Q ss_pred             ccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChhHHHH
Q 017955          282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEE  338 (363)
Q Consensus       282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~~~~~  338 (363)
                      ..|-||...|.   .++...|+|+||..|...-++....|++|-+.+..-.....+.
T Consensus       242 f~c~icr~~f~---~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~~~~akeL  295 (313)
T KOG1813|consen  242 FKCFICRKYFY---RPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGSFNVAKEL  295 (313)
T ss_pred             ccccccccccc---cchhhcCCceeehhhhccccccCCcceecccccccccchHHHH
Confidence            45999999998   6778889999999999999999999999998887655444433

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

Probab=96.50  E-value=0.0015  Score=73.53  Aligned_cols=52  Identities=27%  Similarity=0.641  Sum_probs=43.1

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC----------CCCCcCcCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN----------TCPVCRFELPTD  331 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~----------sCPlCR~~l~~~  331 (363)
                      .+..|.||+-+--.....++|.|+|+||..|...-|.++-          +||+|+.+|...
T Consensus      3485 ~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH~ 3546 (3738)
T KOG1428|consen 3485 ADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINHI 3546 (3738)
T ss_pred             cCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhhH
Confidence            5678999998766666788999999999999998887642          799999988653

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

Probab=96.42  E-value=0.0015  Score=65.62  Aligned_cols=46  Identities=24%  Similarity=0.551  Sum_probs=38.2

Q ss_pred             cccccccccccccCCceEEeCCCCcccHhhHHHHHhcC--------CCCCCcCc
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR--------NTCPVCRF  326 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~--------~sCPlCR~  326 (363)
                      -..|.||++....++....|||+|+||+.|++.++...        -.||-+.-
T Consensus       184 lf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  184 LFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             cccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            36799999999877899999999999999999998642        26877643

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

Probab=96.42  E-value=0.0023  Score=45.63  Aligned_cols=40  Identities=28%  Similarity=0.801  Sum_probs=27.3

Q ss_pred             ccccccccccCCceEEeCC--CC---cccHhhHHHHHhc--CCCCCCc
Q 017955          284 CAICKDTVNVGETATKLPC--GH---VYHGDCIVPWLDS--RNTCPVC  324 (363)
Q Consensus       284 C~ICle~f~~~e~~~~LPC--~H---~Fh~~CI~~WLk~--~~sCPlC  324 (363)
                      |-||++.-.... ..+.||  +-   +.|..||..|+..  +.+|++|
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            779999866443 566785  33   8899999999974  4579988

>PF04641 Rtf2: Rtf2 RING-finger

Probab=96.27  E-value=0.0078  Score=57.74  Aligned_cols=91  Identities=18%  Similarity=0.384  Sum_probs=57.8

Q ss_pred             hHHHHHHHHHHhcCCCCCCCh-hhHHHHHcCCceeeec--------------ccccccccccccccccCCc-eEEeCCCC
Q 017955          241 GYEALLQNLAESDGGRRGAPR-AAKSAVLELPTVEILS--------------EQETIVCAICKDTVNVGET-ATKLPCGH  304 (363)
Q Consensus       241 ~~e~Ll~~L~~~~~~~~~~~~-~s~~~i~~lp~~~~~~--------------~~~~~~C~ICle~f~~~e~-~~~LPC~H  304 (363)
                      +.+.||..|............ .-...+..+..+.+..              ......|||....|..... +...||||
T Consensus        58 nKeaile~Ll~~~~~~~~~~~~~hI~~LKDl~~l~~~~n~~~~~~~~~~~~~~~~~~~CPvt~~~~~~~~~fv~l~~cG~  137 (260)
T PF04641_consen   58 NKEAILEFLLDKKKNKDLPKTFSHIKSLKDLVELKFTKNPSYKEEDKSSGDNSEGRFICPVTGKEFNGKHKFVYLRPCGC  137 (260)
T ss_pred             cHHHHHHHHHhcCcCCCCccccccccCccceeeEEeEecCccccccccccccCCceeECCCCCcccCCceeEEEEcCCCC
Confidence            577888888766422111111 1112233333444332              2356789999999965443 55558999


Q ss_pred             cccHhhHHHHHhcCCCCCCcCcCCCCCC
Q 017955          305 VYHGDCIVPWLDSRNTCPVCRFELPTDD  332 (363)
Q Consensus       305 ~Fh~~CI~~WLk~~~sCPlCR~~l~~~d  332 (363)
                      +|...+|.+- +....||+|-.+|...|
T Consensus       138 V~s~~alke~-k~~~~Cp~c~~~f~~~D  164 (260)
T PF04641_consen  138 VFSEKALKEL-KKSKKCPVCGKPFTEED  164 (260)
T ss_pred             EeeHHHHHhh-cccccccccCCccccCC
Confidence            9999999987 33568999999987665

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

Probab=96.20  E-value=0.0044  Score=59.38  Aligned_cols=49  Identities=24%  Similarity=0.534  Sum_probs=37.5

Q ss_pred             cccccccccccccccCCceEEeCCCCcccHhhHHHHHhcC--CCCCCcCcCCC
Q 017955          279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR--NTCPVCRFELP  329 (363)
Q Consensus       279 ~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~--~sCPlCR~~l~  329 (363)
                      ..+.+|++|-+.-..  .-...+|+|+||..||..-+...  -+||.|-..+.
T Consensus       237 t~~~~C~~Cg~~Pti--P~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  237 TSDTECPVCGEPPTI--PHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cCCceeeccCCCCCC--CeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            366889999987552  33445699999999999876543  58999988765

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

Probab=96.16  E-value=0.0021  Score=66.27  Aligned_cols=56  Identities=30%  Similarity=0.647  Sum_probs=44.3

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc-----CCCCCCcCcCCCCCChhHHHH
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS-----RNTCPVCRFELPTDDPEYEEE  338 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~-----~~sCPlCR~~l~~~d~~~~~~  338 (363)
                      ....|.+|.+.-.   ..+...|.|.||+.||+++...     +-+||+|-..+.-+.....-.
T Consensus       535 ~~~~C~lc~d~ae---d~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~ale  595 (791)
T KOG1002|consen  535 GEVECGLCHDPAE---DYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPALE  595 (791)
T ss_pred             CceeecccCChhh---hhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccccccccchhhh
Confidence            5677999998755   5566779999999999999753     348999999888776665544

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

Probab=96.14  E-value=0.0033  Score=45.05  Aligned_cols=45  Identities=22%  Similarity=0.560  Sum_probs=22.8

Q ss_pred             cccccccccc-CCceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCC
Q 017955          284 CAICKDTVNV-GETATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFEL  328 (363)
Q Consensus       284 C~ICle~f~~-~e~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l  328 (363)
                      |++|.+.+.. +.....-+|++.+|+.|...-++. ...||-||++.
T Consensus         1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            7999999843 224444458999999998887764 67999999864

>PHA03096 p28-like protein; Provisional

Probab=96.04  E-value=0.003  Score=61.41  Aligned_cols=45  Identities=24%  Similarity=0.475  Sum_probs=32.3

Q ss_pred             ccccccccccccC----CceEEeC-CCCcccHhhHHHHHhcC---CCCCCcCc
Q 017955          282 IVCAICKDTVNVG----ETATKLP-CGHVYHGDCIVPWLDSR---NTCPVCRF  326 (363)
Q Consensus       282 ~~C~ICle~f~~~----e~~~~LP-C~H~Fh~~CI~~WLk~~---~sCPlCR~  326 (363)
                      ..|.||++.....    ..-..|+ |.|.||..||..|-..+   .+||.||.
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~  231 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRR  231 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccc
Confidence            5699999976632    2445666 99999999999997653   24555543

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

Probab=95.92  E-value=0.0043  Score=60.06  Aligned_cols=42  Identities=31%  Similarity=0.768  Sum_probs=34.5

Q ss_pred             ccccccccccccCCceEEeC-CCCcccHhhHHHHHhcC-CCCCCcCc
Q 017955          282 IVCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSR-NTCPVCRF  326 (363)
Q Consensus       282 ~~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~WLk~~-~sCPlCR~  326 (363)
                      +.|+.|...+.   .+.+.| |+|.||..||..-|... ..||.|-+
T Consensus       275 LkCplc~~Llr---np~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLR---NPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhh---CcccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            78999998877   566677 89999999999887654 58999944

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

Probab=95.90  E-value=0.0039  Score=61.62  Aligned_cols=49  Identities=27%  Similarity=0.459  Sum_probs=42.2

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD  331 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~  331 (363)
                      ++..|+||+-.-.   ..+..||+|.-|+.||.+.|.+.+.|=.|+..+.+.
T Consensus       421 Ed~lCpICyA~pi---~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~~  469 (489)
T KOG4692|consen  421 EDNLCPICYAGPI---NAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVIDV  469 (489)
T ss_pred             ccccCcceecccc---hhhccCCCCchHHHHHHHHHhcCCeeeEecceeeeh
Confidence            6778999987533   567789999999999999999999999999988753

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

Probab=95.80  E-value=0.0032  Score=62.33  Aligned_cols=46  Identities=33%  Similarity=0.712  Sum_probs=34.6

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD  331 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~  331 (363)
                      ....|.||++...   ...-+||||.-|  |+.--. ...+||+||..+.-.
T Consensus       304 ~p~lcVVcl~e~~---~~~fvpcGh~cc--ct~cs~-~l~~CPvCR~rI~~~  349 (355)
T KOG1571|consen  304 QPDLCVVCLDEPK---SAVFVPCGHVCC--CTLCSK-HLPQCPVCRQRIRLV  349 (355)
T ss_pred             CCCceEEecCCcc---ceeeecCCcEEE--chHHHh-hCCCCchhHHHHHHH
Confidence            3467999999987   478899999877  765543 344599999877543

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

Probab=95.77  E-value=0.0052  Score=66.56  Aligned_cols=70  Identities=26%  Similarity=0.434  Sum_probs=44.8

Q ss_pred             ccccccccccccccCC-ceEEeCCCCcccHhhHHHHHhcCC-------CCCCcCcCCCCCChhHHHHHHhhhccCCCC
Q 017955          280 ETIVCAICKDTVNVGE-TATKLPCGHVYHGDCIVPWLDSRN-------TCPVCRFELPTDDPEYEEERKKRVSAGASV  349 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e-~~~~LPC~H~Fh~~CI~~WLk~~~-------sCPlCR~~l~~~d~~~~~~~~~~~~~~~~~  349 (363)
                      ....|.||++.+.... ....-.|-|+||+.||.+|.+...       .||.|.....+-...|-=+=.+..-|...+
T Consensus       190 ~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~~~~~~y~C~CGk~~nP~~~~  267 (950)
T KOG1952|consen  190 RKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSKTVPKTYLCFCGKVKNPEFSR  267 (950)
T ss_pred             CceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhccCCcccceecCcccCCCCCC
Confidence            4577999999987433 333334899999999999986522       699998544333334443334444444433

>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins

Probab=95.60  E-value=0.0041  Score=63.18  Aligned_cols=10  Identities=20%  Similarity=0.238  Sum_probs=4.4

Q ss_pred             HHHHHHHHhc
Q 017955          244 ALLQNLAESD  253 (363)
Q Consensus       244 ~Ll~~L~~~~  253 (363)
                      +.|..|....
T Consensus       209 AY~Scle~Rr  218 (458)
T PF10446_consen  209 AYISCLEARR  218 (458)
T ss_pred             HHHHHHHHHH
Confidence            3444444433

>PHA02862 5L protein; Provisional

Probab=95.60  E-value=0.0086  Score=52.38  Aligned_cols=45  Identities=27%  Similarity=0.721  Sum_probs=33.9

Q ss_pred             ccccccccccccCCceEEeCCC-----CcccHhhHHHHHhcC--CCCCCcCcCCCC
Q 017955          282 IVCAICKDTVNVGETATKLPCG-----HVYHGDCIVPWLDSR--NTCPVCRFELPT  330 (363)
Q Consensus       282 ~~C~ICle~f~~~e~~~~LPC~-----H~Fh~~CI~~WLk~~--~sCPlCR~~l~~  330 (363)
                      ..|-||++.-..  .  .-||.     ..-|..|+.+|++.+  .+||+|+.++..
T Consensus         3 diCWIC~~~~~e--~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I   54 (156)
T PHA02862          3 DICWICNDVCDE--R--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI   54 (156)
T ss_pred             CEEEEecCcCCC--C--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence            569999997542  2  24553     578999999999754  489999998753

>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=95.59  E-value=0.0074  Score=52.23  Aligned_cols=44  Identities=27%  Similarity=0.601  Sum_probs=33.4

Q ss_pred             cccccccccccccCCceEEeCCC------CcccHhhHHHHHhcCCCCCCc
Q 017955          281 TIVCAICKDTVNVGETATKLPCG------HVYHGDCIVPWLDSRNTCPVC  324 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~------H~Fh~~CI~~WLk~~~sCPlC  324 (363)
                      ...|.||++.+.....++.++|+      |.||..|+++|-+.++.=|.=
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~rDPfn   75 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWRRERNRDPFN   75 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHHhhccCCCcc
Confidence            45699999999874567777886      899999999995544444443

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.

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

Probab=95.54  E-value=0.0041  Score=55.31  Aligned_cols=29  Identities=34%  Similarity=0.855  Sum_probs=26.8

Q ss_pred             ccccccccccccccCCceEEeCCCCcccH
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHG  308 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~  308 (363)
                      ..-.|.|||+++..++.+.+|||-.|||+
T Consensus       176 dkGECvICLEdL~~GdtIARLPCLCIYHK  204 (205)
T KOG0801|consen  176 DKGECVICLEDLEAGDTIARLPCLCIYHK  204 (205)
T ss_pred             cCCcEEEEhhhccCCCceeccceEEEeec
Confidence            45679999999999999999999999996

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

Probab=95.48  E-value=0.011  Score=58.27  Aligned_cols=46  Identities=35%  Similarity=0.816  Sum_probs=38.9

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHH--HhcCCCCCCcCcCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPW--LDSRNTCPVCRFEL  328 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~W--Lk~~~sCPlCR~~l  328 (363)
                      +...|.||-..+.   ....+||+|..|..|....  |-..+.||+||.+.
T Consensus        60 en~~C~ICA~~~T---Ys~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~  107 (493)
T COG5236          60 ENMNCQICAGSTT---YSARYPCGHQICHACAVRLRALYMQKGCPLCRTET  107 (493)
T ss_pred             ccceeEEecCCce---EEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence            5567999999877   6789999999999998764  56788999999864

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

Probab=95.46  E-value=0.014  Score=56.54  Aligned_cols=51  Identities=27%  Similarity=0.615  Sum_probs=40.7

Q ss_pred             ccccccccccccC---CceEEeCCCCcccHhhHHHHHhcCC-CCCCcCcCCCCCC
Q 017955          282 IVCAICKDTVNVG---ETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELPTDD  332 (363)
Q Consensus       282 ~~C~ICle~f~~~---e~~~~LPC~H~Fh~~CI~~WLk~~~-sCPlCR~~l~~~d  332 (363)
                      ..|-||-++|...   ..++.|.|||.||..|+.+-+.... .||.||.......
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~~~~~   58 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETTEIPD   58 (296)
T ss_pred             CceeecCccccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcccCCc
Confidence            4699999999865   3677888999999999987776644 7999999854333

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

Probab=95.28  E-value=0.0032  Score=60.78  Aligned_cols=41  Identities=39%  Similarity=0.794  Sum_probs=32.7

Q ss_pred             cccccccccccccCCceEEeCCCC-cccHhhHHHHHhcCCCCCCcCcCC
Q 017955          281 TIVCAICKDTVNVGETATKLPCGH-VYHGDCIVPWLDSRNTCPVCRFEL  328 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H-~Fh~~CI~~WLk~~~sCPlCR~~l  328 (363)
                      ...|.|||+.-.   ....|+||| +-|..|-+.    -+.||+||+.|
T Consensus       300 ~~LC~ICmDaP~---DCvfLeCGHmVtCt~CGkr----m~eCPICRqyi  341 (350)
T KOG4275|consen  300 RRLCAICMDAPR---DCVFLECGHMVTCTKCGKR----MNECPICRQYI  341 (350)
T ss_pred             HHHHHHHhcCCc---ceEEeecCcEEeehhhccc----cccCchHHHHH
Confidence            467999999866   677899999 678888644    34899999855

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=95.22  E-value=0.013  Score=52.01  Aligned_cols=48  Identities=23%  Similarity=0.662  Sum_probs=35.0

Q ss_pred             ccccccccccccccCCceEEeCC--CC---cccHhhHHHHHhcC--CCCCCcCcCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPC--GH---VYHGDCIVPWLDSR--NTCPVCRFELPTD  331 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC--~H---~Fh~~CI~~WLk~~--~sCPlCR~~l~~~  331 (363)
                      ....|-||++...  ..  .-||  ..   .-|.+|+..|+..+  .+|++|+.++...
T Consensus         7 ~~~~CRIC~~~~~--~~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          7 MDKCCWICKDEYD--VV--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCCeeEecCCCCC--Cc--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            4567999998743  22  2464  44   66999999999764  4899999877543

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.20  E-value=0.018  Score=54.46  Aligned_cols=58  Identities=22%  Similarity=0.381  Sum_probs=48.0

Q ss_pred             ccccccccccccccCCceEEe-CCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChhHHH
Q 017955          280 ETIVCAICKDTVNVGETATKL-PCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEE  337 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~L-PC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~~~~  337 (363)
                      ....|+||.+.+...-....| ||||+|++.|+.+.++.-..||+|-.++...|....+
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI~Lq  278 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDIIGLQ  278 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceEeee
Confidence            346799999998865544444 6999999999999999999999999999998876543

>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=95.20  E-value=0.0088  Score=48.74  Aligned_cols=32  Identities=34%  Similarity=0.812  Sum_probs=27.1

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHH
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIV  312 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~  312 (363)
                      ....|+||...+.. ......||+|+||..|+.
T Consensus        77 ~~~~C~vC~k~l~~-~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   77 ESTKCSVCGKPLGN-SVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCCccCcCCcCCC-ceEEEeCCCeEEeccccc
Confidence            45679999998875 477788999999999975

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 [].

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

Probab=95.19  E-value=0.02  Score=56.23  Aligned_cols=46  Identities=26%  Similarity=0.591  Sum_probs=36.8

Q ss_pred             ccccccccccccccCCceEEeC-CCCcccHhhHHHHHhcCCCCCCcCcCC
Q 017955          280 ETIVCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSRNTCPVCRFEL  328 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~WLk~~~sCPlCR~~l  328 (363)
                      ....|+||+....   .++.+. -|-+||..||..++++++.||+=-.+.
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            5678999998755   344444 599999999999999999999865544

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=94.98  E-value=0.013  Score=43.15  Aligned_cols=47  Identities=36%  Similarity=0.805  Sum_probs=34.9

Q ss_pred             ccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCCh
Q 017955          282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDP  333 (363)
Q Consensus       282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~  333 (363)
                      ..|..|...   +.+...+||+|+.|..|..  +.+-+.||+|-++|...++
T Consensus         8 ~~~~~~~~~---~~~~~~~pCgH~I~~~~f~--~~rYngCPfC~~~~~~~~~   54 (55)
T PF14447_consen    8 QPCVFCGFV---GTKGTVLPCGHLICDNCFP--GERYNGCPFCGTPFEFDDP   54 (55)
T ss_pred             eeEEEcccc---ccccccccccceeeccccC--hhhccCCCCCCCcccCCCC
Confidence            345555544   3367889999999999954  3567789999999987664

>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]

Probab=94.90  E-value=0.022  Score=62.36  Aligned_cols=13  Identities=23%  Similarity=0.371  Sum_probs=7.0

Q ss_pred             CCceecccCCCCc
Q 017955           41 LPDVICHECKNGF   53 (363)
Q Consensus        41 ~~~~~c~~C~~gF   53 (363)
                      ..||-|++=+.-|
T Consensus      1326 ~sdvh~~r~k~p~ 1338 (1516)
T KOG1832|consen 1326 MSDVHTRRVKHPL 1338 (1516)
T ss_pred             hhhhcccccccch
Confidence            4556666655443

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

Probab=94.78  E-value=0.019  Score=55.56  Aligned_cols=57  Identities=28%  Similarity=0.549  Sum_probs=44.1

Q ss_pred             ccccccccccccc-CCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChhHHHH
Q 017955          281 TIVCAICKDTVNV-GETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEE  338 (363)
Q Consensus       281 ~~~C~ICle~f~~-~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~~~~~  338 (363)
                      ...||||.+.+.. ...+..++|+|+-|..|+.+....+-+||+|.+ +......+...
T Consensus       158 ~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~-~~d~~~~~~~~  215 (276)
T KOG1940|consen  158 EFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK-PGDMSHYFRKL  215 (276)
T ss_pred             cCCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc-hHHHHHHHHHH
Confidence            3449999997664 347888999999999999999888899999988 55554444333

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

Probab=94.72  E-value=0.01  Score=55.97  Aligned_cols=46  Identities=20%  Similarity=0.533  Sum_probs=34.0

Q ss_pred             ccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955          282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPT  330 (363)
Q Consensus       282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~  330 (363)
                      ..|..|..--. +.....+.|.|+||..|...-.  ...||+||+.+..
T Consensus         4 VhCn~C~~~~~-~~~f~LTaC~HvfC~~C~k~~~--~~~C~lCkk~ir~   49 (233)
T KOG4739|consen    4 VHCNKCFRFPS-QDPFFLTACRHVFCEPCLKASS--PDVCPLCKKSIRI   49 (233)
T ss_pred             EEeccccccCC-CCceeeeechhhhhhhhcccCC--ccccccccceeee
Confidence            35777776444 6677788899999999976532  2389999998654

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

Probab=94.68  E-value=0.0031  Score=62.92  Aligned_cols=57  Identities=28%  Similarity=0.631  Sum_probs=46.3

Q ss_pred             cccccccccccccC-CceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChhHHH
Q 017955          281 TIVCAICKDTVNVG-ETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEE  337 (363)
Q Consensus       281 ~~~C~ICle~f~~~-e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~~~~  337 (363)
                      ...|.||...++.. +.+..+-|+|++|..||.+||.....||.||+.|+-.-.+.+.
T Consensus       196 v~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~~~~~e~k~  253 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELPKNGFEEKL  253 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhhhhhHHHHH
Confidence            46799999988744 3566677999999999999999999999999999765544443

>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar

Probab=94.67  E-value=0.024  Score=62.44  Aligned_cols=7  Identities=29%  Similarity=0.140  Sum_probs=2.5

Q ss_pred             hhhHHHH
Q 017955          239 AAGYEAL  245 (363)
Q Consensus       239 ~~~~e~L  245 (363)
                      ...+.+|
T Consensus       731 De~m~~l  737 (784)
T PF04931_consen  731 DEQMMAL  737 (784)
T ss_pred             HHHHHHH
Confidence            3333333

The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent

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

Probab=94.54  E-value=0.026  Score=47.77  Aligned_cols=35  Identities=26%  Similarity=0.570  Sum_probs=29.4

Q ss_pred             CCCceeeeecCCcceeeeccCCCceecccCCCCceeecc
Q 017955           20 DPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIP   58 (363)
Q Consensus        20 ~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~   58 (363)
                      -+..+||..|.    ..+.+...++.||.|++..++=+.
T Consensus        67 ~p~~~~C~~C~----~~~~~e~~~~~CP~C~s~~~~i~~  101 (115)
T COG0375          67 EPAECWCLDCG----QEVELEELDYRCPKCGSINLRIIG  101 (115)
T ss_pred             eccEEEeccCC----CeecchhheeECCCCCCCceEEec
Confidence            46789999999    777777788999999999887664

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

Probab=94.54  E-value=0.044  Score=54.97  Aligned_cols=69  Identities=28%  Similarity=0.484  Sum_probs=41.2

Q ss_pred             HHHHHcCCceeee-ccccccccccccccccc-------------CC----ceEEeC--CCCcccHhhHHHHHhcC-----
Q 017955          264 KSAVLELPTVEIL-SEQETIVCAICKDTVNV-------------GE----TATKLP--CGHVYHGDCIVPWLDSR-----  318 (363)
Q Consensus       264 ~~~i~~lp~~~~~-~~~~~~~C~ICle~f~~-------------~e----~~~~LP--C~H~Fh~~CI~~WLk~~-----  318 (363)
                      ++.|..-|..... ..++...|.-|+..-..             |.    ...+.+  |...+|.+|+-+|+..+     
T Consensus       253 ~~~V~~Np~y~~~~~~~e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~  332 (358)
T PF10272_consen  253 KEQVEQNPRYSYPESGQELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQH  332 (358)
T ss_pred             HHHHHhCCccccCCCccccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCC
Confidence            3445555555544 33456678878764321             00    001112  56778999999998532     


Q ss_pred             --------CCCCCcCcCCCCCC
Q 017955          319 --------NTCPVCRFELPTDD  332 (363)
Q Consensus       319 --------~sCPlCR~~l~~~d  332 (363)
                              -.||.||+.|+--|
T Consensus       333 ~~~Wl~~~~~CPtCRa~FCilD  354 (358)
T PF10272_consen  333 PETWLSGKCPCPTCRAKFCILD  354 (358)
T ss_pred             hhhhhcCCCCCCCCcccceeee
Confidence                    27999999987543

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

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=94.51  E-value=0.019  Score=56.62  Aligned_cols=56  Identities=21%  Similarity=0.528  Sum_probs=40.8

Q ss_pred             ccccccccccccccccCC-ceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCCCCCCh
Q 017955          278 EQETIVCAICKDTVNVGE-TATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFELPTDDP  333 (363)
Q Consensus       278 ~~~~~~C~ICle~f~~~e-~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l~~~d~  333 (363)
                      +.++.-|+.|++.+...+ .....|||...|.-|....-+. +..||.||+.....+.
T Consensus        11 edeed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv   68 (480)
T COG5175          11 EDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENV   68 (480)
T ss_pred             ccccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccce
Confidence            334455999999988554 4556779998888886554433 5689999998776663

>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=94.34  E-value=0.018  Score=40.28  Aligned_cols=41  Identities=32%  Similarity=0.865  Sum_probs=23.3

Q ss_pred             ccccccccccCCceEEeCCCCcccHhhHHHHHhcCC--CCCCc
Q 017955          284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN--TCPVC  324 (363)
Q Consensus       284 C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~--sCPlC  324 (363)
                      |.+|.+....|..-....|+-.+|..|+..+++...  .||.|
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            678888777443222223999999999999998766  79988

; PDB: 3NW0_A 2CT0_A.

>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins

Probab=94.26  E-value=0.015  Score=59.15  Aligned_cols=6  Identities=33%  Similarity=0.036  Sum_probs=2.2

Q ss_pred             ccccCC
Q 017955          117 IELDGW  122 (363)
Q Consensus       117 ~~~~~~  122 (363)
                      ||+-+.
T Consensus        38 IRkLge   43 (458)
T PF10446_consen   38 IRKLGE   43 (458)
T ss_pred             HhhhhH
Confidence            333333

>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=93.71  E-value=0.019  Score=40.95  Aligned_cols=33  Identities=30%  Similarity=0.744  Sum_probs=23.6

Q ss_pred             EeCC-CCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955          299 KLPC-GHVYHGDCIVPWLDSRNTCPVCRFELPTD  331 (363)
Q Consensus       299 ~LPC-~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~  331 (363)
                      .+.| .|+.|..|+...|..+..||+|..++|++
T Consensus        15 Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen   15 LIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPTK   48 (50)
T ss_dssp             EEE-SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred             eeeecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence            4457 49999999999999999999999999875

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.

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

Probab=93.30  E-value=0.053  Score=49.10  Aligned_cols=50  Identities=30%  Similarity=0.740  Sum_probs=34.3

Q ss_pred             ccccccccccccCC----ceEEeCCCCcccHhhHHHHHhc----C-------CCCCCcCcCCCCC
Q 017955          282 IVCAICKDTVNVGE----TATKLPCGHVYHGDCIVPWLDS----R-------NTCPVCRFELPTD  331 (363)
Q Consensus       282 ~~C~ICle~f~~~e----~~~~LPC~H~Fh~~CI~~WLk~----~-------~sCPlCR~~l~~~  331 (363)
                      ..|.||+-.--.|.    ..--..|+.-||.-|+..||+.    +       ..||.|-.++.-+
T Consensus       166 ~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialK  230 (234)
T KOG3268|consen  166 GACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALK  230 (234)
T ss_pred             hcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceee
Confidence            45888875433332    2222349999999999999974    1       2699999887544

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

Probab=93.23  E-value=0.021  Score=61.86  Aligned_cols=48  Identities=27%  Similarity=0.599  Sum_probs=39.2

Q ss_pred             ccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC--CCCCcCcCCCCCCh
Q 017955          282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN--TCPVCRFELPTDDP  333 (363)
Q Consensus       282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~--sCPlCR~~l~~~d~  333 (363)
                      ..|.||++    .+.+.+.+|+|.||..|+.+-+....  .||+||..+..+..
T Consensus       455 ~~c~ic~~----~~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~l  504 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVLKEKKL  504 (674)
T ss_pred             cccccccc----cccceeecccchHHHHHHHhccccccCCCCcHHHHHHHHHHH
Confidence            77999999    34778889999999999999886643  69999987765543

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

Probab=92.80  E-value=0.044  Score=53.50  Aligned_cols=43  Identities=28%  Similarity=0.693  Sum_probs=30.5

Q ss_pred             ccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCC
Q 017955          282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFEL  328 (363)
Q Consensus       282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l  328 (363)
                      ..|--|-..+.  -..+.+||+|+||++|...  ..-+.||.|-..|
T Consensus        91 HfCd~Cd~PI~--IYGRmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V  133 (389)
T KOG2932|consen   91 HFCDRCDFPIA--IYGRMIPCKHVFCLECARS--DSDKICPLCDDRV  133 (389)
T ss_pred             EeecccCCcce--eeecccccchhhhhhhhhc--CccccCcCcccHH
Confidence            45666755444  2567789999999999643  4466899996544

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

Probab=92.11  E-value=0.064  Score=60.82  Aligned_cols=45  Identities=31%  Similarity=0.699  Sum_probs=37.7

Q ss_pred             cccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcC
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFE  327 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~  327 (363)
                      ...|.||++.+..  ...+.-|+|.||..|+..|+..+..||+|...
T Consensus      1153 ~~~c~ic~dil~~--~~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi 1197 (1394)
T KOG0298|consen 1153 HFVCEICLDILRN--QGGIAGCGHEPCCRCDELWLYASSRCPICKSI 1197 (1394)
T ss_pred             ccchHHHHHHHHh--cCCeeeechhHhhhHHHHHHHHhccCcchhhh
Confidence            3579999998873  23455699999999999999999999999743

>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=92.07  E-value=0.18  Score=44.92  Aligned_cols=53  Identities=25%  Similarity=0.543  Sum_probs=36.7

Q ss_pred             cccccccccccccCCceEEeC------------CC-CcccHhhHHHHHhc------------------------------
Q 017955          281 TIVCAICKDTVNVGETATKLP------------CG-HVYHGDCIVPWLDS------------------------------  317 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LP------------C~-H~Fh~~CI~~WLk~------------------------------  317 (363)
                      +..|+|||+.-.   ..+.|-            |+ -+-|..||.++-|.                              
T Consensus         2 d~~CpICme~PH---NAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (162)
T PF07800_consen    2 DVTCPICMEHPH---NAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQ   78 (162)
T ss_pred             CccCceeccCCC---ceEEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCccccccccccc
Confidence            457999999754   344443            33 24678899988541                              


Q ss_pred             -CCCCCCcCcCCCCCChhHH
Q 017955          318 -RNTCPVCRFELPTDDPEYE  336 (363)
Q Consensus       318 -~~sCPlCR~~l~~~d~~~~  336 (363)
                       .-.||+||..|..+.....
T Consensus        79 ~~L~CPLCRG~V~GWtvve~   98 (162)
T PF07800_consen   79 PELACPLCRGEVKGWTVVEP   98 (162)
T ss_pred             ccccCccccCceeceEEchH
Confidence             1169999999998877654

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.

>TIGR00100 hypA hydrogenase nickel insertion protein HypA

Probab=91.93  E-value=0.12  Score=43.70  Aligned_cols=35  Identities=20%  Similarity=0.505  Sum_probs=25.6

Q ss_pred             CCCceeeeecCCcceeeeccCCCceecccCCCCceeecc
Q 017955           20 DPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIP   58 (363)
Q Consensus        20 ~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~   58 (363)
                      -+.++||..|.+.+..    .-..+.||.|++..++-+.
T Consensus        67 ~p~~~~C~~Cg~~~~~----~~~~~~CP~Cgs~~~~i~~  101 (115)
T TIGR00100        67 EPVECECEDCSEEVSP----EIDLYRCPKCHGIMLQVRA  101 (115)
T ss_pred             eCcEEEcccCCCEEec----CCcCccCcCCcCCCcEEec
Confidence            5779999999944443    3335889999998766543

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.

>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional

Probab=91.09  E-value=0.16  Score=42.87  Aligned_cols=35  Identities=26%  Similarity=0.607  Sum_probs=25.0

Q ss_pred             CCCceeeeecCCcceeeeccCCCceecccCCCCceeecc
Q 017955           20 DPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIP   58 (363)
Q Consensus        20 ~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~   58 (363)
                      -+.++||..|...+    ...-..+.||.|++.-++-+.
T Consensus        67 vp~~~~C~~Cg~~~----~~~~~~~~CP~Cgs~~~~i~~  101 (113)
T PRK12380         67 KPAQAWCWDCSQVV----EIHQHDAQCPHCHGERLRVDT  101 (113)
T ss_pred             eCcEEEcccCCCEE----ecCCcCccCcCCCCCCcEEcc
Confidence            46799999999443    333345679999988766543

>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional

Probab=90.88  E-value=0.17  Score=43.38  Aligned_cols=38  Identities=16%  Similarity=0.274  Sum_probs=26.0

Q ss_pred             CCCceeeeecCCcceee---eccCCCceecccCCCCceeecc
Q 017955           20 DPTQYWCHHCEKRVSIE---TLANLPDVICHECKNGFVESIP   58 (363)
Q Consensus        20 ~~~~~~C~~C~~~~~~~---~~~~~~~~~c~~C~~gFve~~~   58 (363)
                      -+.++|| .|...+...   +....+.+.||.|++..++-+.
T Consensus        67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~  107 (124)
T PRK00762         67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILG  107 (124)
T ss_pred             cCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEec
Confidence            5779999 999665543   1112245679999998876553

>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=90.86  E-value=0.076  Score=44.67  Aligned_cols=35  Identities=29%  Similarity=0.450  Sum_probs=22.5

Q ss_pred             CCCceeeeecCCcceeeeccCCCceecccCCCCceeecc
Q 017955           20 DPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIP   58 (363)
Q Consensus        20 ~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~   58 (363)
                      .+.++||..|.    .+..+.-..+.||.|++..++-+.
T Consensus        67 ~p~~~~C~~Cg----~~~~~~~~~~~CP~Cgs~~~~i~~  101 (113)
T PF01155_consen   67 VPARARCRDCG----HEFEPDEFDFSCPRCGSPDVEIIS  101 (113)
T ss_dssp             E--EEEETTTS-----EEECHHCCHH-SSSSSS-EEEEE
T ss_pred             cCCcEECCCCC----CEEecCCCCCCCcCCcCCCcEEcc
Confidence            46799999999    554444445889999999876543

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.

>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]

Probab=90.69  E-value=0.11  Score=48.48  Aligned_cols=40  Identities=33%  Similarity=0.722  Sum_probs=30.6

Q ss_pred             ccccccccccCCceEEeCCCC-cccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955          284 CAICKDTVNVGETATKLPCGH-VYHGDCIVPWLDSRNTCPVCRFELPT  330 (363)
Q Consensus       284 C~ICle~f~~~e~~~~LPC~H-~Fh~~CI~~WLk~~~sCPlCR~~l~~  330 (363)
                      |-+|.+.=.   .+..+||.| .+|..|=..    ...||+|+.....
T Consensus       161 Cr~C~~~~~---~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~~s  201 (207)
T KOG1100|consen  161 CRKCGEREA---TVLLLPCRHLCLCGICDES----LRICPICRSPKTS  201 (207)
T ss_pred             ceecCcCCc---eEEeecccceEeccccccc----CccCCCCcChhhc
Confidence            888877643   788999998 789999643    4569999886543

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

Probab=90.56  E-value=0.13  Score=56.08  Aligned_cols=46  Identities=33%  Similarity=0.825  Sum_probs=35.1

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~  330 (363)
                      ....|.+|--.+..  ..+..-|+|.||..|+.   .....||-|+..+..
T Consensus       839 q~skCs~C~~~Ldl--P~VhF~CgHsyHqhC~e---~~~~~CP~C~~e~~~  884 (933)
T KOG2114|consen  839 QVSKCSACEGTLDL--PFVHFLCGHSYHQHCLE---DKEDKCPKCLPELRG  884 (933)
T ss_pred             eeeeecccCCcccc--ceeeeecccHHHHHhhc---cCcccCCccchhhhh
Confidence            34679999887763  45566799999999997   455689999885543

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

Probab=90.48  E-value=0.22  Score=50.25  Aligned_cols=49  Identities=24%  Similarity=0.553  Sum_probs=41.1

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC---CCCCcCcCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN---TCPVCRFEL  328 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~---sCPlCR~~l  328 (363)
                      ..-.|||=.+.-.....+..|.|||+.+++-|.+..++..   .||.|-...
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~  384 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQ  384 (394)
T ss_pred             ceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCccc
Confidence            4567999888877777899999999999999999888765   799995543

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

Probab=90.45  E-value=0.15  Score=55.08  Aligned_cols=28  Identities=32%  Similarity=0.864  Sum_probs=24.4

Q ss_pred             ceEEeCCCCcccHhhHHHHHhcCCCCCC
Q 017955          296 TATKLPCGHVYHGDCIVPWLDSRNTCPV  323 (363)
Q Consensus       296 ~~~~LPC~H~Fh~~CI~~WLk~~~sCPl  323 (363)
                      ...+..|+|+-|.+|.++|+.....||.
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            3455679999999999999999999985

>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]

Probab=90.40  E-value=0.22  Score=54.94  Aligned_cols=11  Identities=9%  Similarity=-0.018  Sum_probs=4.1

Q ss_pred             ccccCCCcccc
Q 017955          117 IELDGWENDAR  127 (363)
Q Consensus       117 ~~~~~~~~~~~  127 (363)
                      .|.+..+++++
T Consensus      1400 ~r~~~dd~Dee 1410 (1516)
T KOG1832|consen 1400 RRPTDDDSDEE 1410 (1516)
T ss_pred             cCCCccccCcc
Confidence            33333333333

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=90.36  E-value=0.26  Score=36.20  Aligned_cols=33  Identities=30%  Similarity=0.738  Sum_probs=27.8

Q ss_pred             cccccccccccccCCceEEeC-CCCcccHhhHHH
Q 017955          281 TIVCAICKDTVNVGETATKLP-CGHVYHGDCIVP  313 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~  313 (363)
                      ...|++|-+.|+.++.+++-| |+-.||+.|..+
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            457999999998777777787 999999999543

>PRK03681 hypA hydrogenase nickel incorporation protein; Validated

Probab=90.31  E-value=0.2  Score=42.29  Aligned_cols=36  Identities=19%  Similarity=0.636  Sum_probs=24.8

Q ss_pred             CCCceeeeecCCcceeeeccCCCceecccCCCCceeecc
Q 017955           20 DPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIP   58 (363)
Q Consensus        20 ~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~   58 (363)
                      -+.++||..|...+.....   .-+.||.|++..++-+.
T Consensus        67 ~p~~~~C~~Cg~~~~~~~~---~~~~CP~Cgs~~~~i~~  102 (114)
T PRK03681         67 QEAECWCETCQQYVTLLTQ---RVRRCPQCHGDMLRIVA  102 (114)
T ss_pred             eCcEEEcccCCCeeecCCc---cCCcCcCcCCCCcEEcc
Confidence            5779999999954443211   12569999988776554

>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues

Probab=89.48  E-value=0.72  Score=38.67  Aligned_cols=34  Identities=21%  Similarity=0.430  Sum_probs=25.4

Q ss_pred             CCceeeeecCCcceeeeccCCCceecccCCCCceeec
Q 017955           21 PTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESI   57 (363)
Q Consensus        21 ~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~   57 (363)
                      +.+.-|..|.++|-   .++-.-+|||+|+.-|.-+.
T Consensus         7 GtKR~Cp~CG~kFY---DLnk~PivCP~CG~~~~~~~   40 (108)
T PF09538_consen    7 GTKRTCPSCGAKFY---DLNKDPIVCPKCGTEFPPEP   40 (108)
T ss_pred             CCcccCCCCcchhc---cCCCCCccCCCCCCccCccc
Confidence            45788999996664   34444588999999997773

The function of members of this family is unknown.

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

Probab=89.20  E-value=0.38  Score=47.32  Aligned_cols=53  Identities=23%  Similarity=0.606  Sum_probs=38.5

Q ss_pred             ccccccccccccccCCceEEeCC--CCcccHhhHHHHHhcCCCCCCcCcCCCCCChhHHHHHH
Q 017955          280 ETIVCAICKDTVNVGETATKLPC--GHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEEERK  340 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC--~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~~~~~~~  340 (363)
                      .-..||||.+.+..    -++.|  ||+-|..|-.   +.++.||.||.++. +-..+.-++.
T Consensus        47 ~lleCPvC~~~l~~----Pi~QC~nGHlaCssC~~---~~~~~CP~Cr~~~g-~~R~~amEkV  101 (299)
T KOG3002|consen   47 DLLDCPVCFNPLSP----PIFQCDNGHLACSSCRT---KVSNKCPTCRLPIG-NIRCRAMEKV  101 (299)
T ss_pred             hhccCchhhccCcc----cceecCCCcEehhhhhh---hhcccCCccccccc-cHHHHHHHHH
Confidence            44679999999872    34557  7999988864   56889999999998 4444444433

>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional

Probab=88.84  E-value=0.27  Score=41.68  Aligned_cols=35  Identities=17%  Similarity=0.420  Sum_probs=24.4

Q ss_pred             CCCceeeeecCCcceeeeccCCCce-ecccCCCCceeecc
Q 017955           20 DPTQYWCHHCEKRVSIETLANLPDV-ICHECKNGFVESIP   58 (363)
Q Consensus        20 ~~~~~~C~~C~~~~~~~~~~~~~~~-~c~~C~~gFve~~~   58 (363)
                      -+.++||..|...+...    -..+ .||.|++-.++-+.
T Consensus        68 vp~~~~C~~Cg~~~~~~----~~~~~~CP~Cgs~~~~i~~  103 (117)
T PRK00564         68 EKVELECKDCSHVFKPN----ALDYGVCEKCHSKNVIITQ  103 (117)
T ss_pred             cCCEEEhhhCCCccccC----CccCCcCcCCCCCceEEec
Confidence            57799999999444332    2234 49999998877553

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

Probab=88.70  E-value=0.32  Score=42.12  Aligned_cols=56  Identities=21%  Similarity=0.474  Sum_probs=41.0

Q ss_pred             ccccccccccccccccCCceEEeC-CCCcccHhhHHHHHhc---CCCCCCcCcCCCCCCh
Q 017955          278 EQETIVCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDS---RNTCPVCRFELPTDDP  333 (363)
Q Consensus       278 ~~~~~~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~WLk~---~~sCPlCR~~l~~~d~  333 (363)
                      +..-.+|.||.+......-.+.=- ||-..|..|....+|.   +..||+|+..+.....
T Consensus        77 d~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~~  136 (140)
T PF05290_consen   77 DPKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSSS  136 (140)
T ss_pred             CCCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccccc
Confidence            336678999999876433222222 8999999998888775   5589999999976553

>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]

Probab=88.63  E-value=0.25  Score=35.60  Aligned_cols=31  Identities=23%  Similarity=0.563  Sum_probs=24.9

Q ss_pred             CceeeeecCCcceeeeccCCCceecccCCCCce
Q 017955           22 TQYWCHHCEKRVSIETLANLPDVICHECKNGFV   54 (363)
Q Consensus        22 ~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFv   54 (363)
                      .-|-|-.|.+.|  +.+-..+.+-||+|++--+
T Consensus         5 ~~Y~C~~Cg~~~--~~~~~~~~irCp~Cg~rIl   35 (49)
T COG1996           5 MEYKCARCGREV--ELDQETRGIRCPYCGSRIL   35 (49)
T ss_pred             EEEEhhhcCCee--ehhhccCceeCCCCCcEEE
Confidence            469999999777  5566778999999997543

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

Probab=88.55  E-value=0.25  Score=50.40  Aligned_cols=35  Identities=26%  Similarity=0.543  Sum_probs=30.2

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS  317 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~  317 (363)
                      +...|+||..-|.   .+++|||+|..|..|...-+.+
T Consensus         3 eelkc~vc~~f~~---epiil~c~h~lc~~ca~~~~~~   37 (699)
T KOG4367|consen    3 EELKCPVCGSFYR---EPIILPCSHNLCQACARNILVQ   37 (699)
T ss_pred             ccccCceehhhcc---CceEeecccHHHHHHHHhhccc
Confidence            4578999999887   7899999999999999876654

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

Probab=87.70  E-value=0.33  Score=53.45  Aligned_cols=37  Identities=24%  Similarity=0.654  Sum_probs=29.7

Q ss_pred             cccccccccccccccCCceEEeCCCCcccHhhHHHHHh
Q 017955          279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLD  316 (363)
Q Consensus       279 ~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk  316 (363)
                      .....|.||...+... .-.+.||+|.||++||.+-..
T Consensus       815 ep~d~C~~C~~~ll~~-pF~vf~CgH~FH~~Cl~~~v~  851 (911)
T KOG2034|consen  815 EPQDSCDHCGRPLLIK-PFYVFPCGHCFHRDCLIRHVL  851 (911)
T ss_pred             cCccchHHhcchhhcC-cceeeeccchHHHHHHHHHHH
Confidence            3567899999887653 566789999999999988743

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

Probab=87.43  E-value=0.45  Score=48.36  Aligned_cols=39  Identities=23%  Similarity=0.536  Sum_probs=28.6

Q ss_pred             ccccccccccccccC-CceEEeCCCCcccHhhHHHHHhcC
Q 017955          280 ETIVCAICKDTVNVG-ETATKLPCGHVYHGDCIVPWLDSR  318 (363)
Q Consensus       280 ~~~~C~ICle~f~~~-e~~~~LPC~H~Fh~~CI~~WLk~~  318 (363)
                      ....|.||+..+... .....+.|+|.||..|+++.+..+
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~  184 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVK  184 (384)
T ss_pred             ccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhh
Confidence            467899999544433 333455699999999999988743

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.22  E-value=0.28  Score=47.70  Aligned_cols=31  Identities=23%  Similarity=0.641  Sum_probs=24.6

Q ss_pred             CCCcccHhhHHHHHh-------------cCCCCCCcCcCCCCCC
Q 017955          302 CGHVYHGDCIVPWLD-------------SRNTCPVCRFELPTDD  332 (363)
Q Consensus       302 C~H~Fh~~CI~~WLk-------------~~~sCPlCR~~l~~~d  332 (363)
                      |...+|.+|+-+|+.             ++-+||.||+.++--|
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~d  368 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRD  368 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEee
Confidence            677899999999974             2448999999987544

>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional

Probab=85.97  E-value=0.44  Score=41.40  Aligned_cols=39  Identities=15%  Similarity=0.398  Sum_probs=26.2

Q ss_pred             CCCCceeeeecCCcceeee---------------ccC--CCceecccCCCCceeec
Q 017955           19 TDPTQYWCHHCEKRVSIET---------------LAN--LPDVICHECKNGFVESI   57 (363)
Q Consensus        19 ~~~~~~~C~~C~~~~~~~~---------------~~~--~~~~~c~~C~~gFve~~   57 (363)
                      ..+.+|||..|...+...-               .|.  ...+.||+|++.-++-+
T Consensus        66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~  121 (135)
T PRK03824         66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIV  121 (135)
T ss_pred             ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEe
Confidence            3568999999997666641               010  23466999998766544

>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues

Probab=84.99  E-value=0.6  Score=44.79  Aligned_cols=7  Identities=29%  Similarity=1.260  Sum_probs=2.9

Q ss_pred             eeeeecC
Q 017955           24 YWCHHCE   30 (363)
Q Consensus        24 ~~C~~C~   30 (363)
                      |.|-.|+
T Consensus       172 ~KC~SCN  178 (314)
T PF06524_consen  172 FKCQSCN  178 (314)
T ss_pred             ccccccc
Confidence            4444443

The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus

>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues

Probab=84.69  E-value=0.66  Score=44.50  Aligned_cols=10  Identities=40%  Similarity=0.800  Sum_probs=4.9

Q ss_pred             eeeecCCcce
Q 017955           25 WCHHCEKRVS   34 (363)
Q Consensus        25 ~C~~C~~~~~   34 (363)
                      -|..|.+.||
T Consensus       127 ~C~EC~R~vw  136 (314)
T PF06524_consen  127 VCIECERGVW  136 (314)
T ss_pred             Eeeeeecccc
Confidence            4555554444

The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus

>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]

Probab=84.67  E-value=0.43  Score=46.10  Aligned_cols=51  Identities=22%  Similarity=0.576  Sum_probs=36.9

Q ss_pred             cccccccccccccCCc-eEEeCCC-----CcccHhhHHHHHh--cCCCCCCcCcCCCCC
Q 017955          281 TIVCAICKDTVNVGET-ATKLPCG-----HVYHGDCIVPWLD--SRNTCPVCRFELPTD  331 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~-~~~LPC~-----H~Fh~~CI~~WLk--~~~sCPlCR~~l~~~  331 (363)
                      ...|-||+........ ....||.     ++.|..|+..|+.  .+..|.+|...+...
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~~  136 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFINV  136 (323)
T ss_pred             CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccceec
Confidence            4679999997653211 4567763     6789999999997  455899998865443

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

Probab=83.97  E-value=0.25  Score=53.26  Aligned_cols=46  Identities=24%  Similarity=0.758  Sum_probs=36.5

Q ss_pred             cccccccccccccCCceEEeCCCCcccHhhHHHHHhcC---CCCCCcCcCCC
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR---NTCPVCRFELP  329 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~---~sCPlCR~~l~  329 (363)
                      ...|+||+..+.   .+..+.|.|+|+..|+..-|...   ..||+|+..+.
T Consensus        21 ~lEc~ic~~~~~---~p~~~kc~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e   69 (684)
T KOG4362|consen   21 ILECPICLEHVK---EPSLLKCDHIFLKFCLNKLFESKKGPKQCALCKSDIE   69 (684)
T ss_pred             hccCCceeEEee---ccchhhhhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence            467999999988   45678899999999987766443   47999986554

>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=83.83  E-value=0.86  Score=44.31  Aligned_cols=47  Identities=23%  Similarity=0.509  Sum_probs=33.8

Q ss_pred             cccccccccccCC--ceEEeCCCCcccHhhHHHHHhcC-CCCCCcCcCCC
Q 017955          283 VCAICKDTVNVGE--TATKLPCGHVYHGDCIVPWLDSR-NTCPVCRFELP  329 (363)
Q Consensus       283 ~C~ICle~f~~~e--~~~~LPC~H~Fh~~CI~~WLk~~-~sCPlCR~~l~  329 (363)
                      .|++|.-......  ...+-+|+|..|.+|+...+... ..||.|-+.+-
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLR   51 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILR   51 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhh
Confidence            4999987544322  23333799999999999988654 48999977654

>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=83.81  E-value=1.3  Score=31.89  Aligned_cols=43  Identities=21%  Similarity=0.566  Sum_probs=19.8

Q ss_pred             ccccccccccccCCceEEeCCCCcccHhhHHHHHhc---CC--CCCCcCcC
Q 017955          282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS---RN--TCPVCRFE  327 (363)
Q Consensus       282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~---~~--sCPlCR~~  327 (363)
                      ..|+|.+..+..  .++-..|.|+-|.+ +..||+.   .+  .||+|.++
T Consensus         3 L~CPls~~~i~~--P~Rg~~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRI--PVRGKNCKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SS--EEEETT--SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEEEe--CccCCcCcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            569998887762  44445599985543 3455543   22  69999763

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.

>smart00834 CxxC_CXXC_SSSS Putative regulatory protein

Probab=82.29  E-value=1  Score=30.21  Aligned_cols=29  Identities=24%  Similarity=0.619  Sum_probs=22.2

Q ss_pred             ceeeeecCCcceeeeccC-CCceecccCCC
Q 017955           23 QYWCHHCEKRVSIETLAN-LPDVICHECKN   51 (363)
Q Consensus        23 ~~~C~~C~~~~~~~~~~~-~~~~~c~~C~~   51 (363)
                      .|.|..|.+.|.+..... .....||.|++
T Consensus         5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~   34 (41)
T smart00834        5 EYRCEDCGHTFEVLQKISDDPLATCPECGG   34 (41)
T ss_pred             EEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence            689999998777664322 56688999998

CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=82.00  E-value=0.55  Score=44.94  Aligned_cols=49  Identities=31%  Similarity=0.670  Sum_probs=33.6

Q ss_pred             ccccccccccccccCCce-EEeCC-----CCcccHhhHHHHHhcCC--------CCCCcCcCC
Q 017955          280 ETIVCAICKDTVNVGETA-TKLPC-----GHVYHGDCIVPWLDSRN--------TCPVCRFEL  328 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~-~~LPC-----~H~Fh~~CI~~WLk~~~--------sCPlCR~~l  328 (363)
                      .+..|-||+..=++.... -.-||     .|-.|..||..|+..++        +||.|+.+.
T Consensus        19 ~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEY   81 (293)
T KOG3053|consen   19 LERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEY   81 (293)
T ss_pred             cceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchh
Confidence            456699999875533221 22355     37899999999985332        699999864

>KOG0269 consensus WD40 repeat-containing protein [Function unknown]

Probab=81.48  E-value=1.3  Score=48.26  Aligned_cols=44  Identities=23%  Similarity=0.573  Sum_probs=31.6

Q ss_pred             ccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCC--cCc
Q 017955          282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPV--CRF  326 (363)
Q Consensus       282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPl--CR~  326 (363)
                      ..|.+|-..+. |..+-+--|+|.-|.+|+++|+..+.-||.  |-.
T Consensus       780 ~~CtVC~~vi~-G~~~~c~~C~H~gH~sh~~sw~~~~s~ca~~~C~~  825 (839)
T KOG0269|consen  780 AKCTVCDLVIR-GVDVWCQVCGHGGHDSHLKSWFFKASPCAKSICPH  825 (839)
T ss_pred             cCceeecceee-eeEeecccccccccHHHHHHHHhcCCCCccccCCc
Confidence            36888877655 112222239999999999999999988876  544

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

Probab=81.28  E-value=0.82  Score=50.02  Aligned_cols=52  Identities=23%  Similarity=0.716  Sum_probs=38.2

Q ss_pred             ccccccccccccccCCceEEeCCC-----CcccHhhHHHHHhcCC--CCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCG-----HVYHGDCIVPWLDSRN--TCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~-----H~Fh~~CI~~WLk~~~--sCPlCR~~l~~~d  332 (363)
                      ++..|-||...=..+ .+..-||+     .+.|.+|+.+|+.-+.  .|-+|..++.-++
T Consensus        11 d~~~CRICr~e~~~d-~pLfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~   69 (1175)
T COG5183          11 DKRSCRICRTEDIRD-DPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKD   69 (1175)
T ss_pred             cchhceeecCCCCCC-CcCcccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeee
Confidence            457899999865433 33345665     4789999999997644  7999998876554

>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=80.99  E-value=1  Score=33.93  Aligned_cols=22  Identities=23%  Similarity=0.601  Sum_probs=18.0

Q ss_pred             cceeeeccCCCceecccCCCCce
Q 017955           32 RVSIETLANLPDVICHECKNGFV   54 (363)
Q Consensus        32 ~~~~~~~~~~~~~~c~~C~~gFv   54 (363)
                      +|++++ .+.-+++||||+.-|.
T Consensus        38 rV~L~m-g~~gev~CPYC~t~y~   59 (62)
T COG4391          38 RVFLDM-GDEGEVVCPYCSTRYR   59 (62)
T ss_pred             EEEEEc-CCCCcEecCccccEEE
Confidence            577887 6678999999998774

>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46

Probab=80.44  E-value=1  Score=48.54  Aligned_cols=18  Identities=11%  Similarity=0.253  Sum_probs=11.5

Q ss_pred             ccChhhHHHHHHHHHHhc
Q 017955          236 YMDAAGYEALLQNLAESD  253 (363)
Q Consensus       236 ~~~~~~~e~Ll~~L~~~~  253 (363)
                      .+....|..++..|....
T Consensus       253 ~i~~~~Y~~~~~~L~~eV  270 (622)
T PF02724_consen  253 RISSERYDRYVPLLQDEV  270 (622)
T ss_pred             ccchhhHHHHHHHHHHHH
Confidence            356677777777666544

Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation

>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]

Probab=80.15  E-value=0.62  Score=49.58  Aligned_cols=42  Identities=24%  Similarity=0.707  Sum_probs=27.1

Q ss_pred             cccccccccc-----ccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCc
Q 017955          280 ETIVCAICKD-----TVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVC  324 (363)
Q Consensus       280 ~~~~C~ICle-----~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlC  324 (363)
                      ....|.||..     .|......++..|+++||..|+.   ..+..||.|
T Consensus       510 ~gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~---r~s~~CPrC  556 (580)
T KOG1829|consen  510 KGFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLR---RKSPCCPRC  556 (580)
T ss_pred             CeeeeeeccCCCcccccccccceeHHHHHHHHHHHHHh---ccCCCCCch
Confidence            3456788833     23222345556699999999954   344459999

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	363
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		5e-09
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		2e-08
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		1e-05
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		2e-05
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		3e-04
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		3e-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 = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 32/45 (71%)
Query: 284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFEL 328
           C +CK+   +GE+  +LPC H++H  CIVPWL+  ++CPVCR  L
Sbjct: 18  CPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSL 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 = 57.0 bits (136), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 38/74 (51%), Gaps = 4/74 (5%)
Query: 260 PRAAKSAVLELPTVEILSEQ----ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWL 315
           P A+K ++  LP + +  +     + + C IC      G+ AT+LPC H +H  C+  WL
Sbjct: 15  PPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWL 74
Query: 316 DSRNTCPVCRFELP 329
               TCPVCR   P
Sbjct: 75  QKSGTCPVCRCMFP 88

>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain Length = 69

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 18/50 (36%), Positives = 27/50 (54%)
Query: 284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDP 333
           C IC   +  GE   +LPC H++H  C+  WL +   CP+CR ++    P
Sbjct: 17  CTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQLP 66

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 29/46 (63%), Gaps = 1/46 (2%)
Query: 284 CAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSRNTCPVCRFEL 328
           CA+C   +  GE A  LP CGH +H +C+  WL S +TCP+CR  +
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 = 43.1 bits (100), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/42 (33%), Positives = 23/42 (54%)
Query: 283 VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVC 324
           +CA+C +     +     PC H +H  C++ WL+ R  CP+C
Sbjct: 17  LCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLC 58

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 16/48 (33%), Positives = 24/48 (50%)
Query: 278 EQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCR 325
           + E  +C +C       +    LPC H +H  C+  WL +  TCP+CR
Sbjct: 20  QSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICR 67

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	363
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	2e-35
2ect_A	78	Ring finger protein 126; metal binding protein, st	2e-26
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	9e-20
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	2e-19
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	2e-19
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	6e-18
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	5e-16
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	7e-15
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	8e-15
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	8e-15
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	8e-15
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	9e-15
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	3e-13
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	2e-11
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	3e-11
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	6e-11
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	6e-11
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	5e-10
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	4e-07
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	9e-10
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	6e-09
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	6e-09
3nw0_A	238	Non-structural maintenance of chromosomes element	9e-09
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	1e-08
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	2e-08
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	6e-08
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	1e-07
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	8e-07
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	1e-06
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	2e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	9e-06
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	1e-05
1z6u_A	150	NP95-like ring finger protein isoform B; structura	1e-05
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	1e-05
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	2e-05
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	2e-05
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	3e-05
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	5e-05
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	5e-05
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	5e-05
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	6e-05
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	9e-05
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	1e-04
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	2e-04
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	2e-04
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	4e-04
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	4e-04
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	6e-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 =  123 bits (311), Expect = 2e-35
 Identities = 26/89 (29%), Positives = 40/89 (44%), Gaps = 4/89 (4%)

Query: 246 LQNLAESDGGRRGAPRAAKSAVLELPTVEILSEQ----ETIVCAICKDTVNVGETATKLP 301
           + +           P A+K ++  LP + +  +     + + C IC      G+ AT+LP
Sbjct: 1   MGHHHHHHSHMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP 60

Query: 302 CGHVYHGDCIVPWLDSRNTCPVCRFELPT 330
           C H +H  C+  WL    TCPVCR   P 
Sbjct: 61  CHHYFHKPCVSIWLQKSGTCPVCRCMFPP 89

>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 = 99.4 bits (248), Expect = 2e-26
 Identities = 22/54 (40%), Positives = 33/54 (61%)

Query: 284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEYEE 337
           C +CK+   +GE+  +LPC H++H  CIVPWL+  ++CPVCR  L   +     
Sbjct: 18  CPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATNP 71

>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 = 81.3 bits (201), Expect = 9e-20
 Identities = 20/60 (33%), Positives = 29/60 (48%)

Query: 274 EILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDP 333
           E   E     C IC   +  GE   +LPC H++H  C+  WL +   CP+CR ++    P
Sbjct: 7   EGTEEDTEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQLP 66

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

 Score = 80.6 bits (199), Expect = 2e-19
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 272 TVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD 331
            V+ L+  E   CA+C +     +     PC H +H  C++ WL+ R  CP+C   +   
Sbjct: 8   KVKELNLHEL--CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQL 65

Query: 332 D 332
            
Sbjct: 66  A 66

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

 Score = 80.4 bits (199), Expect = 2e-19
 Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 3/73 (4%)

Query: 262 AAKSAVLELPTV---EILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR 318
            +  +  +LP+        + E  +C +C       +    LPC H +H  C+  WL + 
Sbjct: 1   GSSGSSGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKAN 60

Query: 319 NTCPVCRFELPTD 331
            TCP+CR +    
Sbjct: 61  RTCPICRADSGPS 73

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

 Score = 76.3 bits (188), Expect = 6e-18
 Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 6/62 (9%)

Query: 271 PTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPT 330
             V+ L+++E   C IC D    G     LPC H +   CI  W D    CP+CR ++  
Sbjct: 7   GRVKQLTDEEE--CCICMD----GRADLILPCAHSFCQKCIDKWSDRHRNCPICRLQMTG 60

Query: 331 DD 332
            +
Sbjct: 61  AN 62

>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 = 70.8 bits (174), Expect = 5e-16
 Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 284 CAICKDTVNVG-ETATKLPCGHVYHGDCIVPWLDSRNTCPVCRF 326
           C IC + ++     A  LPCGH+ H  C    L     CP+C  
Sbjct: 8   CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCSG 51

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

 Score = 68.0 bits (166), Expect = 7e-15
 Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 4/61 (6%)

Query: 272 TVEILSEQETIVCAIC----KDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFE 327
           +   L    T+ C IC     + V  G       CGHV+   C+   L + NTCP CR +
Sbjct: 6   SGTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKK 65

Query: 328 L 328
           +
Sbjct: 66  I 66

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

 Score = 67.2 bits (165), Expect = 8e-15
 Identities = 21/46 (45%), Positives = 29/46 (63%), Gaps = 1/46 (2%)

Query: 284 CAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSRNTCPVCRFEL 328
           CA+C   +  GE A  LP CGH +H +C+  WL S +TCP+CR  +
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

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

 Score = 67.5 bits (165), Expect = 8e-15
 Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 4/57 (7%)

Query: 280 ETIVCAIC----KDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD 332
             + C IC     + V  G       CGHV+   C+   L + NTCP CR ++    
Sbjct: 2   AMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR 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 = 67.6 bits (165), Expect = 8e-15
 Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 4/61 (6%)

Query: 276 LSEQETIVCAIC----KDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD 331
           L    T+ C IC     + V  G       CGHV+   C+   L + NTCP CR ++   
Sbjct: 5   LRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 64

Query: 332 D 332
            
Sbjct: 65  R 65

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

 Score = 67.4 bits (165), Expect = 9e-15
 Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 8/60 (13%)

Query: 284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPT------DDPEYEE 337
           C IC +  +    +  LPC H +   CI  W+    TCP+C+  + +       D E+ +
Sbjct: 8   CPICLE--DPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVESVVHTIESDSEFGD 65

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

 Score = 63.2 bits (154), Expect = 3e-13
 Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 2/55 (3%)

Query: 279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDP 333
              I+C+ICK  +   +  T   C H +   CIV      N CP C   +    P
Sbjct: 13  TPYILCSICKGYLI--DATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQP 65

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

 Score = 58.4 bits (141), Expect = 2e-11
 Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 1/43 (2%)

Query: 284 CAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSRNTCPVCR 325
           C  C+      +       C H +H  C+  W+   N CP+C+
Sbjct: 29  CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 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 = 57.6 bits (139), Expect = 3e-11
 Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 4/54 (7%)

Query: 283 VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN--TCPVCRFELPTDDPE 334
           +C IC   +  G++     CG   H  C+  +  S     CP C    P + P+
Sbjct: 17  ICNICHSLLIQGQSCE--TCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIPK 68

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

 Score = 56.8 bits (137), Expect = 6e-11
 Identities = 17/48 (35%), Positives = 21/48 (43%), Gaps = 3/48 (6%)

Query: 284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD 331
           CAIC  T         LPC HV+   C+         C +CR E+P D
Sbjct: 18  CAICLQTC---VHPVSLPCKHVFCYLCVKGASWLGKRCALCRQEIPED 62

>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 = 57.9 bits (140), Expect = 6e-11
 Identities = 14/67 (20%), Positives = 28/67 (41%), Gaps = 2/67 (2%)

Query: 269 ELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFEL 328
               ++I      ++C +C       +  T + C H +   CIV +L++   CP+C  ++
Sbjct: 3   RTTRIKITELNPHLMCVLCGGYFI--DATTIIECLHSFCKTCIVRYLETSKYCPICDVQV 60

Query: 329 PTDDPEY 335
               P  
Sbjct: 61  HKTRPLL 67

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

 Score = 56.3 bits (135), Expect = 5e-10
 Identities = 20/71 (28%), Positives = 27/71 (38%), Gaps = 4/71 (5%)

Query: 279 QETIVCAIC----KDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPE 334
             T+ C IC     + V  G       CGHV+   C+   L + NTCP CR ++      
Sbjct: 5   SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYH 64

Query: 335 YEEERKKRVSA 345
                   VS 
Sbjct: 65  PIYIGSGTVSC 75

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

 Score = 47.9 bits (113), Expect = 4e-07
 Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 4/51 (7%)

Query: 279 QETIVCAIC----KDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCR 325
             T+ C IC     + V  G       CGHV+   C+   L + NTCP CR
Sbjct: 70  SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCR 120

>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 = 54.5 bits (131), Expect = 9e-10
 Identities = 15/55 (27%), Positives = 21/55 (38%), Gaps = 3/55 (5%)

Query: 279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWL-DSRNTCPVCRFELPTDD 332
            E   C IC + +   +      C  +    CI  WL + R  CP CR  L   +
Sbjct: 20  AEVFRCFICMEKLR--DARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRE 72

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

 Score = 51.4 bits (123), Expect = 6e-09
 Identities = 9/48 (18%), Positives = 16/48 (33%), Gaps = 3/48 (6%)

Query: 278 EQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCR 325
           E+    C IC+      +      C H +   C +    +   C +C 
Sbjct: 12  EEIPFRCFICRQAF---QNPVVTKCRHYFCESCALEHFRATPRCYICD 56

>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 = 52.1 bits (124), Expect = 6e-09
 Identities = 15/58 (25%), Positives = 21/58 (36%), Gaps = 15/58 (25%)

Query: 283 VCAICKDTVNV---------------GETATKLPCGHVYHGDCIVPWLDSRNTCPVCR 325
            CAIC++ +                   T     C H +H  CI  WL +R  CP+  
Sbjct: 39  NCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 96

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

 Score = 54.4 bits (130), Expect = 9e-09
 Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 5/72 (6%)

Query: 266 AVLELPTVEILSEQETI-VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN--TCP 322
           A+LE+      +  + + +C IC   +  G++     CG   H  C+  +  S     CP
Sbjct: 164 AILEMEQYIRETYPDAVKICNICHSLLIQGQSCET--CGIRMHLPCVAKYFQSNAEPRCP 221

Query: 323 VCRFELPTDDPE 334
            C    P + P+
Sbjct: 222 HCNDYWPHEIPK 233

>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 = 55.2 bits (132), Expect = 1e-08
 Identities = 17/66 (25%), Positives = 25/66 (37%), Gaps = 4/66 (6%)

Query: 269 ELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFE 327
           E   +         +C IC +           PCGH+    C+  W +S    CP CR E
Sbjct: 320 EQYELYCEMGSTFQLCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCE 376

Query: 328 LPTDDP 333
           +   +P
Sbjct: 377 IKGTEP 382

>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 = 51.0 bits (121), Expect = 2e-08
 Identities = 15/58 (25%), Positives = 21/58 (36%), Gaps = 15/58 (25%)

Query: 283 VCAICKDTVNV---------------GETATKLPCGHVYHGDCIVPWLDSRNTCPVCR 325
            CAIC++ +                   T     C H +H  CI  WL +R  CP+  
Sbjct: 50  NCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

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

 Score = 50.4 bits (120), Expect = 6e-08
 Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 3/94 (3%)

Query: 242 YEALLQNLAESDGGRRGAPRAAKSAVLELPTVEILSEQETIVCAICKDTVNVGETATKLP 301
           +EA++Q   +     +      ++   E+ +      +  + C IC +      T   L 
Sbjct: 25  FEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYFIEAVT---LN 81

Query: 302 CGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEY 335
           C H +   CI  W+  +  CP+CR ++ +     
Sbjct: 82  CAHSFCSYCINEWMKRKIECPICRKDIKSKTYSL 115

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

 Score = 48.2 bits (115), Expect = 1e-07
 Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 6/65 (9%)

Query: 269 ELPTVEILSEQETIVCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSRNTCPVCRFE 327
            L  ++ +   + + C IC +  N    A  +P C H Y   CI  +L  +  CP C   
Sbjct: 12  GLAVMKTI--DDLLRCGICFEYFN---IAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVT 66

Query: 328 LPTDD 332
           +   D
Sbjct: 67  VTEPD 71

>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 = 46.4 bits (109), Expect = 8e-07
 Identities = 16/87 (18%), Positives = 25/87 (28%), Gaps = 21/87 (24%)

Query: 259 APRAAKSAVLELPTVEILSEQETIVCAICKDTVNVGETAT---------------KLPCG 303
                   V+   T E+    E   C IC + + V    +                  C 
Sbjct: 4   GSSGEPEQVIRKYTEELKVAPEED-CIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCS 62

Query: 304 HVYHGDCIVPWL-----DSRNTCPVCR 325
           H +H  C++        D    CP C+
Sbjct: 63  HAFHLLCLLAMYCNGNKDGSLQCPSCK 89

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

 Score = 44.4 bits (105), Expect = 1e-06
 Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 4/55 (7%)

Query: 279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELPTDD 332
           ++   C  C   +    +  +  CGH +   C+   L S +  C  C+  +  D 
Sbjct: 13  EDKYKCEKCHLVL---CSPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDK 64

>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 = 46.5 bits (110), Expect = 2e-06
 Identities = 28/98 (28%), Positives = 42/98 (42%), Gaps = 4/98 (4%)

Query: 237 MDAAGYEALLQNLAESDGGRRGAPRAAKSAVLELPTVEILSEQETIVCAICKDTVNVGET 296
           +   G + L +    S    +  P+ A +  LE+  V   S    ++C IC D +    T
Sbjct: 11  VQTNGTQPLSKTWELSLYELQRTPQEAITDGLEI-VVSPRSLHSELMCPICLDMLK--NT 67

Query: 297 ATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELPTDDP 333
            T   C H +  DCI+  L S N  CP CR +L +   
Sbjct: 68  MTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRS 105

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 48.7 bits (115), Expect = 2e-06
 Identities = 35/247 (14%), Positives = 69/247 (27%), Gaps = 78/247 (31%)

Query: 24  YWCH--HCEKRVSI-ETLANLPDVICHECKNGFVESIPVTLTPPFSPPSLTPDHVDDPSF 80
           +W +  +C    ++ E L  L     ++            + P ++      DH  +   
Sbjct: 185 FWLNLKNCNSPETVLEMLQKL----LYQ------------IDPNWTSR---SDHSSNIKL 225

Query: 81  GSQFLQVLRLIAQAARDEDAPQQLTQDPQYGHDFLRIELDG-WEN---DA---------- 126
               +Q               ++L +   Y +  L + L         +A          
Sbjct: 226 RIHSIQ------------AELRRLLKSKPYENCLL-V-LLNVQNAKAWNAFNLSCKILLT 271

Query: 127 -REDENDENEENRNVDEEGDENENENEDDEENEGGEDRSDNENEE---NIENEDEEDLRR 182
            R          + V +        +   + +      + +E +       +   +DL R
Sbjct: 272 TR---------FKQVTDFLSAATTTHISLDHHSMTL--TPDEVKSLLLKYLDCRPQDLPR 320

Query: 183 RWRDVLPLRIRDFATRSRSGRNRILDWAEI----LNNSIEFRLEAPESDRYIGNPADYMD 238
                 P R+   A   R G     +W  +    L   IE  L   E       PA+Y  
Sbjct: 321 EVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLE-------PAEYRK 373

Query: 239 AAGYEAL 245
              ++ L
Sbjct: 374 M--FDRL 378

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

 Score = 42.4 bits (99), Expect = 9e-06
 Identities = 15/72 (20%), Positives = 29/72 (40%), Gaps = 5/72 (6%)

Query: 277 SEQETIVCAICKDTVNVGETATK-LPCGHVYHGDCIVPWLDSRNT-CPVCRFELPTDDPE 334
           ++++ + C +C + + + +       CG+     C        N  CP CR   P D   
Sbjct: 7   AKEDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAV 66

Query: 335 Y---EEERKKRV 343
           Y    +E  +R+
Sbjct: 67  YKPLSQEELQRI 78

>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 = 43.4 bits (102), Expect = 1e-05
 Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 4/52 (7%)

Query: 279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR-NTCPVCRFELP 329
           +ET  C  C++ V    T     C H    DC+     ++  +CP CR++L 
Sbjct: 50  EETFQCICCQELVFRPIT---TVCQHNVCKDCLDRSFRAQVFSCPACRYDLG 98

>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 = 43.8 bits (103), Expect = 1e-05
 Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 20/78 (25%)

Query: 279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELPTDD----- 332
           +++ +C  C++ V   +  T   C H    DC+     ++  +CP CR +L  +      
Sbjct: 76  EQSFMCVCCQELVY--QPVT-TECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYIMIPN 132

Query: 333 -----------PEYEEER 339
                      P Y + R
Sbjct: 133 EILQTLLDLFFPGYSKGR 150

>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 = 43.0 bits (101), Expect = 1e-05
 Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 5/66 (7%)

Query: 269 ELPTVEILSE-QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRF 326
           +L  V+  +   ++I C IC+  +       +  C H++   CI+  L      CP CR+
Sbjct: 10  KLLAVDFPAHFVKSISCQICEHIL---ADPVETSCKHLFCRICILRCLKVMGSYCPSCRY 66

Query: 327 ELPTDD 332
                D
Sbjct: 67  PCFPTD 72

>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 = 43.9 bits (103), Expect = 2e-05
 Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 4/54 (7%)

Query: 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWL-DSRNTCPVCRFELPTDD 332
               C IC   +     A + PCGH +   CI+  + D+ + CPV    L  + 
Sbjct: 17  SKYECPICLMAL---REAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQ 67

>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 = 42.2 bits (99), Expect = 2e-05
 Identities = 12/57 (21%), Positives = 20/57 (35%), Gaps = 4/57 (7%)

Query: 274 EILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELP 329
           + +       C IC + +        LPC H     C    ++  +  CP CR  + 
Sbjct: 8   DAIPSLSECQCGICMEIL---VEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVS 61

>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 = 15/54 (27%), Positives = 22/54 (40%), Gaps = 4/54 (7%)

Query: 280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWL-DSRNTCPVCRFELPTDD 332
               C IC         A + PCGH +   CI+  + D+ + CPV    L  + 
Sbjct: 17  SKYECPICLM---ALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQ 67

>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 = 40.1 bits (94), Expect = 5e-05
 Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 6/58 (10%)

Query: 279 QETIVCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSRN--TCPVCRFELPTDDP 333
            + ++C ICKD +     A  +P CG+ Y  +CI   L   +  TCP C     + D 
Sbjct: 13  PDELLCLICKDIM---TDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA 67

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

 Score = 43.7 bits (102), Expect = 5e-05
 Identities = 13/67 (19%), Positives = 19/67 (28%), Gaps = 16/67 (23%)

Query: 278 EQETIVCAICKDTVNVGETATK-----LPCGHVYHGDCIVPWLDSRN-----------TC 321
           + E + C IC      G            C    H  C+  W  +              C
Sbjct: 305 DNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQC 364

Query: 322 PVCRFEL 328
           P C+ +L
Sbjct: 365 PFCKAKL 371

>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 = 41.4 bits (97), Expect = 5e-05
 Identities = 11/54 (20%), Positives = 23/54 (42%), Gaps = 4/54 (7%)

Query: 279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD 332
           ++ + C+ C + +   E      C H++  +C+   + +   CPVC       D
Sbjct: 20  EKLLRCSRCTNILR--EPVCLGGCEHIFCSNCVSDCIGTG--CPVCYTPAWIQD 69

>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 = 41.6 bits (97), Expect = 6e-05
 Identities = 14/60 (23%), Positives = 22/60 (36%), Gaps = 4/60 (6%)

Query: 283 VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELPTDDPEYEEERKK 341
           +C+ C++   V     +  CGH Y   C+   L S    C  C  E   ++     E   
Sbjct: 33  LCSACRN---VLRRPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIYEEGISILESSS 89

>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 Length = 61

 Score = 39.3 bits (92), Expect = 9e-05
 Identities = 6/52 (11%), Positives = 17/52 (32%), Gaps = 2/52 (3%)

Query: 281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD 332
            ++CAI          + K     ++    +  ++      P+    L  ++
Sbjct: 3   HMLCAISGKVPRRPVLSPK--SRTIFEKSLLEQYVKDTGNDPITNEPLSIEE 52

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 73

 Score = 38.9 bits (91), Expect = 1e-04
 Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 14/61 (22%)

Query: 279 QETIVCAIC----KDTVNVGETATKLPCGHVYHGDCIVPWLDSRNT---CPVCRFELPTD 331
           QE ++C IC    +  V        + CGH +   CI    ++      CP+C+  +  +
Sbjct: 18  QEEVICPICLDILQKPVT-------IDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKN 70

Query: 332 D 332
            
Sbjct: 71  A 71

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 15/60 (25%), Positives = 21/60 (35%), Gaps = 4/60 (6%)

Query: 279 QETIVCAICKDTVNVGETATK-LPCGHVYHGDCIVPWLDSRN---TCPVCRFELPTDDPE 334
           +E + C IC ++    +   K L CGH     C+   L S      CP C          
Sbjct: 13  REVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITSLT 72

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

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 6/52 (11%)

Query: 278 EQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP 329
           E + + C  C+           LPC H     C+     S   CP+C+   P
Sbjct: 3   EFQFLRCQQCQAEAK---CPKLLPCLHTLCSGCLE---ASGMQCPICQAPWP 48

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

 Score = 38.2 bits (89), Expect = 4e-04
 Identities = 17/45 (37%), Positives = 22/45 (48%), Gaps = 6/45 (13%)

Query: 284 CAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSRN--TCPVCR 325
           C ICKD +     A  +P CG+ Y  +CI   L   +  TCP C 
Sbjct: 16  CLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCH 57

>2ecw_A Tripartite motif-containing protein 30; metal binding protein, structural genomics, NPPSFA; NMR {Mus musculus} Length = 85

 Score = 37.7 bits (88), Expect = 4e-04
 Identities = 17/65 (26%), Positives = 24/65 (36%), Gaps = 17/65 (26%)

Query: 279 QETIVCAIC----KDTVNVGETATKLPCGHVYHGDCIVPWLDSRNT------CPVCRFEL 328
           +E + C IC    K+ V+         C H +   CI    +S         CPVCR   
Sbjct: 17  KEEVTCPICLELLKEPVS-------ADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPY 69

Query: 329 PTDDP 333
           P  + 
Sbjct: 70  PFGNL 74

>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 Length = 112

 Score = 38.2 bits (89), Expect = 6e-04
 Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 14/62 (22%)

Query: 279 QETIVCAIC----KDTVNVGETATKLPCGHVYHGDCIVPWLDSRN---TCPVCRFELPTD 331
           Q+ + C IC    K+ V          C H++   C++  L+ +     CP+C+ ++   
Sbjct: 19  QKILECPICLELIKEPV-------STKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR 71

Query: 332 DP 333
             
Sbjct: 72  SL 73

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	363
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.64
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.57
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.5
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.49
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.49
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.47
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.42
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.37
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.37
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.37
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.37
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.37
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.36
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.35
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.33
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.31
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.3
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.3
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.3
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.3
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.3
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.28
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.28
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.25
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.24
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.23
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.23
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.23
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.21
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.2
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.17
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.17
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.17
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.16
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.15
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.15
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.12
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.11
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.11
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.11
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.1
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.08
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.08
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.08
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.07
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.07
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.05
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.02
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	98.98
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	98.96
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	98.95
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.92
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.91
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.89
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.88
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	98.88
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.86
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.84
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.83
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.73
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.7
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.58
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.57
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.57
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.56
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.55
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.5
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.48
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.39
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.19
3nw0_A	238	Non-structural maintenance of chromosomes element	97.8
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	96.56
4ayb_P	48	DNA-directed RNA polymerase; transferase, multi-su	95.05
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	94.44
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	92.2
2kdx_A	119	HYPA, hydrogenase/urease nickel incorporation prot	90.8
2lv2_A	85	Insulinoma-associated protein 1; structural genomi	88.55
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	88.52
3a43_A	139	HYPD, hydrogenase nickel incorporation protein HYP	86.15
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	85.49
2ct7_A	86	Ring finger protein 31; IBR, structural genomics,	85.3
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	84.99
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	83.03
2eps_A	54	POZ-, at HOOK-, and zinc finger-containing protein	82.98
2lce_A	74	B-cell lymphoma 6 protein; structural genomics, no	81.53
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	81.04
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	80.38
3h0g_L	63	DNA-directed RNA polymerases I, II, and III subuni	80.3

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

Probab=99.64  E-value=1.8e-16  Score=126.71  Aligned_cols=76  Identities=34%  Similarity=0.794  Sum_probs=66.3

Q ss_pred             CCCCChhhHHHHHcCCceeeeccc----ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955          256 RRGAPRAAKSAVLELPTVEILSEQ----ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD  331 (363)
Q Consensus       256 ~~~~~~~s~~~i~~lp~~~~~~~~----~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~  331 (363)
                      .....++++..|..||.+.+....    ....|+||++.|..+..++.|||+|+||..||.+||+.+.+||+||+.|+..
T Consensus        11 ~~~~~~~s~~~i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~~   90 (91)
T 2l0b_A           11 MVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSGTCPVCRCMFPPP   90 (91)
T ss_dssp             SSCCCCCCHHHHHTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEETTTEEEEHHHHHHHHTTTCBCTTTCCBSSCC
T ss_pred             CcCCCCCCHHHHHhCCCeeecccccccCCCCCCcccChhhcCCCcEEecCCCChHHHHHHHHHHHcCCcCcCcCccCCCC
Confidence            445677899999999998876543    4568999999999888899999999999999999999999999999998753

>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=1.3e-15  Score=116.81  Aligned_cols=65  Identities=28%  Similarity=0.720  Sum_probs=54.6

Q ss_pred             HHcCCceeeecc---cccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955          267 VLELPTVEILSE---QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD  331 (363)
Q Consensus       267 i~~lp~~~~~~~---~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~  331 (363)
                      +..+|...+...   .....|+||++.|..+..++.+||+|+||..||.+||+.+.+||+||+.|...
T Consensus         6 i~~lp~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A            6 SGQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             CSSCCCEEBCSSSCSSSCCEETTTTEECCBTCEEEEETTTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             HhhCCcEEecCccccCCCCCCeECCcccCCCCeEEEECCCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            445666665542   25678999999999888889999999999999999999999999999998764

>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=99.50  E-value=1.4e-14  Score=109.04  Aligned_cols=54  Identities=33%  Similarity=0.902  Sum_probs=48.7

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCCh
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDP  333 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~  333 (363)
                      ....|+||++.|..+..++.+||+|+||..||.+|++.+.+||+||..|....+
T Consensus        13 ~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   66 (69)
T 2kiz_A           13 TEEKCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRVDIEAQLP   66 (69)
T ss_dssp             CCCSBTTTTBCCCSSSCEEECTTSCEEEHHHHHHHHHHCSBCTTTCSBSCSCCC
T ss_pred             CCCCCeeCCccccCCCcEEEeCCCCHHHHHHHHHHHHcCCCCcCcCccccCcCC
Confidence            557899999999877788999999999999999999999999999999876543

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

Probab=99.49  E-value=1.1e-14  Score=104.65  Aligned_cols=50  Identities=42%  Similarity=1.046  Sum_probs=45.8

Q ss_pred             ccccccccccccccCCceEEeC-CCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSRNTCPVCRFELP  329 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~WLk~~~sCPlCR~~l~  329 (363)
                      ....|+||++.|..++.+..++ |+|+||..||.+|++.+.+||+||+.|.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            4567999999999888888898 9999999999999999999999999874

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

Probab=99.49  E-value=1.8e-14  Score=109.87  Aligned_cols=53  Identities=26%  Similarity=0.797  Sum_probs=47.7

Q ss_pred             cccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955          279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD  331 (363)
Q Consensus       279 ~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~  331 (363)
                      .....|+||++.|.....+..|||+|+||..||.+|++.+.+||+||+.|...
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNMPVLQL   65 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEETTTEEEEHHHHHHHHHHCSBCTTTCCBCSSC
T ss_pred             CCCCCCcCCCcccCCCCcEEEcCCCCEecHHHHHHHHHcCCcCCCcCcccccc
Confidence            35678999999999888888899999999999999999999999999998653

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

Probab=99.47  E-value=2.1e-14  Score=110.67  Aligned_cols=54  Identities=41%  Similarity=1.125  Sum_probs=48.8

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCCh
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDP  333 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~  333 (363)
                      ....|+||++.|.....+..|+|+|+||..||.+|++.+.+||+||..|...+.
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   67 (78)
T 2ect_A           14 SGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNT   67 (78)
T ss_dssp             SSCCCTTTTSCCCTTSCEEECTTSCEEETTTTHHHHTTTCSCTTTCCCCCCSCS
T ss_pred             CCCCCeeCCccccCCCCEEEeCCCCeecHHHHHHHHHcCCcCcCcCCccCCccc
Confidence            467899999999877788889999999999999999999999999999987554

>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=99.42  E-value=1.1e-13  Score=99.23  Aligned_cols=50  Identities=30%  Similarity=0.690  Sum_probs=43.8

Q ss_pred             ccccccccccccccC-CceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955          280 ETIVCAICKDTVNVG-ETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP  329 (363)
Q Consensus       280 ~~~~C~ICle~f~~~-e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~  329 (363)
                      ....|+||++.|..+ ..++.++|+|+||..||.+|++.+.+||+||+.|.
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            356799999998643 45788899999999999999999999999999885

>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=99.37  E-value=5.4e-13  Score=109.98  Aligned_cols=52  Identities=23%  Similarity=0.561  Sum_probs=42.2

Q ss_pred             ccccccccccccccCC---------------ceEEeCCCCcccHhhHHHHH-----hcCCCCCCcCcCCCCC
Q 017955          280 ETIVCAICKDTVNVGE---------------TATKLPCGHVYHGDCIVPWL-----DSRNTCPVCRFELPTD  331 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e---------------~~~~LPC~H~Fh~~CI~~WL-----k~~~sCPlCR~~l~~~  331 (363)
                      .+..|+|||+.|....               .++.++|+|+||..||..||     +.+.+||+||..+...
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            4468999999986432               34478899999999999999     4567999999988654

>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=99.37  E-value=4.3e-13  Score=110.50  Aligned_cols=50  Identities=32%  Similarity=0.606  Sum_probs=43.2

Q ss_pred             ccccccccccccccCC---------------ceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955          280 ETIVCAICKDTVNVGE---------------TATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP  329 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e---------------~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~  329 (363)
                      .+..|+||++.|...-               .++.++|+|.||..||.+||+.+.+||+||+.+.
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            5678999999987431               3667899999999999999999999999999864

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

Probab=99.37  E-value=2.1e-13  Score=102.76  Aligned_cols=53  Identities=34%  Similarity=0.763  Sum_probs=45.9

Q ss_pred             cccccccccccccc----CCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNV----GETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~----~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d  332 (363)
                      ....|+||++.|..    +..++.++|+|.||..||.+|++.+.+||+||..+...+
T Consensus         9 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   65 (71)
T 3ng2_A            9 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR   65 (71)
T ss_dssp             TCCBCTTTCCBHHHHHTTTCCEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCCCS
T ss_pred             CCCCCcccChhhhccccccCCeEeCCCCChHhHHHHHHHHHcCCCCCCCCCccChhh
Confidence            56789999999874    234588999999999999999999999999999998654

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

Probab=99.37  E-value=1.4e-13  Score=107.66  Aligned_cols=51  Identities=29%  Similarity=0.734  Sum_probs=41.8

Q ss_pred             cccccccccccccc-----------CCceEEeC-CCCcccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955          280 ETIVCAICKDTVNV-----------GETATKLP-CGHVYHGDCIVPWLDSRNTCPVCRFELPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~-----------~e~~~~LP-C~H~Fh~~CI~~WLk~~~sCPlCR~~l~~  330 (363)
                      .+..|+||++.|..           ++.++.++ |+|+||..||.+||+++++||+||+.+..
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            45668888888753           34455665 99999999999999999999999998864

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

Probab=99.37  E-value=2.2e-13  Score=101.88  Aligned_cols=51  Identities=33%  Similarity=0.720  Sum_probs=44.2

Q ss_pred             ccccccccccccccC----CceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955          280 ETIVCAICKDTVNVG----ETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~~----e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~  330 (363)
                      ....|+||++.|...    ..++.++|+|+||..||.+|++.+.+||+||..|..
T Consensus        14 ~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           14 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             CCCCCTTTCCCHHHHTTTTCCEEECSSSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCcccCccccccccccCCeEeCCCCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            567899999998742    344789999999999999999999999999999864

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

Probab=99.36  E-value=5.4e-13  Score=101.45  Aligned_cols=53  Identities=32%  Similarity=0.680  Sum_probs=45.5

Q ss_pred             cccccccccccccccCCceEEe-CCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChh
Q 017955          279 QETIVCAICKDTVNVGETATKL-PCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPE  334 (363)
Q Consensus       279 ~~~~~C~ICle~f~~~e~~~~L-PC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~  334 (363)
                      .....|+||++.|.   .++.+ +|+|.||..||..|++.+.+||+||+.+...++.
T Consensus        13 ~~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   66 (72)
T 2djb_A           13 TPYILCSICKGYLI---DATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPL   66 (72)
T ss_dssp             CGGGSCTTTSSCCS---SCEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCSSCSC
T ss_pred             CCCCCCCCCChHHH---CcCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCccccc
Confidence            35678999999987   35555 9999999999999999999999999999876543

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

Probab=99.35  E-value=3.3e-13  Score=99.38  Aligned_cols=52  Identities=31%  Similarity=0.692  Sum_probs=45.0

Q ss_pred             cccccccccccccC----CceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCC
Q 017955          281 TIVCAICKDTVNVG----ETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD  332 (363)
Q Consensus       281 ~~~C~ICle~f~~~----e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d  332 (363)
                      ...|+||++.|...    ..+..++|+|.||..||.+|++.+.+||+||..+...+
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   58 (64)
T 2xeu_A            3 MVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR   58 (64)
T ss_dssp             CCBCTTTCCBHHHHHHTTCCEEEETTSCEEEHHHHHHHHHHCSBCTTTCCBCTTTC
T ss_pred             CCCCCccChhhhCccccCCCEEeCCCCCchhHHHHHHHHHcCCCCCCCCccCCccc
Confidence            46799999998742    34578899999999999999999999999999998765

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

Probab=99.33  E-value=4e-13  Score=101.90  Aligned_cols=48  Identities=33%  Similarity=0.627  Sum_probs=43.4

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~  330 (363)
                      ....|+||++.|.   .++.+||+|+||..||..|++.+.+||+||..|..
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            4578999999987   56788999999999999999999999999999864

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

Probab=99.31  E-value=1.9e-13  Score=103.06  Aligned_cols=51  Identities=31%  Similarity=0.826  Sum_probs=45.4

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChh
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPE  334 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~  334 (363)
                      ....|+||++.+..    +.+||+|.||..||.+|++.+.+||+||..+...+..
T Consensus        14 ~~~~C~IC~~~~~~----~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   64 (70)
T 2ecn_A           14 DEEECCICMDGRAD----LILPCAHSFCQKCIDKWSDRHRNCPICRLQMTGANES   64 (70)
T ss_dssp             CCCCCSSSCCSCCS----EEETTTEEECHHHHHHSSCCCSSCHHHHHCTTCCCCC
T ss_pred             CCCCCeeCCcCccC----cccCCCCcccHHHHHHHHHCcCcCCCcCCcccCCCcc
Confidence            56789999999874    7899999999999999999999999999999876643

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

Probab=99.30  E-value=1e-12  Score=98.34  Aligned_cols=49  Identities=29%  Similarity=0.745  Sum_probs=43.0

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~  330 (363)
                      ....|+||++.+..  .++.+||+|.||..||..|++.+.+||+||..+..
T Consensus         4 ~~~~C~IC~~~~~~--~~~~~~C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPSN--YSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCeeCCccccC--CcEecCCCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            35679999999872  45789999999999999999999999999998864

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

Probab=99.30  E-value=1.4e-12  Score=99.77  Aligned_cols=52  Identities=35%  Similarity=0.795  Sum_probs=44.3

Q ss_pred             cccccccccccccccCCceEEeC-CCCcccHhhHHHHHhcC--CCCCCcCcCCCCCCh
Q 017955          279 QETIVCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSR--NTCPVCRFELPTDDP  333 (363)
Q Consensus       279 ~~~~~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~WLk~~--~sCPlCR~~l~~~d~  333 (363)
                      .....|+||++.|.   .++.++ |+|.||..||..|++.+  .+||+||+.+...+.
T Consensus        13 ~~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~~   67 (74)
T 2yur_A           13 PDELLCLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA   67 (74)
T ss_dssp             CGGGSCSSSCCCCT---TCEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTTT
T ss_pred             CCCCCCcCCChHHh---CCeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCccc
Confidence            35678999999998   567799 99999999999999876  689999998765554

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

Probab=99.30  E-value=2e-12  Score=101.25  Aligned_cols=54  Identities=26%  Similarity=0.582  Sum_probs=46.2

Q ss_pred             cccccccccccccccCCc-eEEeCCCCcccHhhHHHHHhcC---CCCCCcCcCCCCCC
Q 017955          279 QETIVCAICKDTVNVGET-ATKLPCGHVYHGDCIVPWLDSR---NTCPVCRFELPTDD  332 (363)
Q Consensus       279 ~~~~~C~ICle~f~~~e~-~~~LPC~H~Fh~~CI~~WLk~~---~sCPlCR~~l~~~d  332 (363)
                      .....|+||++.|..... ++.++|+|.||..||..|++.+   ..||+||+.+...+
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   70 (88)
T 2ct2_A           13 REVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSKITRITS   70 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSSCEEECSSSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCSS
T ss_pred             cCCCCCccCCccccccCCCeEECCCCChhhHHHHHHHHHcCCCCcCCCCCCCcccchh
Confidence            356789999999985443 8889999999999999999886   69999999887654

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

Probab=99.30  E-value=2.6e-12  Score=99.70  Aligned_cols=48  Identities=17%  Similarity=0.490  Sum_probs=43.2

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~  330 (363)
                      ....|+||++.|.   .++.++|+|+||..||..|++...+||+||..+..
T Consensus        14 ~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   61 (81)
T 2csy_A           14 IPFRCFICRQAFQ---NPVVTKCRHYFCESCALEHFRATPRCYICDQPTGG   61 (81)
T ss_dssp             CCSBCSSSCSBCC---SEEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCCS
T ss_pred             CCCCCcCCCchhc---CeeEccCCCHhHHHHHHHHHHCCCcCCCcCccccc
Confidence            4578999999997   46779999999999999999999999999999864

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

Probab=99.30  E-value=9.8e-13  Score=112.56  Aligned_cols=50  Identities=28%  Similarity=0.815  Sum_probs=44.7

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d  332 (363)
                      ....|+||++.|.   .++.+||||.||..||..|++.+.+||+||..+....
T Consensus        52 ~~~~C~iC~~~~~---~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~  101 (138)
T 4ayc_A           52 NELQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKT  101 (138)
T ss_dssp             HHSBCTTTCSBCS---SEEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCCEE
T ss_pred             ccCCCcccCcccC---CceECCCCCCccHHHHHHHHHcCCcCCCCCCcCCCCC
Confidence            3467999999997   5778999999999999999999999999999997654

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

Probab=99.28  E-value=2.2e-12  Score=97.77  Aligned_cols=51  Identities=27%  Similarity=0.723  Sum_probs=43.8

Q ss_pred             cccccccccccccccCCceEEeCCCCcccHhhHHHHHh---cCCCCCCcCcCCCCCC
Q 017955          279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLD---SRNTCPVCRFELPTDD  332 (363)
Q Consensus       279 ~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk---~~~sCPlCR~~l~~~d  332 (363)
                      .....|+||++.|.   .++.++|+|.||..||..|++   .+..||+||..+..++
T Consensus        18 ~~~~~C~IC~~~~~---~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           18 QEEVICPICLDILQ---KPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCCBCTTTCSBCS---SEEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             ccCCEeccCCcccC---CeEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            35678999999988   577789999999999999997   4558999999997654

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

Probab=99.28  E-value=2.1e-12  Score=96.39  Aligned_cols=50  Identities=22%  Similarity=0.612  Sum_probs=42.7

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHh-cCCCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLD-SRNTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk-~~~sCPlCR~~l~~~d  332 (363)
                      ....|+||++.+.   .++.++|+|.||..||.+|++ .+.+||+||..+..++
T Consensus        14 ~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   64 (66)
T 2ecy_A           14 DKYKCEKCHLVLC---SPKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDK   64 (66)
T ss_dssp             CCEECTTTCCEES---SCCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTT
T ss_pred             cCCCCCCCChHhc---CeeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCChhh
Confidence            5678999999987   455589999999999999994 5669999999997654

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

Probab=99.25  E-value=3.8e-12  Score=97.85  Aligned_cols=50  Identities=26%  Similarity=0.533  Sum_probs=44.3

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l~~~d  332 (363)
                      ....|+||++.|.   .++.++|||.||..||..|++. +.+||+||..+...+
T Consensus         7 ~~~~C~IC~~~~~---~Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~   57 (78)
T 1t1h_A            7 EYFRCPISLELMK---DPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAG   57 (78)
T ss_dssp             SSSSCTTTSCCCS---SEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCC
T ss_pred             ccCCCCCcccccc---CCEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCChhh
Confidence            4578999999998   5778899999999999999987 779999999997654

>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=99.24  E-value=1.1e-12  Score=109.82  Aligned_cols=50  Identities=34%  Similarity=0.650  Sum_probs=1.2

Q ss_pred             ccccccccccccccC-------------C--ceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955          280 ETIVCAICKDTVNVG-------------E--TATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP  329 (363)
Q Consensus       280 ~~~~C~ICle~f~~~-------------e--~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~  329 (363)
                      .+..|+||++.|...             +  .+..++|+|.||..||.+||+.+++||+||+++.
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~  111 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWE  111 (117)
T ss_dssp             CC---------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeee
Confidence            567899999999742             1  2334589999999999999999999999999864

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

Probab=99.23  E-value=7.2e-12  Score=97.00  Aligned_cols=50  Identities=30%  Similarity=0.785  Sum_probs=43.7

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc------CCCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS------RNTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~------~~sCPlCR~~l~~~d  332 (363)
                      ....|+||++.|.   .++.++|+|.||..||..|++.      ...||+||..+...+
T Consensus        18 ~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~   73 (85)
T 2ecw_A           18 EEVTCPICLELLK---EPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGN   73 (85)
T ss_dssp             TTTSCTTTCSCCS---SCEECTTSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTC
T ss_pred             cCCCCcCCChhhC---cceeCCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHh
Confidence            5678999999987   4568999999999999999987      668999999987653

>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=99.23  E-value=2.6e-12  Score=104.13  Aligned_cols=50  Identities=30%  Similarity=0.686  Sum_probs=43.7

Q ss_pred             ccccccccccccccCCceEE-eCCCCcccHhhHHHHHhcC-CCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATK-LPCGHVYHGDCIVPWLDSR-NTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~-LPC~H~Fh~~CI~~WLk~~-~sCPlCR~~l~~~d  332 (363)
                      ....|+||++.|.   .++. ++|+|.||..||..|++.+ .+||+||..+...+
T Consensus        21 ~~~~C~IC~~~~~---~p~~~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (100)
T 3lrq_A           21 EVFRCFICMEKLR---DARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRE   72 (100)
T ss_dssp             HHTBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CCCCCccCCcccc---CccccCCCCChhhHHHHHHHHHHCcCCCCCCCCcCCHHH
Confidence            4578999999997   4666 8999999999999999988 69999999997654

>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=99.23  E-value=5.8e-12  Score=103.05  Aligned_cols=51  Identities=25%  Similarity=0.712  Sum_probs=44.9

Q ss_pred             ccccccccccccccccCCceEEe-CCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955          278 EQETIVCAICKDTVNVGETATKL-PCGHVYHGDCIVPWLDSRNTCPVCRFELPTD  331 (363)
Q Consensus       278 ~~~~~~C~ICle~f~~~e~~~~L-PC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~  331 (363)
                      ......|+||++.|.   .++.+ +|+|.||..||..|++.+.+||+||..+...
T Consensus        12 ~~~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           12 LNPHLMCVLCGGYFI---DATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             HGGGTBCTTTSSBCS---SEEEETTTCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             cCCcCCCccCChHHh---CcCEeCCCCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            346688999999997   45666 9999999999999999999999999999865

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

Probab=99.21  E-value=5.6e-12  Score=98.71  Aligned_cols=52  Identities=25%  Similarity=0.721  Sum_probs=43.7

Q ss_pred             ccccccccccccccCCceEEeCCC-----CcccHhhHHHHHhcCC--CCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCG-----HVYHGDCIVPWLDSRN--TCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~-----H~Fh~~CI~~WLk~~~--sCPlCR~~l~~~d  332 (363)
                      ....|.||++.|..+..+ ++||+     |+||..||.+||+.++  +||+||..+....
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            456799999999766554 68996     9999999999998764  8999999997654

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

Probab=99.20  E-value=8.1e-12  Score=96.70  Aligned_cols=50  Identities=28%  Similarity=0.804  Sum_probs=43.6

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc------CCCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS------RNTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~------~~sCPlCR~~l~~~d  332 (363)
                      ....|+||++.|.   .++.++|+|.||..||..|++.      ...||+||..+...+
T Consensus        18 ~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~   73 (85)
T 2ecv_A           18 EEVTCPICLELLT---QPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPEN   73 (85)
T ss_dssp             CCCCCTTTCSCCS---SCBCCSSSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSS
T ss_pred             CCCCCCCCCcccC---CceeCCCCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHh
Confidence            5678999999987   4567899999999999999987      779999999987643

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

Probab=99.17  E-value=3.6e-12  Score=97.90  Aligned_cols=50  Identities=28%  Similarity=0.713  Sum_probs=43.2

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc-------CCCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS-------RNTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~-------~~sCPlCR~~l~~~d  332 (363)
                      ....|+||++.|.   .++.+||+|.||..||..|++.       ...||+||..+...+
T Consensus        11 ~~~~C~IC~~~~~---~p~~l~CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~   67 (79)
T 2egp_A           11 EEVTCPICLELLT---EPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEH   67 (79)
T ss_dssp             CCCEETTTTEECS---SCCCCSSSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSG
T ss_pred             cCCCCcCCCcccC---CeeECCCCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhh
Confidence            5678999999987   4566899999999999999987       568999999997643

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

Probab=99.17  E-value=1.4e-11  Score=99.06  Aligned_cols=49  Identities=29%  Similarity=0.702  Sum_probs=43.1

Q ss_pred             ccccccccccccccCCceEEe-CCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKL-PCGHVYHGDCIVPWLDSRNTCPVCRFELPTD  331 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~L-PC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~  331 (363)
                      ....|+||++.|.   .++.+ +|+|.||..||..|++.+.+||+||..+...
T Consensus        21 ~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   70 (99)
T 2y43_A           21 DLLRCGICFEYFN---IAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEP   70 (99)
T ss_dssp             HHTBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGG
T ss_pred             CCCCcccCChhhC---CcCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCChh
Confidence            4578999999998   45566 8999999999999999999999999998754

>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=99.17  E-value=1.5e-11  Score=103.02  Aligned_cols=48  Identities=29%  Similarity=0.681  Sum_probs=42.6

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC-CCCCcCcCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~-sCPlCR~~l~~  330 (363)
                      ....|+||++.|.   .++.+||||.||..||..|++.+. +||+||..+..
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            4578999999998   677889999999999999998655 89999999976

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

Probab=99.16  E-value=2.1e-11  Score=89.99  Aligned_cols=43  Identities=33%  Similarity=0.829  Sum_probs=37.5

Q ss_pred             cccccccccccccccCCceEEeCCCCcccHhhHHHHHh---cCCCCCCc
Q 017955          279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLD---SRNTCPVC  324 (363)
Q Consensus       279 ~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk---~~~sCPlC  324 (363)
                      .....|+||++.|.   .++.++|+|.||..||.+|++   .+.+||+|
T Consensus        18 ~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           18 QEEVICPICLDILQ---KPVTIDCGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCBCTTTCSBCS---SCEECTTSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             ccCCCCCcCCchhC---CeEEeCCCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            35678999999998   577789999999999999998   45589998

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

Probab=99.15  E-value=2e-11  Score=96.65  Aligned_cols=47  Identities=36%  Similarity=0.840  Sum_probs=41.4

Q ss_pred             ccccccccccccccCCceEEeC-CCCcccHhhHHHHHhcC--CCCCCcCcCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSR--NTCPVCRFELP  329 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~WLk~~--~sCPlCR~~l~  329 (363)
                      ....|+||++.|.   .++.+| |+|.||..||..|++.+  ..||+||..+.
T Consensus        12 ~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           12 DELLCLICKDIMT---DAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             TTTEETTTTEECS---SCEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             cCCCCCCCChhhc---CceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            5678999999998   577899 99999999999999754  48999999973

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

Probab=99.15  E-value=1.7e-11  Score=102.43  Aligned_cols=54  Identities=33%  Similarity=0.730  Sum_probs=46.2

Q ss_pred             cccccccccccccc----CCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCCh
Q 017955          280 ETIVCAICKDTVNV----GETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDP  333 (363)
Q Consensus       280 ~~~~C~ICle~f~~----~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~  333 (363)
                      ....|+||++.|..    +..++.++|||.||..||.+||+.+++||+||+.+.....
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            45789999999873    2345889999999999999999999999999999976553

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

Probab=99.12  E-value=4.2e-11  Score=88.98  Aligned_cols=53  Identities=21%  Similarity=0.403  Sum_probs=41.9

Q ss_pred             ccccccccc-ccccCC-ceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCCCCCCh
Q 017955          281 TIVCAICKD-TVNVGE-TATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFELPTDDP  333 (363)
Q Consensus       281 ~~~C~ICle-~f~~~e-~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l~~~d~  333 (363)
                      ...|+||++ .|.... .+..++|||.||..||.+|+.. +..||+||+.+...+.
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~   58 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNF   58 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCC
T ss_pred             CCcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHHcCCCcCCCCCCccccccc
Confidence            467999999 776432 2356799999999999999765 4589999999976553

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

Probab=99.11  E-value=2.7e-11  Score=93.46  Aligned_cols=53  Identities=26%  Similarity=0.644  Sum_probs=43.9

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcC--CCCCCcCcCCCCCChh
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR--NTCPVCRFELPTDDPE  334 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~--~sCPlCR~~l~~~d~~  334 (363)
                      ....|+||++.|..+.  ....|+|.||..||.+||+++  .+||+||..+..+.+.
T Consensus        14 ~i~~C~IC~~~i~~g~--~C~~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~~~~   68 (74)
T 2ct0_A           14 AVKICNICHSLLIQGQ--SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHEIPK   68 (74)
T ss_dssp             SSCBCSSSCCBCSSSE--ECSSSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSCCCC
T ss_pred             CCCcCcchhhHcccCC--ccCCCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCCCCC
Confidence            4567999999998543  233799999999999999988  7999999998876654

>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=99.11  E-value=3e-11  Score=97.98  Aligned_cols=53  Identities=21%  Similarity=0.169  Sum_probs=47.3

Q ss_pred             ccccccccccccccCCceEEeCCC-CcccHhhHHHHHhcCCCCCCcCcCCCCCChhH
Q 017955          280 ETIVCAICKDTVNVGETATKLPCG-HVYHGDCIVPWLDSRNTCPVCRFELPTDDPEY  335 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~-H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~~  335 (363)
                      ....|+||++.|.   .++.++|| |.||+.||.+||+.+.+||+||.++...+...
T Consensus        21 ~~~~CpI~~~~m~---dPV~~~cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~L~p   74 (98)
T 1wgm_A           21 DEFLDPIMSTLMC---DPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRP   74 (98)
T ss_dssp             TTTBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEE
T ss_pred             HhcCCcCcccccc---CCeECCCCCeEECHHHHHHHHHhCCCCCCCCCCCChhhceE
Confidence            4678999999998   68889999 99999999999998889999999998776443

>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=99.11  E-value=3.2e-11  Score=98.63  Aligned_cols=49  Identities=20%  Similarity=0.751  Sum_probs=42.3

Q ss_pred             cccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC---CCCCcCcCCCCCC
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN---TCPVCRFELPTDD  332 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~---sCPlCR~~l~~~d  332 (363)
                      ...|+||++.|.   .++.++|+|.||..||..|++.+.   +||+||..+...+
T Consensus        21 ~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   72 (112)
T 1jm7_A           21 ILECPICLELIK---EPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS   72 (112)
T ss_dssp             HTSCSSSCCCCS---SCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTT
T ss_pred             CCCCcccChhhc---CeEECCCCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhh
Confidence            467999999987   456689999999999999998764   8999999987654

>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=99.10  E-value=2.7e-11  Score=100.80  Aligned_cols=51  Identities=27%  Similarity=0.616  Sum_probs=44.7

Q ss_pred             cccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC-CCCCcCcCCCCCC
Q 017955          279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELPTDD  332 (363)
Q Consensus       279 ~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~-sCPlCR~~l~~~d  332 (363)
                      .....|+||++.|.   .++.++|+|.||..||..|++.++ +||+||..+...+
T Consensus        16 ~~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   67 (118)
T 3hct_A           16 ESKYECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQ   67 (118)
T ss_dssp             CGGGBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCcCChhhc---CeEECCcCChhhHHHHHHHHhhCCCCCCCCCCCcCHHh
Confidence            35678999999997   567789999999999999998876 9999999998754

>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=99.08  E-value=5.8e-11  Score=103.32  Aligned_cols=49  Identities=24%  Similarity=0.668  Sum_probs=43.4

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC-CCCCcCcCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELPTD  331 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~-sCPlCR~~l~~~  331 (363)
                      ....|+||++.|.   .++.+||+|.||..||..|++... .||+||..+...
T Consensus        77 ~~~~C~IC~~~~~---~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVY---QPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCS---SEEECTTSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhhc---CCEEcCCCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            4578999999997   567799999999999999998765 899999999865

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

Probab=99.08  E-value=4.1e-11  Score=94.52  Aligned_cols=52  Identities=21%  Similarity=0.238  Sum_probs=46.5

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChh
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPE  334 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~  334 (363)
                      ....|+||++.|.   .++.++|||.||+.||..||+.+.+||+||..+...+..
T Consensus        13 ~~~~CpI~~~~m~---dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~l~   64 (85)
T 2kr4_A           13 DEFRDPLMDTLMT---DPVRLPSGTVMDRSIILRHLLNSPTDPFNRQMLTESMLE   64 (85)
T ss_dssp             TTTBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHCSBCTTTCCBCCGGGCE
T ss_pred             hheECcccCchhc---CCeECCCCCEECHHHHHHHHhcCCCCCCCcCCCChHhcc
Confidence            4678999999998   688899999999999999999889999999999876543

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

Probab=99.08  E-value=3.8e-11  Score=86.68  Aligned_cols=42  Identities=29%  Similarity=0.878  Sum_probs=36.0

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHh---cCCCCCCc
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLD---SRNTCPVC  324 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk---~~~sCPlC  324 (363)
                      ....|+||++.|.   .++.++|+|+||..||..|++   .+.+||+|
T Consensus        14 ~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           14 VEASCSVCLEYLK---EPVIIECGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCBCSSSCCBCS---SCCCCSSCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cCCCCccCCcccC---ccEeCCCCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            5678999999998   456789999999999999954   56789998

>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=99.08  E-value=5.2e-11  Score=104.50  Aligned_cols=48  Identities=33%  Similarity=0.793  Sum_probs=41.5

Q ss_pred             ccccccccccccccCCceEEe-CCCCcccHhhHHHHHhc-CCCCCCcCcCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKL-PCGHVYHGDCIVPWLDS-RNTCPVCRFELPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~L-PC~H~Fh~~CI~~WLk~-~~sCPlCR~~l~~  330 (363)
                      ....|+||++.|.   .++.+ +|+|.||..||..|++. +..||+||..+..
T Consensus        53 ~~~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           53 SELMCPICLDMLK---NTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHHBCTTTSSBCS---SEEEETTTCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCcccChHhh---CcCEeCCCCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            4568999999998   35555 99999999999999997 7789999999864

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

Probab=99.07  E-value=4.2e-11  Score=100.03  Aligned_cols=55  Identities=33%  Similarity=0.732  Sum_probs=46.7

Q ss_pred             cccccccccccccccc----CCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCC
Q 017955          278 EQETIVCAICKDTVNV----GETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD  332 (363)
Q Consensus       278 ~~~~~~C~ICle~f~~----~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d  332 (363)
                      ......|+||++.|..    ...++.++|+|.||..||.+||+.+++||+||..+..++
T Consensus        69 ~~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~  127 (133)
T 4ap4_A           69 GSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR  127 (133)
T ss_dssp             SSSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChhc
Confidence            3466789999999873    234478899999999999999999999999999997654

>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=99.07  E-value=5.9e-11  Score=96.58  Aligned_cols=53  Identities=19%  Similarity=0.224  Sum_probs=47.6

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCChhH
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDPEY  335 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~~  335 (363)
                      ....|+||++.|.   .++.++|||.||+.||..||..+.+||+||.++...+...
T Consensus        28 ~~~~CpI~~~~m~---dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~L~p   80 (100)
T 2kre_A           28 DEFRDPLMDTLMT---DPVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTESMLEP   80 (100)
T ss_dssp             TTTBCTTTCSBCS---SEEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCTTSSEE
T ss_pred             HhhCCcCccCccc---CCeECCCCCEEchHHHHHHHHcCCCCCCCCCCCChhhceE
Confidence            4678999999998   7888999999999999999998889999999998776544

>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=99.05  E-value=1.9e-11  Score=100.98  Aligned_cols=48  Identities=25%  Similarity=0.675  Sum_probs=42.3

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFELPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l~~  330 (363)
                      ....|+||++.|.   .++.++|+|.||..||..|++. +.+||+||..+..
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            4578999999987   5778899999999999999977 6689999999863

>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=99.02  E-value=1.1e-10  Score=96.44  Aligned_cols=50  Identities=28%  Similarity=0.721  Sum_probs=43.6

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l~~~d  332 (363)
                      ....|+||++.|.   .++.++|+|.||..||..|++. ..+||+||..+...+
T Consensus        22 ~~~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   72 (116)
T 1rmd_A           22 KSISCQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (116)
T ss_dssp             HHTBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCcHhc---CcEEcCCCCcccHHHHHHHHhHCcCcCCCCCCCCCHhh
Confidence            3577999999997   5677999999999999999987 679999999987644

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

Probab=98.98  E-value=1.9e-10  Score=89.53  Aligned_cols=56  Identities=20%  Similarity=0.518  Sum_probs=43.1

Q ss_pred             cccccccccccccccCC-ceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCCCCCChh
Q 017955          279 QETIVCAICKDTVNVGE-TATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFELPTDDPE  334 (363)
Q Consensus       279 ~~~~~C~ICle~f~~~e-~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l~~~d~~  334 (363)
                      ++...|+||++.+...+ ....++|||.||..||..|++. ...||+||+.+......
T Consensus         9 ~~~~~CpICle~~~~~d~~~~p~~CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~~   66 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAV   66 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTTTCCSSTTSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSSC
T ss_pred             ccCCcCCccCccCccccccccccCCCCCcCHHHHHHHHhcCCCCCCCCCCccCCCchh
Confidence            45678999999886432 2223459999999999999854 56899999999876654

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

Probab=98.96  E-value=9e-11  Score=85.17  Aligned_cols=47  Identities=23%  Similarity=0.631  Sum_probs=40.0

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d  332 (363)
                      +...|+||++.|.   .++.|||+|.||..||..|   ...||+||+.+....
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            5678999999998   5678999999999999884   668999999987543

>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=98.95  E-value=3.5e-10  Score=84.39  Aligned_cols=48  Identities=23%  Similarity=0.500  Sum_probs=41.1

Q ss_pred             ccccccccccccccCCceEEe--CCCCc-ccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKL--PCGHV-YHGDCIVPWLDSRNTCPVCRFELPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~L--PC~H~-Fh~~CI~~WLk~~~sCPlCR~~l~~  330 (363)
                      ....|+||++.+.   .+..+  ||||. ||..|+..|++.+..||+||..+..
T Consensus         7 ~~~~C~IC~~~~~---~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~~   57 (64)
T 2vje_A            7 AIEPCVICQGRPK---NGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQM   57 (64)
T ss_dssp             GGSCCTTTSSSCS---CEEEEETTEEEEEECHHHHHHHHHTTCCCTTTCCCCCE
T ss_pred             CcCCCCcCCCCCC---CEEEECCCCCChhhHHHHHHHHHHcCCcCCCcCcchhc
Confidence            4567999999876   44555  99999 8999999999999999999998853

>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=98.92  E-value=2.2e-10  Score=98.74  Aligned_cols=49  Identities=24%  Similarity=0.613  Sum_probs=42.5

Q ss_pred             cccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC-CCCCcCcCCCC
Q 017955          279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELPT  330 (363)
Q Consensus       279 ~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~-sCPlCR~~l~~  330 (363)
                      .....|+||++.|.   .++.++|||.||..||.+|++... +||+||.++..
T Consensus        29 ~~~~~C~IC~~~~~---~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   78 (141)
T 3knv_A           29 EAKYLCSACRNVLR---RPFQAQCGHRYCSFCLASILSSGPQNCAACVHEGIY   78 (141)
T ss_dssp             CGGGBCTTTCSBCS---SEEECTTSCEEEHHHHHHHGGGSCEECHHHHHTTCC
T ss_pred             CcCcCCCCCChhhc---CcEECCCCCccCHHHHHHHHhcCCCCCCCCCCcccc
Confidence            35678999999998   567789999999999999998765 89999998643

>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=98.91  E-value=1.8e-10  Score=95.67  Aligned_cols=48  Identities=23%  Similarity=0.658  Sum_probs=41.7

Q ss_pred             ccccccccccccccCCceEEe-CCCCcccHhhHHHHHhcCCCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKL-PCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~L-PC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d  332 (363)
                      ....|+||++.|.   .++.+ +|||.||..||..|++  ..||+||..+...+
T Consensus        21 ~~~~C~IC~~~~~---~pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~   69 (117)
T 1jm7_B           21 KLLRCSRCTNILR---EPVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQD   69 (117)
T ss_dssp             HTTSCSSSCSCCS---SCBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSS
T ss_pred             hCCCCCCCChHhh---CccEeCCCCCHHHHHHHHHHhc--CCCcCCCCcCcccc
Confidence            4578999999997   56677 9999999999999998  88999999996544

>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=98.89  E-value=5.9e-10  Score=89.32  Aligned_cols=51  Identities=33%  Similarity=0.716  Sum_probs=42.6

Q ss_pred             ccccccccccccccCCceEEeC-CCCcccHhhHHHHHhcC------CCCCC--cCcC-CCCCCh
Q 017955          280 ETIVCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSR------NTCPV--CRFE-LPTDDP  333 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~WLk~~------~sCPl--CR~~-l~~~d~  333 (363)
                      ....|+||++.|.   .++.++ |||.||+.||..||..+      .+||+  |+.. +...+.
T Consensus         6 ~~~~CPI~~~~~~---dPV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~~~L   66 (94)
T 2yu4_A            6 SGFTCPITKEEMK---KPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSDL   66 (94)
T ss_dssp             SCCBCTTTCSBCS---SEEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCGGGE
T ss_pred             cEeECcCcCchhc---CCEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCHhhC
Confidence            5578999999998   678886 99999999999999864      48999  9876 655543

>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=98.88  E-value=8.5e-10  Score=82.04  Aligned_cols=48  Identities=19%  Similarity=0.490  Sum_probs=40.6

Q ss_pred             ccccccccccccccCCceEEe--CCCCc-ccHhhHHHHHhcCCCCCCcCcCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKL--PCGHV-YHGDCIVPWLDSRNTCPVCRFELPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~L--PC~H~-Fh~~CI~~WLk~~~sCPlCR~~l~~  330 (363)
                      ....|+||++.+.   .+..+  ||||. ||..|+..|.+.+..||+||.++..
T Consensus         6 ~~~~C~IC~~~~~---~~~~~~~pCgH~~~C~~C~~~~~~~~~~CPiCR~~i~~   56 (63)
T 2vje_B            6 LLKPCSLCEKRPR---DGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQL   56 (63)
T ss_dssp             GGSBCTTTSSSBS---CEEEEETTEEEEEECHHHHHHHHHTTCBCTTTCCBCCE
T ss_pred             cCCCCcccCCcCC---CeEEEecCCCCHhHHHHHHHHHHHhCCcCCCcCchhhc
Confidence            4567999999876   34455  99998 9999999999988999999998853

>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=98.88  E-value=9.2e-10  Score=109.23  Aligned_cols=48  Identities=29%  Similarity=0.832  Sum_probs=42.8

Q ss_pred             cccccccccccccCCceEEeCCCCcccHhhHHHHHh-cCCCCCCcCcCCCCC
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLD-SRNTCPVCRFELPTD  331 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk-~~~sCPlCR~~l~~~  331 (363)
                      ...|+||++.+.   .++.+||+|.||..||..|++ .+.+||+||..+...
T Consensus       332 ~~~C~ICle~~~---~pv~lpCGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~  380 (389)
T 2y1n_A          332 FQLCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT  380 (389)
T ss_dssp             SSBCTTTSSSBC---CEEEETTCCEECHHHHHHHHHHTCSBCTTTCCBCCEE
T ss_pred             CCCCCccCcCCC---CeEEeCCCChhhHHHHHHHHhcCCCCCCCCCCccCCc
Confidence            368999999987   678899999999999999998 688999999988754

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

Probab=98.86  E-value=5.8e-10  Score=85.42  Aligned_cols=45  Identities=29%  Similarity=0.686  Sum_probs=39.4

Q ss_pred             ccccccccccccccCCceEEeCCCCc-ccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHV-YHGDCIVPWLDSRNTCPVCRFELPTD  331 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~-Fh~~CI~~WLk~~~sCPlCR~~l~~~  331 (363)
                      ....|+||++.+.   .++.+||+|. ||..||..|    ..||+||..+...
T Consensus        23 ~~~~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~~   68 (74)
T 4ic3_A           23 EEKLCKICMDRNI---AIVFVPCGHLVTCKQCAEAV----DKCPMCYTVITFK   68 (74)
T ss_dssp             HHTBCTTTSSSBC---CEEEETTCCBCCCHHHHTTC----SBCTTTCCBCSEE
T ss_pred             cCCCCCCCCCCCC---CEEEcCCCChhHHHHhhhcC----ccCCCcCcCccCc
Confidence            4567999999887   6778999999 999999999    8899999988653

>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=98.84  E-value=9.7e-10  Score=102.73  Aligned_cols=51  Identities=20%  Similarity=0.238  Sum_probs=44.3

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcC-CCCCCcCcCCCCCCh
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR-NTCPVCRFELPTDDP  333 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~-~sCPlCR~~l~~~d~  333 (363)
                      ....|+||++.|.   .++.+||||.||+.||..||..+ .+||+||.++...+.
T Consensus       207 ~~~~c~i~~~~~~---dPv~~~~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~l  258 (281)
T 2c2l_A          207 DYLCGKISFELMR---EPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQL  258 (281)
T ss_dssp             STTBCTTTCSBCS---SEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGC
T ss_pred             cccCCcCcCCHhc---CCeECCCCCEECHHHHHHHHHHCCCCCcCCCCCCchhcC
Confidence            5678999999998   78889999999999999999864 459999999976553

>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=98.83  E-value=1.3e-09  Score=95.95  Aligned_cols=52  Identities=27%  Similarity=0.586  Sum_probs=44.7

Q ss_pred             ccccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC-CCCCcCcCCCCCC
Q 017955          278 EQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRFELPTDD  332 (363)
Q Consensus       278 ~~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~-sCPlCR~~l~~~d  332 (363)
                      ......|+||++.|.   .++.++|+|.||..||.+|++.++ +||+||..|...+
T Consensus        15 ~~~~~~C~IC~~~~~---~pv~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   67 (170)
T 3hcs_A           15 LESKYECPICLMALR---EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQ   67 (170)
T ss_dssp             CCGGGBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCCChhhc---CcEECCCCCHHHHHHHHHHHHhCCCCCCCCccCcchhh
Confidence            335688999999998   567799999999999999998754 9999999998754

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

Probab=98.73  E-value=4.2e-09  Score=94.30  Aligned_cols=53  Identities=21%  Similarity=0.197  Sum_probs=45.5

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcC-CCCCCcCcCCCCCChhH
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR-NTCPVCRFELPTDDPEY  335 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~-~sCPlCR~~l~~~d~~~  335 (363)
                      ....||||++.|.   .++.+||||.||+.||..||..+ .+||+||.++...+...
T Consensus       105 ~~f~CPI~~elm~---DPV~~~~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~L~p  158 (179)
T 2f42_A          105 DYLCGKISFELMR---EPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIP  158 (179)
T ss_dssp             GGGBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEE
T ss_pred             HhhcccCccccCC---CCeECCCCCEECHHHHHHHHHhCCCCCCCCcCCCChhhCcc
Confidence            5678999999998   68889999999999999999874 47999999998765443

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

Probab=98.70  E-value=4.2e-09  Score=80.61  Aligned_cols=47  Identities=28%  Similarity=0.663  Sum_probs=38.8

Q ss_pred             ccccccccccccccCCceEEeCCCCc-ccHhhHHHHHhcCCCCCCcCcCCCCCCh
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHV-YHGDCIVPWLDSRNTCPVCRFELPTDDP  333 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~-Fh~~CI~~WLk~~~sCPlCR~~l~~~d~  333 (363)
                      ....|+||++.+.   .++.+||+|. ||..|+..    ...||+||..+.....
T Consensus        24 ~~~~C~IC~~~~~---~~~~~pCgH~~~C~~C~~~----~~~CP~Cr~~i~~~~~   71 (75)
T 2ecg_A           24 EEKLCKICMDRNI---AIVFVPCGHLVTCKQCAEA----VDKCPMCYTVITFKQK   71 (75)
T ss_dssp             HHHSCSSSCSSCC---CBCCSSSCCCCBCHHHHHH----CSBCTTTCCBCCCCCB
T ss_pred             CCCCCCcCCCCCC---CEEEecCCCHHHHHHHhhC----CCCCccCCceecCcEE
Confidence            3467999999987   5677999999 99999954    4789999999876543

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

Probab=98.58  E-value=3.2e-08  Score=73.10  Aligned_cols=48  Identities=27%  Similarity=0.713  Sum_probs=37.8

Q ss_pred             ccccccccccccccCCceEEeCCC--C---cccHhhHHHHHhc--CCCCCCcCcCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCG--H---VYHGDCIVPWLDS--RNTCPVCRFELPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~--H---~Fh~~CI~~WLk~--~~sCPlCR~~l~~  330 (363)
                      ....|.||++...  +. .++||.  |   +||..||.+|+..  +.+||+||..+..
T Consensus         5 ~~~~CrIC~~~~~--~~-l~~PC~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            5 DVPVCWICNEELG--NE-RFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             SCCEETTTTEECS--CC-CCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCEeEEeecCCC--Cc-eecCcCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            4567999999743  33 368854  4   9999999999975  5689999998864

>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=98.57  E-value=1.7e-08  Score=74.74  Aligned_cols=49  Identities=10%  Similarity=0.264  Sum_probs=43.6

Q ss_pred             ccccccccccccCCceEEe-CCCCcccHhhHHHHHhcCCCCCCcCcCCCCCCh
Q 017955          282 IVCAICKDTVNVGETATKL-PCGHVYHGDCIVPWLDSRNTCPVCRFELPTDDP  333 (363)
Q Consensus       282 ~~C~ICle~f~~~e~~~~L-PC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~  333 (363)
                      ..|+||++.|.   .++.+ +|||+|.+.||.+||+.+.+||+++.+|...+.
T Consensus         4 ~~CpIs~~~m~---dPV~~~~sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~L   53 (61)
T 2bay_A            4 MLCAISGKVPR---RPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEI   53 (61)
T ss_dssp             CCCTTTCSCCS---SEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGC
T ss_pred             EEecCCCCCCC---CCEEeCCCCcEEcHHHHHHHHHhCCCCcCCcCCCChhhc
Confidence            57999999998   56777 899999999999999988899999999976654

>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=98.57  E-value=1.4e-08  Score=78.84  Aligned_cols=45  Identities=31%  Similarity=0.773  Sum_probs=38.5

Q ss_pred             ccccccccccccccCCceEEeCCCCc-ccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHV-YHGDCIVPWLDSRNTCPVCRFELPTD  331 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~-Fh~~CI~~WLk~~~sCPlCR~~l~~~  331 (363)
                      ....|+||++.+.   .++.+||||. ||..|+..|    ..||+||..+...
T Consensus        17 ~~~~C~IC~~~~~---~~v~~pCgH~~~C~~C~~~~----~~CP~Cr~~i~~~   62 (79)
T 2yho_A           17 EAMLCMVCCEEEI---NSTFCPCGHTVCCESCAAQL----QSCPVCRSRVEHV   62 (79)
T ss_dssp             HHTBCTTTSSSBC---CEEEETTCBCCBCHHHHTTC----SBCTTTCCBCCEE
T ss_pred             CCCEeEEeCcccC---cEEEECCCCHHHHHHHHHhc----CcCCCCCchhhCe
Confidence            3467999999887   6788999999 999999887    4999999988754

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

Probab=98.56  E-value=3e-08  Score=74.84  Aligned_cols=45  Identities=24%  Similarity=0.634  Sum_probs=38.6

Q ss_pred             ccccccccccccccCCceEEeCCCCc-ccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHV-YHGDCIVPWLDSRNTCPVCRFELPTD  331 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~-Fh~~CI~~WLk~~~sCPlCR~~l~~~  331 (363)
                      ....|.||++.+.   .++.+||+|. ||..|+..    ...||+||..|...
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            4577999999876   6788999999 99999983    57999999998764

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

Probab=98.55  E-value=1.1e-08  Score=99.63  Aligned_cols=52  Identities=29%  Similarity=0.654  Sum_probs=40.2

Q ss_pred             cccccccccccccc-CCce---EE-eCCCCcccHhhHHHHHhcC-----------CCCCCcCcCCCCC
Q 017955          280 ETIVCAICKDTVNV-GETA---TK-LPCGHVYHGDCIVPWLDSR-----------NTCPVCRFELPTD  331 (363)
Q Consensus       280 ~~~~C~ICle~f~~-~e~~---~~-LPC~H~Fh~~CI~~WLk~~-----------~sCPlCR~~l~~~  331 (363)
                      ....|+||+..+.. +..+   .. .+|+|.||..||.+||+..           ++||+||.+|...
T Consensus       307 ~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~s  374 (381)
T 3k1l_B          307 EELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTS  374 (381)
T ss_dssp             SCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGG
T ss_pred             CCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCcc
Confidence            55689999999886 3322   21 3599999999999999753           4799999988643

>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=98.50  E-value=2.4e-08  Score=93.99  Aligned_cols=55  Identities=22%  Similarity=0.434  Sum_probs=44.6

Q ss_pred             cccccccccccccccccCCceEE-eCCCCcccHhhHHHHHhcC--CCCCC--cCcCCCCCChh
Q 017955          277 SEQETIVCAICKDTVNVGETATK-LPCGHVYHGDCIVPWLDSR--NTCPV--CRFELPTDDPE  334 (363)
Q Consensus       277 ~~~~~~~C~ICle~f~~~e~~~~-LPC~H~Fh~~CI~~WLk~~--~sCPl--CR~~l~~~d~~  334 (363)
                      .......||||++.|.   .++. +.|||.||+.||..|++.+  .+||+  ||+.+...+..
T Consensus       177 ~~~~el~CPIcl~~f~---DPVts~~CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL~  236 (267)
T 3htk_C          177 GGKIELTCPITCKPYE---APLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFV  236 (267)
T ss_dssp             SSBCCSBCTTTSSBCS---SEEEESSSCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGEE
T ss_pred             CCceeeECcCccCccc---CCeeeCCCCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhCC
Confidence            3446688999999998   4554 5899999999999999865  37999  99988766643

>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=98.48  E-value=5.2e-08  Score=77.53  Aligned_cols=51  Identities=20%  Similarity=0.494  Sum_probs=39.3

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcC--------CCCCC--cCcC--CCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR--------NTCPV--CRFE--LPT  330 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~--------~sCPl--CR~~--l~~  330 (363)
                      ....|+||++.+........++|+|.||..||..|++.+        -.||.  ||..  +..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~   66 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQE   66 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECH
T ss_pred             CCcCCcccCcccccccceEcCCCCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCH
Confidence            346799999998754344444799999999999998742        37999  9998  543

>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=98.39  E-value=6.7e-08  Score=94.75  Aligned_cols=45  Identities=29%  Similarity=0.745  Sum_probs=39.7

Q ss_pred             ccccccccccccccCCceEEeCCCCc-ccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHV-YHGDCIVPWLDSRNTCPVCRFELPTD  331 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~-Fh~~CI~~WLk~~~sCPlCR~~l~~~  331 (363)
                      ....|+||++.+.   .++.+||+|. ||..||..|    ..||+||..+...
T Consensus       294 ~~~~C~IC~~~~~---~~v~lpCgH~~fC~~C~~~~----~~CP~CR~~i~~~  339 (345)
T 3t6p_A          294 EERTCKVCMDKEV---SVVFIPCGHLVVCQECAPSL----RKCPICRGIIKGT  339 (345)
T ss_dssp             TTCBCTTTSSSBC---CEEEETTCCEEECTTTGGGC----SBCTTTCCBCCEE
T ss_pred             CCCCCCccCCcCC---ceEEcCCCChhHhHHHHhcC----CcCCCCCCCccCe
Confidence            5678999999987   6788999999 999999988    7899999988653

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

Probab=98.19  E-value=1e-06  Score=71.18  Aligned_cols=45  Identities=27%  Similarity=0.643  Sum_probs=38.6

Q ss_pred             cccccccccccCCceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCCC
Q 017955          283 VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFELP  329 (363)
Q Consensus       283 ~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l~  329 (363)
                      .|.+|--.+..  ..+.+||+|+||.+|+..|.++ .++||.||.+|.
T Consensus         3 fC~~C~~Pi~i--ygRmIPCkHvFCydCa~~~~~~~~k~Cp~C~~~V~   48 (101)
T 3vk6_A            3 FCDKCGLPIKV--YGRMIPCKHVFCYDCAILHEKKGDKMCPGCSDPVQ   48 (101)
T ss_dssp             BCTTTCSBCSE--EEEEETTCCEEEHHHHHHHHHTTCCBCTTTCCBCS
T ss_pred             ecCccCCCeEE--EeeeccccccHHHHHHHHHHhccCCCCcCcCCeee
Confidence            58888877763  6788999999999999999965 579999999875

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

Probab=97.80  E-value=6.9e-06  Score=76.47  Aligned_cols=94  Identities=22%  Similarity=0.417  Sum_probs=57.6

Q ss_pred             hhhHHHHHHHHHHhc--CCCCCCChhhHHHHHcCCceeee-cccccccccccccccccCCceEEeCCCCcccHhhHHHHH
Q 017955          239 AAGYEALLQNLAESD--GGRRGAPRAAKSAVLELPTVEIL-SEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWL  315 (363)
Q Consensus       239 ~~~~e~Ll~~L~~~~--~~~~~~~~~s~~~i~~lp~~~~~-~~~~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WL  315 (363)
                      ....+.+|..|.+..  ....+.-..+...+..|...... -......|.||.+.+..+  ..+-.|+|.||..|+.+|+
T Consensus       135 ~~eae~lL~~lv~~gWl~~~~g~~~l~~R~l~El~~~l~~~~~~~i~~C~iC~~iv~~g--~~C~~C~~~~H~~C~~~~~  212 (238)
T 3nw0_A          135 KKEAEQVLQKFVQNKWLIEKEGEFTLHGRAILEMEQYIRETYPDAVKICNICHSLLIQG--QSCETCGIRMHLPCVAKYF  212 (238)
T ss_dssp             HHHHHHHHHHHHHTTSEEEETTEEEECHHHHHHHHHHHHHHCTTTCCBCTTTCSBCSSC--EECSSSCCEECHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhcchhhhCCEEEecCccHHHHHHHHHHhcCCCCCcCcchhhHHhCC--cccCccChHHHHHHHHHHH
Confidence            445566777666554  11223222333332222211111 112357799999988843  2222399999999999999


Q ss_pred             hcCC--CCCCcCcCCCCCChh
Q 017955          316 DSRN--TCPVCRFELPTDDPE  334 (363)
Q Consensus       316 k~~~--sCPlCR~~l~~~d~~  334 (363)
                      +.+.  .||.|+..++...+.
T Consensus       213 ~~~~~~~CP~C~~~W~~~~~~  233 (238)
T 3nw0_A          213 QSNAEPRCPHCNDYWPHEIPK  233 (238)
T ss_dssp             TTCSSCBCTTTCCBCCSCCCC
T ss_pred             HhCCCCCCCCCCCCCCCCCCC
Confidence            8765  899999998876553

>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=95.05  E-value=0.0075  Score=41.80  Aligned_cols=36  Identities=31%  Similarity=0.535  Sum_probs=30.3

Q ss_pred             ceeeeecCCcceeeeccCCCceecccCCCCceeecc
Q 017955           23 QYWCHHCEKRVSIETLANLPDVICHECKNGFVESIP   58 (363)
Q Consensus        23 ~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~   58 (363)
                      .|-|-+|.+.|+.+-...||.+.||+|+---|-.+-
T Consensus         3 iY~C~rCg~~fs~~el~~lP~IrCpyCGyrii~KvR   38 (48)
T 4ayb_P            3 VYRCGKCWKTFTDEQLKVLPGVRCPYCGYKIIFMVR   38 (48)
T ss_dssp             --CCCCTTTTCCCCCSCCCSSSCCTTTCCSCEECCC
T ss_pred             EEEeeccCCCccHHHHhhCCCcccCccCcEEEEEec
Confidence            689999999999999999999999999977776653

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

Probab=94.44  E-value=0.015  Score=45.95  Aligned_cols=34  Identities=18%  Similarity=0.533  Sum_probs=26.5

Q ss_pred             cccccccccccccCCceEEeCCCCcccHhhHHHH
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPW  314 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~W  314 (363)
                      +..|.||++.+........+.|+|.||..||..|
T Consensus         3 e~~C~~C~~~~~~~av~~C~~C~~~~C~~Cl~~~   36 (101)
T 2jun_A            3 KVLCQFCDQDPAQDAVKTCVTCEVSYCDECLKAT   36 (101)
T ss_dssp             CCBCTTCCSSSCCBCCEEETTTTEEECHHHHHHH
T ss_pred             CCCCcCCCCCCCCCceEECCcCChHHhHHHCHHH
Confidence            4679999987543334455899999999999983

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=92.20  E-value=0.073  Score=39.52  Aligned_cols=46  Identities=24%  Similarity=0.528  Sum_probs=33.7

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC----CCCCcCcCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN----TCPVCRFEL  328 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~----sCPlCR~~l  328 (363)
                      ....|.||.+.   ++.+..-.|...||..|+.+.|....    .||.|+...
T Consensus        11 ~~~~C~vC~~~---~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           11 PGARCGVCGDG---TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             TTCCCTTTSCC---TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCcCCCCCC---CeEEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            34569999853   33444445999999999998887643    799997643

>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}

Probab=90.80  E-value=0.11  Score=42.61  Aligned_cols=36  Identities=19%  Similarity=0.435  Sum_probs=26.6

Q ss_pred             CCCCceeeeecCCcceeeeccCCCce-ecccCCCCceeecc
Q 017955           19 TDPTQYWCHHCEKRVSIETLANLPDV-ICHECKNGFVESIP   58 (363)
Q Consensus        19 ~~~~~~~C~~C~~~~~~~~~~~~~~~-~c~~C~~gFve~~~   58 (363)
                      ..+..|||..|...+..    .-+.+ .||.|++..++-+.
T Consensus        69 ~~p~~~~C~~CG~~~e~----~~~~~~~CP~Cgs~~~~i~~  105 (119)
T 2kdx_A           69 DEKVELECKDCSHVFKP----NALDYGVCEKCHSKNVIITQ  105 (119)
T ss_dssp             EECCEEECSSSSCEECS----CCSTTCCCSSSSSCCCEEEE
T ss_pred             eccceEEcCCCCCEEeC----CCCCCCcCccccCCCcEEec
Confidence            34679999999955544    44567 89999998776443

>2lv2_A Insulinoma-associated protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=88.55  E-value=0.19  Score=38.67  Aligned_cols=40  Identities=15%  Similarity=0.274  Sum_probs=30.1

Q ss_pred             CCCCCCceeeeecCCcceeeecc--------CCCceecccCCCCceee
Q 017955           17 SDTDPTQYWCHHCEKRVSIETLA--------NLPDVICHECKNGFVES   56 (363)
Q Consensus        17 ~~~~~~~~~C~~C~~~~~~~~~~--------~~~~~~c~~C~~gFve~   56 (363)
                      ..+....|-|..|.|.|......        ...-|.|+.|++.|...
T Consensus        22 ~~~~~~~h~C~~Cgk~F~~~~~L~~H~~~H~~~k~~~C~~C~k~F~~~   69 (85)
T 2lv2_A           22 LSASAECHLCPVCGESFASKGAQERHLRLLHAAQVFPCKYCPATFYSS   69 (85)
T ss_dssp             SCCCCTTEECTTSCCEESSHHHHHHHHHTTSCSSSEECTTSSCEESSH
T ss_pred             CCCCCCCEECCCCCCCcCcHHHHhhhhhhccCCCccCCCCCCCEeCCH
Confidence            33456789999999998875332        24569999999999754

>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=88.52  E-value=0.25  Score=53.94  Aligned_cols=51  Identities=20%  Similarity=0.219  Sum_probs=44.7

Q ss_pred             ccccccccccccccCCceEEeCCC-CcccHhhHHHHHhcCCCCCCcCcCCCCCCh
Q 017955          280 ETIVCAICKDTVNVGETATKLPCG-HVYHGDCIVPWLDSRNTCPVCRFELPTDDP  333 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~-H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~  333 (363)
                      +...|||-++.|.   .++++|.| +.|-+.+|.+||..+.+||+=|.++...+.
T Consensus       890 ~~F~cPIs~~lM~---DPVilpsG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~l  941 (968)
T 3m62_A          890 DEFLDPLMYTIMK---DPVILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDV  941 (968)
T ss_dssp             GGGBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGC
T ss_pred             HHhCCcchhhHHh---CCeEcCCCCEEECHHHHHHHHhcCCCCCCCCCCCCcccc
Confidence            3467999999998   78899997 589999999999999999999999987653

>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=86.15  E-value=0.25  Score=41.80  Aligned_cols=37  Identities=16%  Similarity=0.425  Sum_probs=25.6

Q ss_pred             CCCceeeeecCCcceeee-----------c-cCCC-----ceecccCCCCceee
Q 017955           20 DPTQYWCHHCEKRVSIET-----------L-ANLP-----DVICHECKNGFVES   56 (363)
Q Consensus        20 ~~~~~~C~~C~~~~~~~~-----------~-~~~~-----~~~c~~C~~gFve~   56 (363)
                      .+.++||..|...+...-           . .-.|     .+.||.|++.-++-
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            477999999996655433           1 1112     67899999987763

>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=85.49  E-value=0.43  Score=37.18  Aligned_cols=31  Identities=23%  Similarity=0.712  Sum_probs=22.3

Q ss_pred             ccccccccccccccCCceEEeC---CCCcccHhhHHHH
Q 017955          280 ETIVCAICKDTVNVGETATKLP---CGHVYHGDCIVPW  314 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LP---C~H~Fh~~CI~~W  314 (363)
                      .+..|.||-- |..+   .++|   |+.+||..|+.+-
T Consensus        14 ~D~~C~VC~~-~t~~---~l~pCRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           14 NDEMCDVCEV-WTAE---SLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CSCCCTTTCC-CCSS---CCSSCSSSSSCCCHHHHHHH
T ss_pred             CCcccCcccc-cccc---ceeccccccccccHhhcccc
Confidence            4678999973 2322   2344   8999999999996

>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=85.30  E-value=0.41  Score=36.94  Aligned_cols=41  Identities=22%  Similarity=0.547  Sum_probs=30.5

Q ss_pred             CCCCceeeeecCCcceeeeccCCCceecccCCCCceeeccCCC
Q 017955           19 TDPTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESIPVTL   61 (363)
Q Consensus        19 ~~~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~~~~~   61 (363)
                      ..+..+||..|+..|...  +..+.++||.|+.-|-=.=..+-
T Consensus        21 ~~~~~~wCP~C~~~~~~~--~~~~~v~C~~C~~~FC~~C~~~w   61 (86)
T 2ct7_A           21 RDPKFLWCAQCSFGFIYE--REQLEATCPQCHQTFCVRCKRQW   61 (86)
T ss_dssp             SCCCEECCSSSCCCEECC--CSCSCEECTTTCCEECSSSCSBC
T ss_pred             cCCCEeECcCCCchheec--CCCCceEeCCCCCccccccCCch
Confidence            356678999999776544  34567999999999986655554

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=84.99  E-value=0.32  Score=33.62  Aligned_cols=44  Identities=23%  Similarity=0.533  Sum_probs=29.5

Q ss_pred             cccccccccccCCceEEeCCCCcccHhhHHHHHhcCC----CCCCcCc
Q 017955          283 VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN----TCPVCRF  326 (363)
Q Consensus       283 ~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~----sCPlCR~  326 (363)
                      .|.||...-..+..+..-.|...||..|+.+=|....    .||.|+.
T Consensus         2 ~C~vC~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCCEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            4889987543333444445999999999976444322    5999965

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=83.03  E-value=0.41  Score=34.67  Aligned_cols=44  Identities=27%  Similarity=0.658  Sum_probs=31.3

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC----CCCCcCc
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN----TCPVCRF  326 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~----sCPlCR~  326 (363)
                      ....|.||...   ++.+..-.|...||..|+..-+....    .||.|+.
T Consensus        10 ~~~~C~vC~~~---g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A           10 HQDYCEVCQQG---GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             CCSSCTTTSCC---SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCCCCccCCCC---CcEEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            45679999873   33444445889999999988554322    7999965

>2eps_A POZ-, at HOOK-, and zinc finger-containing protein 1; C2H2, zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.1

Probab=82.98  E-value=0.45  Score=32.27  Aligned_cols=38  Identities=18%  Similarity=0.264  Sum_probs=27.2

Q ss_pred             CCCCCceeeeecCCcceeee---------ccCCCceecccCCCCcee
Q 017955           18 DTDPTQYWCHHCEKRVSIET---------LANLPDVICHECKNGFVE   55 (363)
Q Consensus        18 ~~~~~~~~C~~C~~~~~~~~---------~~~~~~~~c~~C~~gFve   55 (363)
                      .+....|-|..|.+.+....         -....-|.|+.|+..|..
T Consensus         7 ~~~~k~~~C~~C~k~f~~~~~L~~H~~~~H~~~k~~~C~~C~k~F~~   53 (54)
T 2eps_A            7 GSVGKPYICQSCGKGFSRPDHLNGHIKQVHTSERPHKCQVWVSGPSS   53 (54)
T ss_dssp             CCSSCCEECSSSCCEESSHHHHHHHHHHTSCCCCCCCSSSSCCSSCC
T ss_pred             CCCCCCeECCCCCcccCCHHHHHHHHHHhcCCCCCccCCCCCCCCCC
Confidence            34466899999998875432         222355899999999953

>2lce_A B-cell lymphoma 6 protein; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=81.53  E-value=0.41  Score=34.43  Aligned_cols=41  Identities=15%  Similarity=0.320  Sum_probs=29.3

Q ss_pred             CCCCCCCceeeeecCCcceeeecc--------CCCceecccCCCCceee
Q 017955           16 ASDTDPTQYWCHHCEKRVSIETLA--------NLPDVICHECKNGFVES   56 (363)
Q Consensus        16 ~~~~~~~~~~C~~C~~~~~~~~~~--------~~~~~~c~~C~~gFve~   56 (363)
                      ...+....|-|..|.+.|......        ...-+.|+.|+..|...
T Consensus        10 ~~~~~~~~~~C~~C~k~f~~~~~l~~H~~~H~~~~~~~C~~C~k~f~~~   58 (74)
T 2lce_A           10 HMTHSDKPYKCDRCQASFRYKGNLASHKTVHTGEKPYRCNICGAQFNRP   58 (74)
T ss_dssp             -CCCCCCSBCCTTSSCCBSCHHHHHHHHHHHCCCCSEECTTTCCEESCH
T ss_pred             cccCCCCCeECCCCCceeCCHHHHHHHHHHcCCCCCEECCCCCchhCCH
Confidence            344556789999999988764322        23459999999999653

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=81.04  E-value=0.58  Score=37.13  Aligned_cols=46  Identities=24%  Similarity=0.307  Sum_probs=31.0

Q ss_pred             cccccccccccccCCceEEeCCCCcccHhhHHHHHhc---CCCCCCcCcC
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS---RNTCPVCRFE  327 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~---~~sCPlCR~~  327 (363)
                      ...| ||......+..+..-.|..-||..|+..=+..   .-.||.|+..
T Consensus        28 ~vrC-iC~~~~~~~~mi~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~~   76 (98)
T 2lv9_A           28 VTRC-ICGFTHDDGYMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQPR   76 (98)
T ss_dssp             BCCC-TTSCCSCSSCEEEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSSS
T ss_pred             CEEe-ECCCccCCCcEEEcCCCCCcCcCcCCCCCccCCCCCEECCCCcCC
Confidence            3557 89876655544544459999999998653322   2279999754

>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=80.38  E-value=0.35  Score=42.43  Aligned_cols=46  Identities=33%  Similarity=0.592  Sum_probs=33.2

Q ss_pred             cccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC----CCCCcCcCCC
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN----TCPVCRFELP  329 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~----sCPlCR~~l~  329 (363)
                      +..|.||...   ++.+..-.|...||..|+.+.|....    .||.|+..-.
T Consensus         4 ~~~C~~C~~~---g~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   53 (184)
T 3o36_A            4 EDWCAVCQNG---GELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSK   53 (184)
T ss_dssp             CSSCTTTCCC---SSCEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSSS
T ss_pred             CCccccCCCC---CeeeecCCCCcccCccccCCCCCCCCCCCEECccccCccc
Confidence            4669999854   44444445999999999987765432    6999987543

>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}

Probab=80.30  E-value=0.63  Score=34.24  Aligned_cols=34  Identities=24%  Similarity=0.575  Sum_probs=25.1

Q ss_pred             CCceeeeecCCcceeeeccCCCceecccCCCCceeec
Q 017955           21 PTQYWCHHCEKRVSIETLANLPDVICHECKNGFVESI   57 (363)
Q Consensus        21 ~~~~~C~~C~~~~~~~~~~~~~~~~c~~C~~gFve~~   57 (363)
                      .-.|-|-.|...|.+.   ....+.||+|+.-.+-..
T Consensus        19 ~v~Y~C~~Cg~~~~l~---~~~~iRC~~CG~RILyK~   52 (63)
T 3h0g_L           19 TMIYLCADCGARNTIQ---AKEVIRCRECGHRVMYKM   52 (63)
T ss_dssp             CCCCBCSSSCCBCCCC---SSSCCCCSSSCCCCCBCC
T ss_pred             CeEEECCCCCCeeecC---CCCceECCCCCcEEEEEe
Confidence            5679999999666544   246689999998766443

---

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	363
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	1e-15
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	7e-14
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	6e-12
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	1e-10
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	3e-09
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	1e-08
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	1e-08
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	2e-08
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	3e-08
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	5e-08
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	1e-07
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	2e-06
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	1e-05
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	0.001
d1fp0a1	70	g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-	0.002

>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 = 68.0 bits (166), Expect = 1e-15
 Identities = 21/50 (42%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 280 ETIVCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSRNTCPVCRFEL 328
           + + CA+C   +  GE A  LP CGH +H +C+  WL S +TCP+CR  +
Sbjct: 4   DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>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 = 63.8 bits (155), Expect = 7e-14
 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 8/61 (13%)

Query: 284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPT------DDPEYEE 337
           C IC +  +    +  LPC H +   CI  W+    TCP+C+  + +       D E+ +
Sbjct: 8   CPICLE--DPSNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVESVVHTIESDSEFGD 65

Query: 338 E 338
           +
Sbjct: 66  Q 66

>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 = 58.9 bits (142), Expect = 6e-12
 Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 6/62 (9%)

Query: 273 VEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR-NTCPVCRFELPTD 331
            E+ S  +  +C IC +     +     PCGH+    C+  W +S    CP CR E+   
Sbjct: 17  CEMGSTFQ--LCKICAEND---KDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGT 71

Query: 332 DP 333
           +P
Sbjct: 72  EP 73

>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 = 16/60 (26%), Positives = 22/60 (36%), Gaps = 15/60 (25%)

Query: 283 VCAICKDTVN---------------VGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFE 327
            CAIC++ +                   T     C H +H  CI  WL +R  CP+   E
Sbjct: 23  NCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNRE 82

>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 = 50.6 bits (121), Expect = 3e-09
 Identities = 12/52 (23%), Positives = 19/52 (36%), Gaps = 6/52 (11%)

Query: 278 EQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP 329
           E + + C  C+      +    LPC H     C+         CP+C+   P
Sbjct: 3   EFQFLRCQQCQAEA---KCPKLLPCLHTLCSGCLEAS---GMQCPICQAPWP 48

>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 = 49.5 bits (118), Expect = 1e-08
 Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 5/66 (7%)

Query: 269 ELPTVEILSE-QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-TCPVCRF 326
           +L  V+  +   ++I C IC+  +       +  C H++   CI+  L      CP CR+
Sbjct: 10  KLLAVDFPAHFVKSISCQICEHIL---ADPVETSCKHLFCRICILRCLKVMGSYCPSCRY 66

Query: 327 ELPTDD 332
                D
Sbjct: 67  PCFPTD 72

>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 = 48.6 bits (115), Expect = 1e-08
 Identities = 12/50 (24%), Positives = 18/50 (36%), Gaps = 2/50 (4%)

Query: 284 CAICKDTVNVGETATK-LPCGHVYHGDCIVPWLDSRNT-CPVCRFELPTD 331
           C +C + + + +       CG+     C        N  CP CR   P D
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED 52

>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 = 48.3 bits (114), Expect = 2e-08
 Identities = 11/59 (18%), Positives = 19/59 (32%), Gaps = 4/59 (6%)

Query: 276 LSEQETIVCAICKDTVNVGE--TATKLPCGHVYHGDCIVPWLDSR--NTCPVCRFELPT 330
           + +++  VC IC + +                 H  C+  WL       C +C     T
Sbjct: 1   MEDEDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT 59

>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 = 48.9 bits (116), Expect = 3e-08
 Identities = 11/57 (19%), Positives = 26/57 (45%), Gaps = 6/57 (10%)

Query: 279 QETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN---TCPVCRFELPTDD 332
           Q+ + C IC + +   +      C H++   C++  L+ +     CP+C+ ++    
Sbjct: 19  QKILECPICLELI---KEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS 72

>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 = 47.5 bits (112), Expect = 5e-08
 Identities = 12/56 (21%), Positives = 17/56 (30%), Gaps = 3/56 (5%)

Query: 280 ETIVCAICKDTVNVGETATKL--PCGHVYHGDCIVPWLDSR-NTCPVCRFELPTDD 332
           +   C  CK T     +   +   CGH     C+          CP C   L   +
Sbjct: 2   DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSN 57

>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 = 45.9 bits (108), Expect = 1e-07
 Identities = 5/50 (10%), Positives = 14/50 (28%), Gaps = 2/50 (4%)

Query: 283 VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD 332
           +CAI                  ++    +  ++      P+    L  ++
Sbjct: 2   LCAISGKVPR--RPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEE 49

>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 = 44.3 bits (103), Expect = 2e-06
 Identities = 10/57 (17%), Positives = 17/57 (29%), Gaps = 5/57 (8%)

Query: 274 EILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN-----TCPVCR 325
           E L+             +          C H +H  C++    + N      CP C+
Sbjct: 33  EKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCK 89

>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 = 15/78 (19%), Positives = 30/78 (38%), Gaps = 12/78 (15%)

Query: 256 RRGAPRAAKSAVLELPTVEILSEQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWL 315
            RGA   +++A+  L        ++ + C+ C + +          C H++  +C+   +
Sbjct: 5   GRGAWAHSRAALDRL--------EKLLRCSRCTNILREPVCLG--GCEHIFCSNCVSDCI 54

Query: 316 DSRNTCPVCRFELPTDDP 333
                CPVC       D 
Sbjct: 55  G--TGCPVCYTPAWIQDL 70

>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 = 35.4 bits (81), Expect = 0.001
 Identities = 8/50 (16%), Positives = 17/50 (34%), Gaps = 8/50 (16%)

Query: 284 CAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN--------TCPVCR 325
           C +C     V +  T   C  ++   C+  +++           +CP   
Sbjct: 8   CKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA 57

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]} Length = 70

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]

 Score = 34.2 bits (78), Expect = 0.002
 Identities = 11/68 (16%), Positives = 24/68 (35%), Gaps = 7/68 (10%)

Query: 278 EQETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNT----CPVCRFELPTDDP 333
           +    +C +C+   ++        C   +H DC +P L         C +C       + 
Sbjct: 4   DDSATICRVCQKPGDLVMCNQ---CEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEE 60

Query: 334 EYEEERKK 341
           + + +  K
Sbjct: 61  DVDLQACK 68

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	363
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.6
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.45
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.41
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.37
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.37
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.37
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.36
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.3
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.23
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.22
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.13
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.06
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.06
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.05
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	98.97
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.96
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.45
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	92.71
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	87.33
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	87.11
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	83.25
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	81.47
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	81.26
d2csha1	53	Zinc finger protein 297b {Human (Homo sapiens) [Ta	80.18

>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=99.60  E-value=1.6e-16  Score=114.38  Aligned_cols=50  Identities=42%  Similarity=1.046  Sum_probs=45.4

Q ss_pred             ccccccccccccccCCceEEeC-CCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSRNTCPVCRFELP  329 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~WLk~~~sCPlCR~~l~  329 (363)
                      ++..|+|||+.|..++.++.++ |+|+||..||.+||+++++||+||++|.
T Consensus         4 d~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            4567999999999888888886 9999999999999999999999999873

>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=1.4e-14  Score=108.13  Aligned_cols=47  Identities=30%  Similarity=0.802  Sum_probs=42.0

Q ss_pred             cccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP  329 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~  329 (363)
                      ...|+||++.|.  +.++.+||+|.||..||.+||+.+++||+||.+|.
T Consensus         5 ~d~C~IC~~~~~--~~~~~~~C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~   51 (68)
T d1chca_           5 AERCPICLEDPS--NYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVE   51 (68)
T ss_dssp             CCCCSSCCSCCC--SCEEETTTTEEESTTHHHHHHHHSCSTTTTCCCCC
T ss_pred             CCCCccCCcCcc--CCcEEeCCCCcCcHHHHHHHHHhCCcCCCCCcchH
Confidence            467999999986  35677899999999999999999999999999875

>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=99.41  E-value=3.1e-14  Score=100.87  Aligned_cols=49  Identities=22%  Similarity=0.556  Sum_probs=41.1

Q ss_pred             cccccccccccCC-ceEEeCCCCcccHhhHHHHHhcC-CCCCCcCcCCCCC
Q 017955          283 VCAICKDTVNVGE-TATKLPCGHVYHGDCIVPWLDSR-NTCPVCRFELPTD  331 (363)
Q Consensus       283 ~C~ICle~f~~~e-~~~~LPC~H~Fh~~CI~~WLk~~-~sCPlCR~~l~~~  331 (363)
                      .|+||++.|..+. .++.++|+|.||..||.+|++.. ++||+||+++..+
T Consensus         2 eCpICl~~~~~~~~~~~~~~CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~d   52 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED   52 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSSSSCCCCHHHHHHHTTTSCCBCTTTCCBCSCC
T ss_pred             CCcCCChhhhCCCceEEecCCCCccchHHHHHHHhhcCCCCCccCCcCCCC
Confidence            6999999997654 45566899999999999999864 4799999998753

>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=99.37  E-value=1.3e-13  Score=101.90  Aligned_cols=53  Identities=23%  Similarity=0.439  Sum_probs=42.1

Q ss_pred             ccccccccccccccC--CceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVG--ETATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~--e~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l~~~d  332 (363)
                      ++..|+||++.+...  ..+..++|+|.||..||.+||+. +++||+||+.|...+
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~   57 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSN   57 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCC
T ss_pred             CCCCCCcCCceeecCCceEEEeCccChHhhHHHHHHHhCcCcCCCCCCCcCccccc
Confidence            357899999976532  24566789999999999999965 558999999986554

>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=99.37  E-value=1.5e-13  Score=107.47  Aligned_cols=50  Identities=32%  Similarity=0.606  Sum_probs=42.4

Q ss_pred             ccccccccccccccCC---------------ceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCC
Q 017955          280 ETIVCAICKDTVNVGE---------------TATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELP  329 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e---------------~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~  329 (363)
                      ....|+||++.+....               .+..++|+|+||..||.+||+.+++||+||+++.
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            4567999998876422               3677899999999999999999999999999875

>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=99.37  E-value=2.9e-13  Score=110.24  Aligned_cols=53  Identities=21%  Similarity=0.461  Sum_probs=42.1

Q ss_pred             cccccccccccccc---------------CCceEEeCCCCcccHhhHHHHHhcC-----CCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNV---------------GETATKLPCGHVYHGDCIVPWLDSR-----NTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~---------------~e~~~~LPC~H~Fh~~CI~~WLk~~-----~sCPlCR~~l~~~d  332 (363)
                      .+..|+||++.|..               ...+..++|+|+||..||..||+.+     .+||+||..+..+.
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~~   96 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKT   96 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESSSCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCS
T ss_pred             ccccccchhheecccccccccccccccccccceEECCCCChhhHHHHHHHHHhcCcCCCCccccccchhccCc
Confidence            35679999998753               2246678899999999999999854     37999999886653

>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=99.36  E-value=2.1e-13  Score=104.66  Aligned_cols=49  Identities=33%  Similarity=0.913  Sum_probs=42.6

Q ss_pred             ccccccccccccCCceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCCCCCCh
Q 017955          282 IVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFELPTDDP  333 (363)
Q Consensus       282 ~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l~~~d~  333 (363)
                      ..|+||++.+.   .++.+||||+||..||..||+. +++||+||..|.....
T Consensus        24 ~~C~IC~~~~~---~~~~~~CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~   73 (79)
T d1fbva4          24 QLCKICAENDK---DVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP   73 (79)
T ss_dssp             TBCTTTSSSBC---CEECSSSCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCC
T ss_pred             CCCccCCCcCC---CeEEeCCCCeeeHHHHHHHHHHCcCcCCCCCcCccCCce
Confidence            46999999987   5788999999999999999975 5689999999976543

>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=99.30  E-value=2.6e-13  Score=97.40  Aligned_cols=49  Identities=12%  Similarity=0.320  Sum_probs=43.3

Q ss_pred             ccccccccccccCCceEEeC-CCCcccHhhHHHHHhcCCCCCCcCcCCCCCCh
Q 017955          282 IVCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSRNTCPVCRFELPTDDP  333 (363)
Q Consensus       282 ~~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~  333 (363)
                      +.|+||++.|.   .++.++ |||+||+.||.+||+.+++||+||.++..++.
T Consensus         1 l~C~Ic~~~~~---~Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dL   50 (56)
T d2baya1           1 MLCAISGKVPR---RPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEI   50 (56)
T ss_dssp             CCCTTTCSCCS---SEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGC
T ss_pred             CCCccCCchHH---hcCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhc
Confidence            36999999998   677775 99999999999999999999999999987654

>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=99.23  E-value=1.9e-12  Score=103.76  Aligned_cols=49  Identities=20%  Similarity=0.751  Sum_probs=42.0

Q ss_pred             cccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC---CCCCcCcCCCCCC
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN---TCPVCRFELPTDD  332 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~---sCPlCR~~l~~~d  332 (363)
                      ...|+||++.|.   .++.++|||+||..||..|++.++   .||+||..+...+
T Consensus        21 ~l~CpIC~~~~~---~pv~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   72 (103)
T d1jm7a_          21 ILECPICLELIK---EPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS   72 (103)
T ss_dssp             HTSCSSSCCCCS---SCCBCTTSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTT
T ss_pred             CcCCCccCchhC---CeEEcCCCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhh
Confidence            467999999997   567789999999999999997754   7999999987554

>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=99.22  E-value=2.5e-12  Score=100.26  Aligned_cols=50  Identities=28%  Similarity=0.716  Sum_probs=43.0

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcC-CCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR-NTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~-~sCPlCR~~l~~~d  332 (363)
                      ....|+||++.|.   .++.++|||.||+.||.+|++.+ .+||+||.++...+
T Consensus        22 ~~l~C~IC~~~~~---~pv~~~CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~   72 (86)
T d1rmda2          22 KSISCQICEHILA---DPVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTD   72 (86)
T ss_dssp             HHTBCTTTCSBCS---SEEECTTSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGG
T ss_pred             cCcCCccCCcchh---cceecCCCChhhHHHHHHHHhhCCCcCcccCCCCChhh
Confidence            3467999999997   67889999999999999999754 58999999987554

>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=99.13  E-value=2.9e-12  Score=91.97  Aligned_cols=45  Identities=24%  Similarity=0.648  Sum_probs=38.9

Q ss_pred             cccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCC
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTD  331 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~  331 (363)
                      ...|+||++.|.   .++.+||+|.||..||.+|   +.+||+||.+++..
T Consensus         6 ~l~C~IC~~~~~---~p~~lpCgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T d1bora_           6 FLRCQQCQAEAK---CPKLLPCLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CSSCSSSCSSCB---CCSCSTTSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             CCCCcccCcccC---CCEEecCCCHHhHHHHHcC---CCcCcCCCCcccCC
Confidence            468999999997   5678999999999999876   66899999999754

>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=99.06  E-value=3.7e-11  Score=86.90  Aligned_cols=49  Identities=22%  Similarity=0.535  Sum_probs=38.0

Q ss_pred             cccccccccccccccCCceEEeC-----CCCcccHhhHHHHHh--cCCCCCCcCcCCCC
Q 017955          279 QETIVCAICKDTVNVGETATKLP-----CGHVYHGDCIVPWLD--SRNTCPVCRFELPT  330 (363)
Q Consensus       279 ~~~~~C~ICle~f~~~e~~~~LP-----C~H~Fh~~CI~~WLk--~~~sCPlCR~~l~~  330 (363)
                      ++...|.||++.+...   ...|     |+|+||..||.+|++  .+.+||+||+++..
T Consensus         4 ed~~~C~IC~~~~~~~---~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           4 EDVPVCWICNEELGNE---RFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEECSCC---CCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCCccCCccCCCc---eeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            3567899999987632   2233     459999999999995  45689999998864

>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=99.06  E-value=3.3e-11  Score=92.04  Aligned_cols=52  Identities=19%  Similarity=0.223  Sum_probs=44.5

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhc-CCCCCCcCcCCCCCChh
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDS-RNTCPVCRFELPTDDPE  334 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~-~~sCPlCR~~l~~~d~~  334 (363)
                      +...|+||++.|.   .++.++|||.||+.||.+||.. +.+||+||.++...+..
T Consensus         6 ~~l~CpIc~~l~~---dPv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~l~   58 (80)
T d2c2la2           6 DYLCGKISFELMR---EPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLI   58 (80)
T ss_dssp             STTBCTTTCSBCS---SEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCE
T ss_pred             ccccCcCcCchhh---hhcccCCcCeecHHHHHHHHhcCCccCCCccccccccccc
Confidence            5678999999998   6778999999999999999975 55899999998765533

>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=99.05  E-value=6e-11  Score=90.05  Aligned_cols=51  Identities=25%  Similarity=0.497  Sum_probs=44.5

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcC-CCCCCcCcCCCCCCh
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR-NTCPVCRFELPTDDP  333 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~-~sCPlCR~~l~~~d~  333 (363)
                      +...|+||++.|.   .++.++|||.||+.||.+|++.+ ..||+||.++...+.
T Consensus         7 ~~l~CpIc~~~m~---dPV~~~cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~l   58 (78)
T d1t1ha_           7 EYFRCPISLELMK---DPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGL   58 (78)
T ss_dssp             SSSSCTTTSCCCS---SEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCC
T ss_pred             ccCCCcCcCchhh---CceEccCCCcchHHHHHHHHHHCCCCCCcccccCCcccc
Confidence            4678999999998   67789999999999999999875 579999999987653

>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=98.97  E-value=3.5e-11  Score=95.12  Aligned_cols=49  Identities=20%  Similarity=0.576  Sum_probs=39.3

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCCCCCCcCcCCCCCC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRNTCPVCRFELPTDD  332 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d  332 (363)
                      ....|+||++.|..  .++..+|+|.||..||.+|++  +.||+||..+...+
T Consensus        21 ~~l~C~IC~~~~~~--pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~   69 (97)
T d1jm7b_          21 KLLRCSRCTNILRE--PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWIQD   69 (97)
T ss_dssp             HTTSCSSSCSCCSS--CBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSCSS
T ss_pred             hcCCCccCCchhhc--CceeCCCCCchhHHHHHHHHh--ccccccCCcCchhh
Confidence            34679999999972  333457999999999999985  45999999886554

>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=98.96  E-value=3.8e-10  Score=89.55  Aligned_cols=52  Identities=21%  Similarity=0.192  Sum_probs=45.9

Q ss_pred             ccccccccccccccCCceEEeCCC-CcccHhhHHHHHhcCCCCCCcCcCCCCCChh
Q 017955          280 ETIVCAICKDTVNVGETATKLPCG-HVYHGDCIVPWLDSRNTCPVCRFELPTDDPE  334 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~-H~Fh~~CI~~WLk~~~sCPlCR~~l~~~d~~  334 (363)
                      ....||||+..|.   .+++++|+ |.|++.||..||+.+.+||+||.+|...+..
T Consensus        21 ~~f~CPI~~~lm~---dPV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L~   73 (98)
T d1wgma_          21 DEFLDPIMSTLMC---DPVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIR   73 (98)
T ss_dssp             TTTBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSE
T ss_pred             HHhCCcCchhHHH---HHHhcccccchhhHHHHHHHHHhcCCcccccccccchhhc
Confidence            4688999999998   78889966 5899999999999999999999999876643

>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=98.45  E-value=1.8e-08  Score=78.43  Aligned_cols=46  Identities=17%  Similarity=0.454  Sum_probs=36.6

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcC----C----CCCCcC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSR----N----TCPVCR  325 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~----~----sCPlCR  325 (363)
                      ....|+||++.+...+.+..++|+|.||..||..|++.+    .    .||.|+
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETTTTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCCcCccCCCcccCCceEEECCCCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            346799999999765566666899999999999999642    1    699864

>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=92.71  E-value=0.017  Score=38.66  Aligned_cols=44  Identities=23%  Similarity=0.533  Sum_probs=30.7

Q ss_pred             cccccccccccCCceEEeCCCCcccHhhHHHHHhcCC----CCCCcCc
Q 017955          283 VCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN----TCPVCRF  326 (363)
Q Consensus       283 ~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~----sCPlCR~  326 (363)
                      .|.||...-..+..+..-.|...||..|+..-+....    .||.||.
T Consensus         2 ~C~vC~~~~~~~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            4889976544333343335999999999988765432    6999975

>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=87.33  E-value=0.06  Score=38.40  Aligned_cols=49  Identities=22%  Similarity=0.636  Sum_probs=33.2

Q ss_pred             cccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC----CCCCcCcCCCCCC
Q 017955          281 TIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN----TCPVCRFELPTDD  332 (363)
Q Consensus       281 ~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~----sCPlCR~~l~~~d  332 (363)
                      ...|.||..   .++.+..-.|...||..|+.+.+....    .||.|+.....+.
T Consensus         7 c~~C~~C~~---~~~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~~~~   59 (70)
T d1fp0a1           7 ATICRVCQK---PGDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKE   59 (70)
T ss_dssp             SSCCSSSCS---SSCCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCSSCC
T ss_pred             CCCCCCCCC---cCEEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCccCc
Confidence            455777764   334444445999999999998875533    6999977554433

>d1wila_ g.50.1.3 (A:) Hypothetical protein KIAA1045 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: variant PHD-like domain
domain: Hypothetical protein KIAA1045
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.11  E-value=0.16  Score=37.51  Aligned_cols=31  Identities=23%  Similarity=0.759  Sum_probs=23.9

Q ss_pred             ccccccccccccccCCceEEeC---CCCcccHhhHHHH
Q 017955          280 ETIVCAICKDTVNVGETATKLP---CGHVYHGDCIVPW  314 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LP---C~H~Fh~~CI~~W  314 (363)
                      .+..|.|| +.|...   .++|   |+.+||..|+.+.
T Consensus        14 ~D~mC~vC-~v~t~~---~l~pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          14 NDEMCDVC-EVWTAE---SLFPCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CSCCCTTT-CCCCSS---CCSSCSSSSSCCCHHHHHHH
T ss_pred             cCcccccc-Cccccc---ceecceeecchhhHHHHHHh
Confidence            56789999 666633   2345   7899999999997

>d1z60a1 g.49.1.2 (A:328-386) TFIIH p44 subunit cysteine-rich domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: TFIIH p44 subunit cysteine-rich domain
domain: TFIIH p44 subunit cysteine-rich domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.25  E-value=0.14  Score=35.45  Aligned_cols=44  Identities=27%  Similarity=0.502  Sum_probs=30.3

Q ss_pred             ccccccccccccccCCceEEeC-CCCcccHhhHHHHHhcCCCCCCc
Q 017955          280 ETIVCAICKDTVNVGETATKLP-CGHVYHGDCIVPWLDSRNTCPVC  324 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LP-C~H~Fh~~CI~~WLk~~~sCPlC  324 (363)
                      ....|--|+..+... .+..-+ |+++||.+|=.---+.-..||-|
T Consensus        14 ~~~~C~gC~~~l~~~-~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKDQ-HVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTTS-EEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCCccCCCCcCCCC-ceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            456799999888643 233344 99999999954333445589987

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.47  E-value=0.1  Score=35.98  Aligned_cols=45  Identities=33%  Similarity=0.660  Sum_probs=31.1

Q ss_pred             ccccccccccccccCCceEEeCCCCcccHhhHHHHHhcCC----CCCCcCcC
Q 017955          280 ETIVCAICKDTVNVGETATKLPCGHVYHGDCIVPWLDSRN----TCPVCRFE  327 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~~~~LPC~H~Fh~~CI~~WLk~~~----sCPlCR~~  327 (363)
                      ....|.||...   +..+..-.|.-.||..||...+....    .||.|+..
T Consensus         8 ~~~~C~~C~~~---g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~   56 (61)
T d1mm2a_           8 HMEFCRVCKDG---GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCP   56 (61)
T ss_dssp             SCSSCTTTCCC---SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTT
T ss_pred             CcCCCcCCCCC---CeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCc
Confidence            34569999853   33444445999999999976654322    69999754

>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=81.26  E-value=0.093  Score=36.45  Aligned_cols=48  Identities=21%  Similarity=0.496  Sum_probs=32.5

Q ss_pred             ccccccccccccccCCc-eEEeCCCCcccHhhHHHHH---h--cCCCCCCcCcC
Q 017955          280 ETIVCAICKDTVNVGET-ATKLPCGHVYHGDCIVPWL---D--SRNTCPVCRFE  327 (363)
Q Consensus       280 ~~~~C~ICle~f~~~e~-~~~LPC~H~Fh~~CI~~WL---k--~~~sCPlCR~~  327 (363)
                      ....|.||...+..+.. +..-.|+.-||..|+..=.   .  ..-.||.|+..
T Consensus         5 ~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            34679999987766554 3344599999999985321   1  12379999754

>d2csha1 g.37.1.1 (A:8-60) Zinc finger protein 297b {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Zinc finger protein 297b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.18  E-value=0.16  Score=33.75  Aligned_cols=33  Identities=24%  Similarity=0.488  Sum_probs=25.4

Q ss_pred             ceeeeecCCcceeeeccC--------CCceecccCCCCceee
Q 017955           23 QYWCHHCEKRVSIETLAN--------LPDVICHECKNGFVES   56 (363)
Q Consensus        23 ~~~C~~C~~~~~~~~~~~--------~~~~~c~~C~~gFve~   56 (363)
                      .|.| .|.+.+.......        .--+.|+.|+.+|...
T Consensus         3 ~y~C-~Cgk~F~~~~~l~~H~~~Ht~ekpy~C~~C~k~F~~~   43 (53)
T d2csha1           3 LYPC-QCGKSFTHKSQRDRHMSMHLGLRPYGCGVCGKKFKMK   43 (53)
T ss_dssp             CEEC-TTSCEESSHHHHHHHHHHHSCCCSEECTTTSCEESSS
T ss_pred             CCCC-CCCCeECCHHHhHHHhhccccccCCcCCCcCCEecCH
Confidence            6999 6999887664433        4559999999999753