Citrus Sinensis ID: 042698

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200---
Protein Sequence
FFGKFHSRKLLIQNPLNEQPVTAAHPYSSESSLNSNAVIVLSVLVCGIICSLGLHFLIRCILVSWSRLEYSGPRANSSTPLAKTGIKKKALKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQPSSLSGISTPVQETVVNIRPLEPEGILRNYEGLS
Secondary Structure (PSIPRED)
cccccccHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHcccEEEccccccccccccccEEccccccccEEccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHccEEEEccccccccccccEEEEEcccccccEEEEcccccccccHHHHHHHHHccccccHHHHHcccccccccccccccccccccccccccEEEccccccccccccccccc
Coil and Loop (DISEMBL)
ffgkfhsrklliqnplneqpvtaahpyssesslnsnAVIVLSVLVCGIICSLGLHFLIRCILVSwsrleysgpransstplaktGIKKKALKAFTIVKYsgelklpgldnecviclsdfapgervrilpkcnhgfhvrCIDKWlrsnsscpkcrhcliesckkiegstqpsslsgistpvqetvvnirplepegilrnyegls
Flexible Loop (DISEMBL)
ffgkfhsrklliqnplneqpVTAAHPYSSESSLNSNAVIVLSVLVCGIICSLGLHFLIRCILVSWSRLEysgpransstplaktgikkKALKAFTIVKYSgelklpgldNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLrsnsscpkcRHCLIESCKKIegstqpsslsgistpvqetvvnirplepegilrnyegls
Low Complexity Region (SEG)
FFGKFHSRKLLIQNPLNEQPVTAAHPYSSESSLNSNAVIVLSVLVCGIICSLGLHFLIRCILVSWSRLEYSGPRANSSTPLAKTGIKKKALKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQPSSLSGISTPVQETVVNIRPLEPEGILRNYEGLS
Disordered region (IsUnstruct)
***********************************NAVIVLSVLVCGIICSLGLHFLIRCILVSWSRLEYS***********KTGIKKKALKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKI***************************************
Disordered Region (DISOPRED)
*****HS*****************************AVIVLSVLVCGIICSLGLHFLIRCILV***************************LKAFTIVKYSGE******DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCL**********************************************
Disordered Region (DISEMBL)
FFGKFHSRKLLIQNPLNEQPVT**********LNSNAVIVLSVLVCGIICSLGLHFLIRCILVSWSRLEYSGPRANSSTPLAKTGIKKKALKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKI***********ISTPVQETVVNIRPLEPEGILRNYEGLS
Disordered Region (DISPRO)
**GKFHSRKLLIQNPL**************SSLNSNAVIVLSVLVCGIICSLGLHFLIRCILVSW******************TGIKKKALKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES*******************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
FFGKFHSRKLLIQNPLNEQPVTAAHPYSSESSLNSNAVIVLSVLVCGIICSLGLHFLIRCILVSWSRLEYSGPRANSSTPLAKTGIKKKALKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQPSSLSGISTPVQETVVNIRPLEPEGILRNYEGLS
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	203	2.2.26 [Sep-21-2011]
Q94BY6	226	RING-H2 finger protein AT	yes	no	0.940	0.845	0.527	1e-52
Q6NML0	225	E3 ubiquitin-protein liga	no	no	0.970	0.875	0.507	2e-52
P0C034	251	RING-H2 finger protein AT	no	no	0.955	0.772	0.514	6e-52
Q6NQG7	219	RING-H2 finger protein AT	no	no	0.975	0.904	0.492	7e-51
Q9LS99	220	RING-H2 finger protein AT	no	no	0.965	0.890	0.465	1e-47
Q9FLC6	176	RING-H2 finger protein AT	no	no	0.694	0.801	0.451	6e-31
Q9SG96	181	RING-H2 finger protein AT	no	no	0.729	0.817	0.413	1e-27
O22755	185	RING-H2 finger protein AT	no	no	0.620	0.681	0.431	7e-24
Q8LC69	185	RING-H2 finger protein AT	no	no	0.674	0.740	0.395	1e-23
Q9LM69	197	RING-H2 finger protein AT	no	no	0.630	0.649	0.407	1e-23

>sp|Q94BY6|ATL75_ARATH RING-H2 finger protein ATL75 OS=Arabidopsis thaliana GN=ATL75 PE=2 SV=1

 Score =  206 bits (523), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 106/201 (52%), Positives = 136/201 (67%), Gaps = 10/201 (4%)

Query: 2   FGKFHSRKLLIQNPL--NEQPVTAAHP---YSSESSLNSNAVIVLSVLVCGIICSLGLHF 56
            G F SRKLL+ NP   N Q   A  P    + E++L+ N +++LSVL+CGIIC LGLH+
Sbjct: 19  LGGFVSRKLLLHNPFDHNTQRAFAVAPSPLITHENNLSGNVLMLLSVLICGIICCLGLHY 78

Query: 57  LIRCILVSWSRLEYSGPRANSSTPLAKT--GIKKKALKAFTIVKYSGELKLPGLDNECVI 114
           +IRC     S    S P A  STP   +  GI KKAL+ F +V YS E+ LPGL  ECVI
Sbjct: 79  IIRCAFRRTSSFMISEPIAGLSTPCGSSNKGINKKALRMFPVVSYSPEMNLPGLGEECVI 138

Query: 115 CLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGS-TQPSSL 173
           CLSDF  GE++R+LPKC+HGFHVRCIDKWL+ + +CPKCRHCL+E+C+KI G  +Q   +
Sbjct: 139 CLSDFVSGEQIRMLPKCHHGFHVRCIDKWLQQHLTCPKCRHCLVETCQKILGDFSQADQV 198

Query: 174 SGISTPVQETVVNIRPLEPEG 194
           +  +TP    +V I PLEPEG
Sbjct: 199 A--ATPTASVIVRIAPLEPEG 217

Arabidopsis thaliana (taxid: 3702)

>sp|Q6NML0|ATL76_ARATH E3 ubiquitin-protein ligase ATL76 OS=Arabidopsis thaliana GN=ATL76 PE=1 SV=1

 Score =  204 bits (520), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 105/207 (50%), Positives = 140/207 (67%), Gaps = 10/207 (4%)

Query: 1   FFGKFHSRKLLIQNPL--NEQPVTAAHP---YSSESSLNSNAVIVLSVLVCGIICSLGLH 55
           F G F +RKLL+ +P   N   V A  P    + E++L  N +++LSVL+CGIIC LGLH
Sbjct: 17  FLGSFVTRKLLLHDPFDHNSLRVFAVAPSPLITHENNLKGNVLMLLSVLICGIICCLGLH 76

Query: 56  FLIRCILVSWSRLEYSGP--RANSSTPLAKTGIKKKALKAFTIVKYSGELKLPGLDNECV 113
           ++IRC     SR   S P    ++    +  GIKKKAL+ F +V YS E+ LPG+  ECV
Sbjct: 77  YIIRCAFRRSSRFMISEPISSLSTPRSSSNKGIKKKALRMFPVVSYSREMNLPGIGEECV 136

Query: 114 ICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGS-TQPSS 172
           ICLSDF  GE++R+LPKCNHGFHVRCIDKWL+ + +CPKCRHCL+E+C+KI G  +Q  S
Sbjct: 137 ICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQHHLTCPKCRHCLVETCQKILGDFSQADS 196

Query: 173 LSGISTPVQETVVNIRPLEPEGILRNY 199
           ++  STP +  +V I PLEPEG +  +
Sbjct: 197 MA--STPTESVIVRIDPLEPEGRVNTF 221

E3 ubiquitin-protein ligase able to catalyze polyubiquitination with ubiquitin-conjugating enzyme E2 UBC8 in vitro.

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 3

EC: .

EC: 2

EC: .

EC: -

>sp|P0C034|ATL10_ARATH RING-H2 finger protein ATL10 OS=Arabidopsis thaliana GN=ATL10 PE=2 SV=1

 Score =  203 bits (517), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 105/204 (51%), Positives = 141/204 (69%), Gaps = 10/204 (4%)

Query: 1   FFGKFHSRKLLIQNPL--NEQPVTAAHP---YSSESSLNSNAVIVLSVLVCGIICSLGLH 55
           F G F SRKLL+ NP   N Q   A  P    + E++L+ N +++LS+L+CGIIC LGLH
Sbjct: 17  FLGGFVSRKLLLHNPFDHNTQRAFAVAPSPLITHENNLSGNVMMLLSILICGIICCLGLH 76

Query: 56  FLIRCILVSWSRLEYSGPRANSSTPLAKT--GIKKKALKAFTIVKYSGELKLPGLDNECV 113
           ++IRC L   +R   S P  + S+    +  GIKKKAL+ F +V YS E+ LPGLD ECV
Sbjct: 77  YIIRCALRRSTRFMISEPVPSLSSTRGSSNKGIKKKALRMFPVVSYSPEMNLPGLDEECV 136

Query: 114 ICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGS-TQPSS 172
           ICLSDF  GE++R+LPKCNHGFHVRCIDKWL+ + +CPKCR+CL+E+C+KI G  +Q  S
Sbjct: 137 ICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQQHLTCPKCRNCLVETCQKILGDFSQADS 196

Query: 173 LSGISTPVQETVVNIRPLEPEGIL 196
           ++  + P +  +V I PLEP  I+
Sbjct: 197 VT--AEPTEIVIVTIVPLEPTEIV 218

Arabidopsis thaliana (taxid: 3702)

>sp|Q6NQG7|ATL78_ARATH RING-H2 finger protein ATL78 OS=Arabidopsis thaliana GN=ATL78 PE=2 SV=1

 Score =  200 bits (508), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 98/199 (49%), Positives = 131/199 (65%), Gaps = 1/199 (0%)

Query: 1   FFGKFHSRKLLIQNPLNEQPVTAAHPYSSESSLNSNAVIVLSVLVCGIICSLGLHFLIRC 60
             G  +SRKLL     ++ P  A  PY  +++ ++N V+VLSVL+C ++CSLGL+ +IRC
Sbjct: 21  ILGSSYSRKLLFHTH-DQSPTPAPSPYVGDNNFDANVVMVLSVLLCALVCSLGLNSIIRC 79

Query: 61  ILVSWSRLEYSGPRANSSTPLAKTGIKKKALKAFTIVKYSGELKLPGLDNECVICLSDFA 120
            L   + +       N    L  TG+K+KALK+F  V YS EL LPGLD EC ICLS+F 
Sbjct: 80  ALRCSNLVPSEAGGDNYPVRLTNTGVKRKALKSFQTVSYSTELNLPGLDTECAICLSEFV 139

Query: 121 PGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQPSSLSGISTPV 180
             ERV++LP C+HGFHVRCIDKWL S+SSCP CRHCLI++C+KI   +Q SSL+    P 
Sbjct: 140 AEERVKLLPTCHHGFHVRCIDKWLSSHSSCPTCRHCLIQTCEKIADCSQTSSLNSTQPPQ 199

Query: 181 QETVVNIRPLEPEGILRNY 199
              ++ I PLEPE  +R +
Sbjct: 200 DSIILQIAPLEPERWIRWF 218

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LS99|ATL77_ARATH RING-H2 finger protein ATL77 OS=Arabidopsis thaliana GN=ATL77 PE=2 SV=1

 Score =  189 bits (480), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 94/202 (46%), Positives = 128/202 (63%), Gaps = 6/202 (2%)

Query: 1   FFGKFHSRKLLIQNPLNEQPVTAAHPYSSESSLNSNAVIVLSVLVCGIICSLGLHFLIRC 60
           F   F SRKLL Q P       A  P   +++L+ N +++LS+L+CGIICSLGLH++IRC
Sbjct: 18  FIDSFVSRKLLQQIPFAHNAQQAHVP--DKNNLSGNVLMLLSILLCGIICSLGLHYIIRC 75

Query: 61  ILVSWSRLEYSGPRANSSTPLAKT---GIKKKALKAFTIVKYSGELKLPGLDNECVICLS 117
             +       S P +  STP   +   GIKKKALK   +V YS E+ LPG+  ECVICLS
Sbjct: 76  AFIRSRSFMISDPISIPSTPRDSSVNKGIKKKALKMLPVVNYSPEINLPGVGEECVICLS 135

Query: 118 DFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQPSSLSGIS 177
           DF  GE++R+LPKCNHGFH+RCIDKWL  + +CPKCRHCL+++C+K+      +     +
Sbjct: 136 DFVAGEQLRVLPKCNHGFHLRCIDKWLTQHMTCPKCRHCLVDTCQKVLSDCDAADQVA-A 194

Query: 178 TPVQETVVNIRPLEPEGILRNY 199
           T  +   + I PLEPE  +  +
Sbjct: 195 TATESIDIRISPLEPEARVATF 216

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FLC6|ATL73_ARATH RING-H2 finger protein ATL73 OS=Arabidopsis thaliana GN=ATL73 PE=2 SV=1

 Score =  134 bits (336), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 65/144 (45%), Positives = 96/144 (66%), Gaps = 3/144 (2%)

Query: 31  SSLNSNAVIVLSVLVCGIICSLGLHFLIRCILVSWSRLEYSGPRANSSTPLAKTGIKKKA 90
           +S++++ VI+L+ L+C +IC+LG++ ++RC+L    R   +    +++  +AK GIKK+A
Sbjct: 35  ASMDTHMVIILAALLCALICALGINSVLRCVLRCTRRFTPNEDPVDTNANVAK-GIKKRA 93

Query: 91  LKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSC 150
           LK   +  YS ELK+     EC+ICL DF  GE VR+LPKCNHGFHV+CID WL S+SSC
Sbjct: 94  LKVIPVDSYSPELKMKA--TECLICLGDFVEGETVRVLPKCNHGFHVKCIDTWLLSHSSC 151

Query: 151 PKCRHCLIESCKKIEGSTQPSSLS 174
           P CR  L+E      GS +   ++
Sbjct: 152 PTCRQSLLEHQTPANGSRRGDDVA 175

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SG96|ATL72_ARATH RING-H2 finger protein ATL72 OS=Arabidopsis thaliana GN=ATL72 PE=2 SV=1

 Score =  123 bits (308), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 69/167 (41%), Positives = 99/167 (59%), Gaps = 19/167 (11%)

Query: 29  SESSLNSNAVIVLSVLVCGIICSLGLHFLIRCILVSWSRLEYSGPRANSSTP-------L 81
           +++  ++N VI+L+ L+C +IC+L L+  +RC+L    R       +N+S          
Sbjct: 25  NDTYFDTNMVIILAALLCALICALSLNSALRCVLRITRRFTSDDQVSNASNANANLGRLA 84

Query: 82  AKTGIKKKALKAFTIVKY-SGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCI 140
           A TG+KK+ALK   +  Y SG + +     EC+ICL DF  GE+VR+LPKCNHGFHVRCI
Sbjct: 85  AATGLKKQALKQIPVGLYGSGIIDMKA--TECLICLGDFEDGEKVRVLPKCNHGFHVRCI 142

Query: 141 DKWLRSNSSCPKCRHCLIESCKKIEGSTQPSSLSGISTPVQETVVNI 187
           D WL S SSCP CR  L+          QPS ++ +S   ++ VV+I
Sbjct: 143 DTWLLSRSSCPTCRQSLLLE--------QPSPMA-VSRRDEDMVVSI 180

Arabidopsis thaliana (taxid: 3702)

>sp|O22755|ATL44_ARATH RING-H2 finger protein ATL44 OS=Arabidopsis thaliana GN=ATL44 PE=2 SV=1

 Score =  110 bits (275), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 60/139 (43%), Positives = 78/139 (56%), Gaps = 13/139 (9%)

Query: 25  HPYSSESSLNSNAVIVLSVLVCGIICSLGLHFLIRCILVSWSRLEYSGPRANSSTPLAKT 84
            P     +  S+ V++LS L+C +IC  GL  ++RC   +W R   +G      +P    
Sbjct: 16  QPSEEMIAAESDMVVILSALLCALICVAGLAAVVRC---AWLRRFTAG----GDSPSPNK 68

Query: 85  GIKKKALKA-----FTIVK-YSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVR 138
           G+KKKAL++     FT  +  SG     G   EC ICL+DFA GE +R+LP C H FHV 
Sbjct: 69  GLKKKALQSLPRSTFTAAESTSGAAAEEGDSTECAICLTDFADGEEIRVLPLCGHSFHVE 128

Query: 139 CIDKWLRSNSSCPKCRHCL 157
           CIDKWL S SSCP CR  L
Sbjct: 129 CIDKWLVSRSSCPSCRRIL 147

Arabidopsis thaliana (taxid: 3702)

>sp|Q8LC69|ATL8_ARATH RING-H2 finger protein ATL8 OS=Arabidopsis thaliana GN=ATL8 PE=2 SV=2

 Score =  109 bits (273), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 57/144 (39%), Positives = 84/144 (58%), Gaps = 7/144 (4%)

Query: 19  QPVTAAHPYSSESSLNSNAVIVLSVLVCGIICSLGLHFLIRCILVSWSRLEYSGPRANSS 78
           Q   +  P  +    NS+ V++L+VL+C + C +GL  + RC   +W R   S  R++ +
Sbjct: 10  QEANSTSPAEASPPFNSDLVLILAVLLCALTCIIGLIAVSRC---AWLRRIASRNRSDQT 66

Query: 79  TP----LAKTGIKKKALKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHG 134
            P     A  G+KKK L++   + YS +        EC ICL++FA G+ +R+LP+C HG
Sbjct: 67  HPPPVAAANKGLKKKVLRSLPKLTYSPDSPPAEKLVECAICLTEFAAGDELRVLPQCGHG 126

Query: 135 FHVRCIDKWLRSNSSCPKCRHCLI 158
           FHV CID WL S+SSCP CR  L+
Sbjct: 127 FHVSCIDTWLGSHSSCPSCRQILV 150

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LM69|ATL80_ARATH RING-H2 finger protein ATL80 OS=Arabidopsis thaliana GN=ATL80 PE=1 SV=1

 Score =  109 bits (272), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 57/140 (40%), Positives = 84/140 (60%), Gaps = 12/140 (8%)

Query: 28  SSESSLNSNAVIVLSVLVCGIICSLGLHFLIRCILVSWSRLEYSGPRANSST-------- 79
           +S ++LNS+ V++L+ L+C +IC LGL  + RC+   W R   +G R  S +        
Sbjct: 21  NSTAALNSDLVVILAALLCALICVLGLIAVSRCV---WLRRLAAGNRTVSGSQTQSPQPP 77

Query: 80  -PLAKTGIKKKALKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVR 138
              A  G+KKK L++   + +S E        EC ICL++F+ G+ +R+LP+C HGFHV 
Sbjct: 78  VAAANKGLKKKVLQSLPKLTFSPESPESEKFAECAICLAEFSAGDELRVLPQCGHGFHVA 137

Query: 139 CIDKWLRSNSSCPKCRHCLI 158
           CID WL S+SSCP CR  L+
Sbjct: 138 CIDTWLGSHSSCPSCRQILV 157

May be involved in the early steps of the plant defense signaling pathway.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	203
224055977	225	predicted protein [Populus trichocarpa]	0.985	0.888	0.570	3e-62
224116596	225	predicted protein [Populus trichocarpa]	0.970	0.875	0.571	5e-61
255562369	223	RING-H2 finger protein ATL1L, putative [	0.980	0.892	0.570	3e-60
225431583	224	PREDICTED: RING-H2 finger protein ATL78	0.980	0.888	0.570	1e-59
357464535	240	Ring-H2 zinc finger protein [Medicago tr	0.965	0.816	0.570	1e-54
388508514	228	unknown [Medicago truncatula]	0.980	0.872	0.557	3e-53
297847202	225	zinc finger family protein [Arabidopsis	0.970	0.875	0.526	5e-53
9293902	222	unnamed protein product [Arabidopsis tha	0.931	0.851	0.531	1e-52
297830534	222	hypothetical protein ARALYDRAFT_479387 [	0.935	0.855	0.519	5e-52
357519845	219	RING-H2 finger protein ATL1L [Medicago t	0.926	0.858	0.504	5e-51

>gi|224055977|ref|XP_002298709.1| predicted protein [Populus trichocarpa] gi|222845967|gb|EEE83514.1| predicted protein [Populus trichocarpa]

 Score =  243 bits (620), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 121/212 (57%), Positives = 151/212 (71%), Gaps = 12/212 (5%)

Query: 1   FFGKFHSRKLLIQNPLNEQPVTAAHP-----------YSSESSLNSNAVIVLSVLVCGII 49
           F G F+SR+LL+  PL +   TA  P            S+++S ++N V+VLS+L+C +I
Sbjct: 15  FLGDFYSRRLLLHTPLYQSSNTATPPAPGNTASSETYTSTDNSFDANVVMVLSILLCALI 74

Query: 50  CSLGLHFLIRCILVSWSRLEYSGPRANSSTPLAKTGIKKKALKAFTIVKYSGELKLPGLD 109
           CSLGL+ +IRC L   S L  S   AN ST  A TG+K+KALK F IVKYS +L LPGLD
Sbjct: 75  CSLGLNSIIRCAL-RCSNLVASESAANPSTQAANTGVKRKALKTFPIVKYSTDLNLPGLD 133

Query: 110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQ 169
            +CVICLS+F PGE VR+LPKCNHGFHV+CIDKWL S+SSCP CRHCLIE+CKKI G +Q
Sbjct: 134 TQCVICLSEFTPGEHVRLLPKCNHGFHVKCIDKWLSSHSSCPTCRHCLIETCKKIAGCSQ 193

Query: 170 PSSLSGISTPVQETVVNIRPLEPEGILRNYEG 201
            S+    S PVQE +V+I PLEPEG++ NY G
Sbjct: 194 ASTSGPTSLPVQEAIVSILPLEPEGLISNYRG 225

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224116596|ref|XP_002331879.1| predicted protein [Populus trichocarpa] gi|222874628|gb|EEF11759.1| predicted protein [Populus trichocarpa]

 Score =  239 bits (610), Expect = 5e-61,   Method: Compositional matrix adjust.
 Identities = 120/210 (57%), Positives = 153/210 (72%), Gaps = 13/210 (6%)

Query: 1   FFGKFHSRKLLIQNPLNEQPVTAAHP-----------YSSESSLNSNAVIVLSVLVCGII 49
           F G F+SR+LL+ NPL +   TA  P             + SS ++N V+VLSVL+C +I
Sbjct: 14  FLGDFYSRRLLLHNPLYQSTNTATPPAPGNSAPSEPSTGTGSSFDANVVMVLSVLLCALI 73

Query: 50  CSLGLHFLIRCILVSWSRLEYSGPRANSSTPLAKTGIKKKALKAFTIVKYSGELKLPGLD 109
           CSLGL+ +IRC L   S +  S   AN ST  A TG+ ++ALK+F +V YS +L LPGLD
Sbjct: 74  CSLGLNSIIRCAL-RCSNIAASESAANPSTQSANTGVNRRALKSFPVVNYSSDLNLPGLD 132

Query: 110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQ 169
            ECVICLS+F PGERVR+LPKC+HGFHV+CIDKWL S+SSCP CRHCLIE+C+KI G +Q
Sbjct: 133 TECVICLSEFTPGERVRLLPKCHHGFHVKCIDKWLSSHSSCPTCRHCLIETCQKIIGCSQ 192

Query: 170 PSSLSGISTPVQETVVNIRPLEPEGILRNY 199
            S+ SG S PVQET+V+I PLEPEG++R+Y
Sbjct: 193 AST-SGTSLPVQETIVSILPLEPEGLIRDY 221

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255562369|ref|XP_002522191.1| RING-H2 finger protein ATL1L, putative [Ricinus communis] gi|223538562|gb|EEF40166.1| RING-H2 finger protein ATL1L, putative [Ricinus communis]

 Score =  236 bits (603), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 122/214 (57%), Positives = 149/214 (69%), Gaps = 15/214 (7%)

Query: 1   FFGKFHSRKLLIQNPLNEQPVT-----------AAHPYSSESSLNSNAVIVLSVLVCGII 49
           F G F+SR+LL+  PL   P             A+ PY+  +S ++N V+VLSVL+C +I
Sbjct: 14  FQGDFYSRRLLLHTPLYHSPTAAAPPAPGYSQEASEPYTGNNSFDANVVMVLSVLLCALI 73

Query: 50  CSLGLHFLIRCILVSWSRLEYSGPRANSSTPLAKTGIKKKALKAFTIVKYSGELKLPGLD 109
           CSLGL+ +IRC L   S L  S    NSS  LA TG+K+KALK F  V YS +L LPGLD
Sbjct: 74  CSLGLNSIIRCAL-RCSSLVASRSADNSSAGLANTGVKRKALKTFPTVNYSTDLNLPGLD 132

Query: 110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQ 169
            EC ICLS+F PGERVR+LPKCNHGFHVRCIDKWL S+SSCP CRHCLIE+C+KI G +Q
Sbjct: 133 TECAICLSEFTPGERVRLLPKCNHGFHVRCIDKWLSSHSSCPTCRHCLIETCQKIVGCSQ 192

Query: 170 PSSLSGISTPVQETVVNIRPLEPEGILRNYEGLS 203
            SS      PVQE++VNI PLEPE ++R+Y G S
Sbjct: 193 TSS---SDPPVQESIVNIAPLEPEALIRSYRGTS 223

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225431583|ref|XP_002282494.1| PREDICTED: RING-H2 finger protein ATL78 [Vitis vinifera] gi|147833208|emb|CAN75293.1| hypothetical protein VITISV_042413 [Vitis vinifera]

 Score =  234 bits (598), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 122/214 (57%), Positives = 152/214 (71%), Gaps = 15/214 (7%)

Query: 1   FFGKFHSRKLLIQNPLNEQPVTAA-----------HPYSSESSLNSNAVIVLSVLVCGII 49
             G F+SR+LL+ +PL+E P TA+            PY+  +S ++N V+VLSVL+C +I
Sbjct: 15  LVGDFYSRRLLLHSPLHESPATASPPATGNSHDSSEPYTGSNSFDTNVVMVLSVLLCALI 74

Query: 50  CSLGLHFLIRCILVSWSRLEYSGPRANSSTPLAKTGIKKKALKAFTIVKYSGELKLPGLD 109
           CSLGL+ +IRC L   S +  + P  + ST LA TG+KKKALK F  + YS  L LPGLD
Sbjct: 75  CSLGLNSIIRCALRCSSLV--ASPGNSPSTRLANTGVKKKALKTFPTLNYSAGLNLPGLD 132

Query: 110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQ 169
            ECVICLSDF PGER+RILPKCNHGFHVRCIDKWL S+SSCP CRHCLIE+C+KI G +Q
Sbjct: 133 TECVICLSDFTPGERIRILPKCNHGFHVRCIDKWLNSHSSCPTCRHCLIETCQKIIGCSQ 192

Query: 170 PSSLSGISTPVQETVVNIRPLEPEGILRNYEGLS 203
            SS S    P+QE+++ I PLEPEG  RNY  +S
Sbjct: 193 ASS-SETPPPLQESMI-IVPLEPEGFSRNYREVS 224

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357464535|ref|XP_003602549.1| Ring-H2 zinc finger protein [Medicago truncatula] gi|355491597|gb|AES72800.1| Ring-H2 zinc finger protein [Medicago truncatula]

 Score =  218 bits (555), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 118/207 (57%), Positives = 146/207 (70%), Gaps = 11/207 (5%)

Query: 4   KFHSRKLLIQ--NPLNEQPVTAAHPYSSESS------LNSNAVIVLSVLVCGIICSLGLH 55
            FHSR+LL+   N  N    T+ H  + ESS       ++N V+VLSVL+C +ICSL L+
Sbjct: 18  NFHSRRLLLHSSNSANPPISTSIHDSTKESSYAGDGNFDANVVMVLSVLLCALICSLCLN 77

Query: 56  FLIRCILVSWSRLEYSGPRANSSTPL--AKTGIKKKALKAFTIVKYSGELKLPGLDNECV 113
            +IRC L   + +  SG R+ ++ P+  A TGIKKKALK FT V YS ELKLP LD+ECV
Sbjct: 78  SIIRCALKCSNLVVMSGDRSANNIPVRAANTGIKKKALKKFTTVSYSDELKLPSLDSECV 137

Query: 114 ICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQPSSL 173
           ICLS+F  G++VR+LPKCNHGFHVRCIDKWL S+SSCPKCR CLIE+C KI GS   SS 
Sbjct: 138 ICLSEFTNGDKVRLLPKCNHGFHVRCIDKWLSSHSSCPKCRQCLIETCNKIVGSQGSSSQ 197

Query: 174 -SGISTPVQETVVNIRPLEPEGILRNY 199
              +  PV ET+V I PLEPEG++RNY
Sbjct: 198 PQPMLFPVPETIVTIAPLEPEGLVRNY 224

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388508514|gb|AFK42323.1| unknown [Medicago truncatula]

 Score =  213 bits (543), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 117/210 (55%), Positives = 146/210 (69%), Gaps = 11/210 (5%)

Query: 5   FHSRKLLIQ--NPLNEQPVTAAHPYSSESS------LNSNAVIVLSVLVCGIICSLGLHF 56
           FHSR+LL+   N  N    T+ H  + ESS       ++N V+VLSVL+C +ICSL L+ 
Sbjct: 19  FHSRRLLLHSSNSANPPISTSIHDSTKESSYAGDGNFDANVVMVLSVLLCALICSLCLNS 78

Query: 57  LIRCILVSWSRLEYSGPRANSSTPL--AKTGIKKKALKAFTIVKYSGELKLPGLDNECVI 114
           +IRC L   + +   G R+ ++ P+  A TGIKKKALK FT V YS ELKL  LD+ECVI
Sbjct: 79  IIRCALKCSNLVVMRGDRSANNIPVRAANTGIKKKALKKFTTVSYSDELKLLSLDSECVI 138

Query: 115 CLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQPSSL- 173
           CLS+F  G++VR+LPKCNHGFHVRCIDKWL S+SSCPKCR CLIE+C KI GS   SS  
Sbjct: 139 CLSEFTNGDKVRLLPKCNHGFHVRCIDKWLSSHSSCPKCRQCLIETCNKIVGSQGSSSQP 198

Query: 174 SGISTPVQETVVNIRPLEPEGILRNYEGLS 203
             +  PV ET+V I PLEPEG++RNY  +S
Sbjct: 199 QPMLFPVPETIVTIAPLEPEGLVRNYREVS 228

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297847202|ref|XP_002891482.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata] gi|297337324|gb|EFH67741.1| zinc finger family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  213 bits (541), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 109/207 (52%), Positives = 142/207 (68%), Gaps = 10/207 (4%)

Query: 1   FFGKFHSRKLLIQNPL--NEQPVTAAHP---YSSESSLNSNAVIVLSVLVCGIICSLGLH 55
           F G F SRKLL+ +P   N   V A  P    + E++L  N +++LSVL+CGIIC LGLH
Sbjct: 17  FLGDFVSRKLLLHDPFDHNSLRVLAVAPSPLITHENNLRGNVLMLLSVLICGIICCLGLH 76

Query: 56  FLIRCILVSWSRLEYSGPRANSSTPLAKT--GIKKKALKAFTIVKYSGELKLPGLDNECV 113
           ++IRC     SR   S P ++  TP   +  GIKKKAL+ F +V YS E+ LPGL  ECV
Sbjct: 77  YIIRCAFRRSSRFMISEPISSLPTPRGSSDKGIKKKALRMFPVVSYSREMNLPGLGEECV 136

Query: 114 ICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGS-TQPSS 172
           ICLSDF  GE++R+LPKCNHGFHVRCIDKWLR + +CPKCRHCL+E+C+KI G  +Q  S
Sbjct: 137 ICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLRQHLTCPKCRHCLVETCQKILGDFSQADS 196

Query: 173 LSGISTPVQETVVNIRPLEPEGILRNY 199
           ++  +TP +  +V I PLEPEG +  +
Sbjct: 197 MA--ATPTESVIVRIAPLEPEGRVNTF 221

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|9293902|dbj|BAB01805.1| unnamed protein product [Arabidopsis thaliana]

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 111/209 (53%), Positives = 141/209 (67%), Gaps = 20/209 (9%)

Query: 3   GKFHSRKLLIQNPLNEQPVTAA-----------HPYSSESSLNSNAVIVLSVLVCGIICS 51
           G F+SR+LL+      QP TAA           H Y S  S ++N V+VLSVL+C ++CS
Sbjct: 21  GDFYSRRLLLHTAY--QPPTAASPPFADAHEASHSYQSHMSFDANVVMVLSVLLCALVCS 78

Query: 52  LGLHFLIRCILVSWSRLEYSGPRANSSTPLAKTGIKKKALKAFTIVKYSGELKLPGLDNE 111
           LGLH +IRC L  +S L  S      S  LA TG+K+KALK+F  V Y+ ELKLPGLD E
Sbjct: 79  LGLHSIIRCAL-RYSNLLSSEASDEFSVRLANTGVKQKALKSFQTVSYTAELKLPGLDTE 137

Query: 112 CVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQPS 171
           C ICLS+FA GERV++LPKC+HGFHVRCIDKWL S+SSCP CRHCLI++CKKI G ++  
Sbjct: 138 CAICLSEFASGERVKLLPKCHHGFHVRCIDKWLSSHSSCPTCRHCLIQTCKKIAGYSETE 197

Query: 172 SLSGISTPVQ-ETVVNIRPLEPEGILRNY 199
                S+P Q +  V+I PL PE ++R +
Sbjct: 198 -----SSPNQPQQNVHISPLGPESLIRGF 221

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297830534|ref|XP_002883149.1| hypothetical protein ARALYDRAFT_479387 [Arabidopsis lyrata subsp. lyrata] gi|297328989|gb|EFH59408.1| hypothetical protein ARALYDRAFT_479387 [Arabidopsis lyrata subsp. lyrata]

 Score =  209 bits (532), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 108/208 (51%), Positives = 142/208 (68%), Gaps = 18/208 (8%)

Query: 3   GKFHSRKLLIQNPLNEQPVTAA----------HPYSSESSLNSNAVIVLSVLVCGIICSL 52
           G F+SR+LL+     + P TA+          H Y+S  S ++N V+VLSVL+C ++CSL
Sbjct: 21  GDFYSRRLLLHTAY-QPPTTASSPFADAHETSHTYASHMSFDANVVMVLSVLLCALVCSL 79

Query: 53  GLHFLIRCILVSWSRLEYSGPRANSSTPLAKTGIKKKALKAFTIVKYSGELKLPGLDNEC 112
           GLH +IRC L  +S L  S      S  LA TG+K+KALK+F  V Y+ ELKLPGLD EC
Sbjct: 80  GLHSIIRCAL-RYSNLLSSEASDELSVRLANTGVKQKALKSFQTVSYTAELKLPGLDTEC 138

Query: 113 VICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQPSS 172
            ICLS+F  GERV++LPKC+HGFHVRCIDKWL S+SSCP CRHCLI++CKKI G ++   
Sbjct: 139 AICLSEFVSGERVKLLPKCHHGFHVRCIDKWLSSHSSCPTCRHCLIQTCKKIAGCSE--- 195

Query: 173 LSGISTPVQ-ETVVNIRPLEPEGILRNY 199
              +S+P Q +  V+I PL PE ++R +
Sbjct: 196 --TVSSPNQPQENVHIAPLGPESLIRGF 221

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357519845|ref|XP_003630211.1| RING-H2 finger protein ATL1L [Medicago truncatula] gi|355524233|gb|AET04687.1| RING-H2 finger protein ATL1L [Medicago truncatula]

 Score =  206 bits (524), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 105/208 (50%), Positives = 136/208 (65%), Gaps = 20/208 (9%)

Query: 6   HSRKLLIQNPLNEQPVTAAH-----------PYSSESSLNSNAVIVLSVLVCGIICSLGL 54
           H+R+LL Q+P+  Q +T +H            Y      +SN +++L+VL+C +ICSL L
Sbjct: 21  HTRRLLFQDPIEHQSLTNSHVLTNNNHNSTDSYFGAREFDSNVIMILAVLLCALICSLAL 80

Query: 55  HFLIRCILVSWSRLEYSGPRANSSTPLAKTGIKKKALKAFTIVKYSGELKLPGLDNECVI 114
           + +IRC L   +   ++ P  +SS      GIKKKALK F  V YS ELKLP LD EC+I
Sbjct: 81  NSIIRCGLRFSNVALHNDPSLSSSN----KGIKKKALKTFPTVSYSAELKLPSLDTECII 136

Query: 115 CLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQPSSLS 174
           CLS+F  GE+VRILPKCNHGFHVRCIDKWL+ + SCPKCR CL+E+C+KI  S QP    
Sbjct: 137 CLSEFTKGEKVRILPKCNHGFHVRCIDKWLKEHPSCPKCRQCLLETCRKIVRSQQP---- 192

Query: 175 GISTPVQETVVNIRPLEPEGILRNYEGL 202
            I  PV ETV+ I+PLE E + RNY  +
Sbjct: 193 -IVMPVLETVIRIQPLEHEALERNYREI 219

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	203
TAIR|locus:2028506	251	AT1G49220 [Arabidopsis thalian	0.955	0.772	0.524	3.7e-54
TAIR|locus:2028406	225	AT1G49210 [Arabidopsis thalian	0.970	0.875	0.521	1.5e-53
TAIR|locus:2028411	226	AT1G49200 [Arabidopsis thalian	0.935	0.840	0.53	9.2e-52
TAIR|locus:2028436	219	AT1G49230 [Arabidopsis thalian	0.955	0.885	0.502	7.4e-50
TAIR|locus:2830088	220	AT3G18773 [Arabidopsis thalian	0.935	0.863	0.479	1.8e-46
TAIR|locus:2153554	176	DAF "DEFECTIVE IN ANTHER DEHIS	0.660	0.761	0.474	2e-31
TAIR|locus:2181032	159	DAFL2 "DAF-Like gene 2" [Arabi	0.630	0.805	0.470	1.6e-29
TAIR|locus:2103162	181	DAFL1 "DAF-Like gene 1" [Arabi	0.822	0.922	0.405	6.4e-28
TAIR|locus:2825708	197	AT1G20823 [Arabidopsis thalian	0.822	0.847	0.393	7.3e-27
TAIR|locus:2011686	185	ATL8 [Arabidopsis thaliana (ta	0.837	0.918	0.373	1.5e-26

TAIR|locus:2028506 AT1G49220 [Arabidopsis thaliana (taxid:3702)]

 Score = 528 (190.9 bits), Expect = 3.7e-54, Sum P(2) = 3.7e-54
 Identities = 107/204 (52%), Positives = 142/204 (69%)

Query:     1 FFGKFHSRKLLIQNPL--NEQPVTAAHP---YSSESSLNSNAVIVLSVLVCGIICSLGLH 55
             F G F SRKLL+ NP   N Q   A  P    + E++L+ N +++LS+L+CGIIC LGLH
Sbjct:    17 FLGGFVSRKLLLHNPFDHNTQRAFAVAPSPLITHENNLSGNVMMLLSILICGIICCLGLH 76

Query:    56 FLIRCILVSWSRLEYSGPRAN-SSTP-LAKTGIKKKALKAFTIVKYSGELKLPGLDNECV 113
             ++IRC L   +R   S P  + SST   +  GIKKKAL+ F +V YS E+ LPGLD ECV
Sbjct:    77 YIIRCALRRSTRFMISEPVPSLSSTRGSSNKGIKKKALRMFPVVSYSPEMNLPGLDEECV 136

Query:   114 ICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGS-TQPSS 172
             ICLSDF  GE++R+LPKCNHGFHVRCIDKWL+ + +CPKCR+CL+E+C+KI G  +Q  S
Sbjct:   137 ICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQQHLTCPKCRNCLVETCQKILGDFSQADS 196

Query:   173 LSGISTPVQETVVNIRPLEPEGIL 196
             ++  + P +  +V I PLEP  I+
Sbjct:   197 VT--AEPTEIVIVTIVPLEPTEIV 218

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

TAIR|locus:2028406 AT1G49210 [Arabidopsis thaliana (taxid:3702)]

 Score = 554 (200.1 bits), Expect = 1.5e-53, P = 1.5e-53
 Identities = 108/207 (52%), Positives = 144/207 (69%)

Query:     1 FFGKFHSRKLLIQNPL--NEQPVTAAHP---YSSESSLNSNAVIVLSVLVCGIICSLGLH 55
             F G F +RKLL+ +P   N   V A  P    + E++L  N +++LSVL+CGIIC LGLH
Sbjct:    17 FLGSFVTRKLLLHDPFDHNSLRVFAVAPSPLITHENNLKGNVLMLLSVLICGIICCLGLH 76

Query:    56 FLIRCILVSWSRLEYSGPRANSSTPLAKT--GIKKKALKAFTIVKYSGELKLPGLDNECV 113
             ++IRC     SR   S P ++ STP + +  GIKKKAL+ F +V YS E+ LPG+  ECV
Sbjct:    77 YIIRCAFRRSSRFMISEPISSLSTPRSSSNKGIKKKALRMFPVVSYSREMNLPGIGEECV 136

Query:   114 ICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGS-TQPSS 172
             ICLSDF  GE++R+LPKCNHGFHVRCIDKWL+ + +CPKCRHCL+E+C+KI G  +Q  S
Sbjct:   137 ICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQHHLTCPKCRHCLVETCQKILGDFSQADS 196

Query:   173 LSGISTPVQETVVNIRPLEPEGILRNY 199
             ++  STP +  +V I PLEPEG +  +
Sbjct:   197 MA--STPTESVIVRIDPLEPEGRVNTF 221

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

TAIR|locus:2028411 AT1G49200 [Arabidopsis thaliana (taxid:3702)]

 Score = 537 (194.1 bits), Expect = 9.2e-52, P = 9.2e-52
 Identities = 106/200 (53%), Positives = 136/200 (68%)

Query:     3 GKFHSRKLLIQNPL--NEQPVTAAHP---YSSESSLNSNAVIVLSVLVCGIICSLGLHFL 57
             G F SRKLL+ NP   N Q   A  P    + E++L+ N +++LSVL+CGIIC LGLH++
Sbjct:    20 GGFVSRKLLLHNPFDHNTQRAFAVAPSPLITHENNLSGNVLMLLSVLICGIICCLGLHYI 79

Query:    58 IRCILVSWSRLEYSGPRANSSTPLAKT--GIKKKALKAFTIVKYSGELKLPGLDNECVIC 115
             IRC     S    S P A  STP   +  GI KKAL+ F +V YS E+ LPGL  ECVIC
Sbjct:    80 IRCAFRRTSSFMISEPIAGLSTPCGSSNKGINKKALRMFPVVSYSPEMNLPGLGEECVIC 139

Query:   116 LSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGS-TQPSSLS 174
             LSDF  GE++R+LPKC+HGFHVRCIDKWL+ + +CPKCRHCL+E+C+KI G  +Q   ++
Sbjct:   140 LSDFVSGEQIRMLPKCHHGFHVRCIDKWLQQHLTCPKCRHCLVETCQKILGDFSQADQVA 199

Query:   175 GISTPVQETVVNIRPLEPEG 194
               +TP    +V I PLEPEG
Sbjct:   200 --ATPTASVIVRIAPLEPEG 217

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

TAIR|locus:2028436 AT1G49230 [Arabidopsis thaliana (taxid:3702)]

 Score = 519 (187.8 bits), Expect = 7.4e-50, P = 7.4e-50
 Identities = 98/195 (50%), Positives = 130/195 (66%)

Query:     3 GKFHSRKLLIQNPLNEQPVTAAHPYSSESSLNSNAVIVLSVLVCGIICSLGLHFLIRCIL 62
             G  +SRKLL     ++ P  A  PY  +++ ++N V+VLSVL+C ++CSLGL+ +IRC L
Sbjct:    23 GSSYSRKLLFHTH-DQSPTPAPSPYVGDNNFDANVVMVLSVLLCALVCSLGLNSIIRCAL 81

Query:    63 VSWSRLEYSGPRANSSTPLAKTGIKKKALKAFTIVKYSGELKLPGLDNECVICLSDFAPG 122
                + +       N    L  TG+K+KALK+F  V YS EL LPGLD EC ICLS+F   
Sbjct:    82 RCSNLVPSEAGGDNYPVRLTNTGVKRKALKSFQTVSYSTELNLPGLDTECAICLSEFVAE 141

Query:   123 ERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQPSSLSGISTPVQE 182
             ERV++LP C+HGFHVRCIDKWL S+SSCP CRHCLI++C+KI   +Q SSL+    P   
Sbjct:   142 ERVKLLPTCHHGFHVRCIDKWLSSHSSCPTCRHCLIQTCEKIADCSQTSSLNSTQPPQDS 201

Query:   183 TVVNIRPLEPEGILR 197
              ++ I PLEPE  +R
Sbjct:   202 IILQIAPLEPERWIR 216

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

TAIR|locus:2830088 AT3G18773 [Arabidopsis thaliana (taxid:3702)]

 Score = 487 (176.5 bits), Expect = 1.8e-46, P = 1.8e-46
 Identities = 94/196 (47%), Positives = 126/196 (64%)

Query:     1 FFGKFHSRKLLIQNPLNEQPVTAAHPYSSESSLNSNAVIVLSVLVCGIICSLGLHFLIRC 60
             F   F SRKLL Q P       A  P   +++L+ N +++LS+L+CGIICSLGLH++IRC
Sbjct:    18 FIDSFVSRKLLQQIPFAHNAQQAHVP--DKNNLSGNVLMLLSILLCGIICSLGLHYIIRC 75

Query:    61 ILVSWSRLEYSGPRANSSTPLAKT---GIKKKALKAFTIVKYSGELKLPGLDNECVICLS 117
               +       S P +  STP   +   GIKKKALK   +V YS E+ LPG+  ECVICLS
Sbjct:    76 AFIRSRSFMISDPISIPSTPRDSSVNKGIKKKALKMLPVVNYSPEINLPGVGEECVICLS 135

Query:   118 DFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQPSSLSGIS 177
             DF  GE++R+LPKCNHGFH+RCIDKWL  + +CPKCRHCL+++C+K+      +     +
Sbjct:   136 DFVAGEQLRVLPKCNHGFHLRCIDKWLTQHMTCPKCRHCLVDTCQKVLSDCDAADQVA-A 194

Query:   178 TPVQETVVNIRPLEPE 193
             T  +   + I PLEPE
Sbjct:   195 TATESIDIRISPLEPE 210

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

TAIR|locus:2153554 DAF "DEFECTIVE IN ANTHER DEHISCENCE1- ( DAD1-) Activating Factor" [Arabidopsis thaliana (taxid:3702)]

 Score = 345 (126.5 bits), Expect = 2.0e-31, P = 2.0e-31
 Identities = 65/137 (47%), Positives = 93/137 (67%)

Query:    31 SSLNSNAVIVLSVLVCGIICSLGLHFLIRCILVSWSRLEYSGPRANSSTPLAKTGIKKKA 90
             +S++++ VI+L+ L+C +IC+LG++ ++RC+L    R   +    +++  +AK GIKK+A
Sbjct:    35 ASMDTHMVIILAALLCALICALGINSVLRCVLRCTRRFTPNEDPVDTNANVAK-GIKKRA 93

Query:    91 LKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSC 150
             LK   +  YS ELK+     EC+ICL DF  GE VR+LPKCNHGFHV+CID WL S+SSC
Sbjct:    94 LKVIPVDSYSPELKMKA--TECLICLGDFVEGETVRVLPKCNHGFHVKCIDTWLLSHSSC 151

Query:   151 PKCRHCLIESCKKIEGS 167
             P CR  L+E      GS
Sbjct:   152 PTCRQSLLEHQTPANGS 168

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

TAIR|locus:2181032 DAFL2 "DAF-Like gene 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 327 (120.2 bits), Expect = 1.6e-29, P = 1.6e-29
 Identities = 63/134 (47%), Positives = 89/134 (66%)

Query:    27 YSSESSLNSNAVIVLSVLVCGIICSLGLHFLIRCILVSWSRLEYSGPRANSSTPLAKTGI 86
             Y+ + + ++N VI+L+ L+C +I +LGL+ ++RC +     L  S   A + T   + G+
Sbjct:    24 YTRDMNFDANMVIILAALLCALILALGLNSILRCAMRCGFGLSSS---AAAGTVADRAGL 80

Query:    87 KKKALKAFTIVKY-SGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR 145
             KK+ LK F + +Y SGE+K+     EC ICL +FA GERVR+LP CNH FH+ CID WL 
Sbjct:    81 KKRELKKFPVAEYGSGEVKIAA--TECAICLGEFADGERVRVLPPCNHSFHMSCIDTWLV 138

Query:   146 SNSSCPKCRHCLIE 159
             S+SSCP CRH LIE
Sbjct:   139 SHSSCPNCRHSLIE 152

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

TAIR|locus:2103162 DAFL1 "DAF-Like gene 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 312 (114.9 bits), Expect = 6.4e-28, P = 6.4e-28
 Identities = 77/190 (40%), Positives = 109/190 (57%)

Query:     9 KLLIQNPLNEQPVTA-AHPYS--SESSLNSNAVIVLSVLVCGIICSLGLHFLIRCILVSW 65
             +LL++ P    P  A   P    +++  ++N VI+L+ L+C +IC+L L+  +RC+L   
Sbjct:     3 RLLLE-PQANAPANANPKPKGGINDTYFDTNMVIILAALLCALICALSLNSALRCVLRIT 61

Query:    66 SRL-------EYSGPRANSSTPLAKTGIKKKALKAFTIVKY-SGELKLPGLDNECVICLS 117
              R          S   AN     A TG+KK+ALK   +  Y SG + +     EC+ICL 
Sbjct:    62 RRFTSDDQVSNASNANANLGRLAAATGLKKQALKQIPVGLYGSGIIDMKA--TECLICLG 119

Query:   118 DFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQPSSLSGIS 177
             DF  GE+VR+LPKCNHGFHVRCID WL S SSCP CR  L+     +E   QPS ++ +S
Sbjct:   120 DFEDGEKVRVLPKCNHGFHVRCIDTWLLSRSSCPTCRQSLL-----LE---QPSPMA-VS 170

Query:   178 TPVQETVVNI 187
                ++ VV+I
Sbjct:   171 RRDEDMVVSI 180

GO:0005634 "nucleus" evidence=ISM

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

GO:0010413 "glucuronoxylan metabolic process" evidence=RCA

GO:0045492 "xylan biosynthetic process" evidence=RCA

TAIR|locus:2825708 AT1G20823 [Arabidopsis thaliana (taxid:3702)]

 Score = 302 (111.4 bits), Expect = 7.3e-27, P = 7.3e-27
 Identities = 70/178 (39%), Positives = 102/178 (57%)

Query:    28 SSESSLNSNAVIVLSVLVCGIICSLGLHFLIRCI----LVSWSRLEYSGPRANSSTP--- 80
             +S ++LNS+ V++L+ L+C +IC LGL  + RC+    L + +R   SG +  S  P   
Sbjct:    21 NSTAALNSDLVVILAALLCALICVLGLIAVSRCVWLRRLAAGNRT-VSGSQTQSPQPPVA 79

Query:    81 LAKTGIKKKALKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCI 140
              A  G+KKK L++   + +S E        EC ICL++F+ G+ +R+LP+C HGFHV CI
Sbjct:    80 AANKGLKKKVLQSLPKLTFSPESPESEKFAECAICLAEFSAGDELRVLPQCGHGFHVACI 139

Query:   141 DKWLRSNSSCPKCRHCLIES-CKKIEGSTQPSSLSGI-STPVQETVVNIRPLEPEGIL 196
             D WL S+SSCP CR  L+ + C K  G    SS SG+ S P  E  +     +P   L
Sbjct:   140 DTWLGSHSSCPSCRQILVVARCHKC-GGLPGSSSSGLESEPEIEIRIKQGEDDPNSFL 196

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

GO:0009507 "chloroplast" evidence=ISM

GO:0010200 "response to chitin" evidence=IEP

TAIR|locus:2011686 ATL8 [Arabidopsis thaliana (taxid:3702)]

 Score = 299 (110.3 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 68/182 (37%), Positives = 100/182 (54%)

Query:    19 QPVTAAHPYSSESSLNSNAVIVLSVLVCGIICSLGLHFLIRCILVSWSRLEYSGPRANSS 78
             Q   +  P  +    NS+ V++L+VL+C + C +GL  + RC   +W R   S  R++ +
Sbjct:    10 QEANSTSPAEASPPFNSDLVLILAVLLCALTCIIGLIAVSRC---AWLRRIASRNRSDQT 66

Query:    79 TP----LAKTGIKKKALKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHG 134
              P     A  G+KKK L++   + YS +        EC ICL++FA G+ +R+LP+C HG
Sbjct:    67 HPPPVAAANKGLKKKVLRSLPKLTYSPDSPPAEKLVECAICLTEFAAGDELRVLPQCGHG 126

Query:   135 FHVRCIDKWLRSNSSCPKCRHCLIES-CKKIEGSTQPSSLSGISTPVQETVVNIRPLEPE 193
             FHV CID WL S+SSCP CR  L+ + C K  G    SS SG   P  +T +  R   P+
Sbjct:   127 FHVSCIDTWLGSHSSCPSCRQILVVTRCHKC-GGLPGSSSSG---PEPDTRIKQREDGPD 182

Query:   194 GI 195
              +
Sbjct:   183 NL 184

GO:0005634 "nucleus" evidence=ISM

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

GO:0009744 "response to sucrose stimulus" evidence=RCA

GO:0009750 "response to fructose stimulus" evidence=RCA

GO:0009855 "determination of bilateral symmetry" evidence=RCA

GO:0009944 "polarity specification of adaxial/abaxial axis" evidence=RCA

GO:0010014 "meristem initiation" evidence=RCA

GO:0010075 "regulation of meristem growth" evidence=RCA

---

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)
Q94BY6	ATL75_ARATH	No assigned EC number	0.5273	0.9408	0.8451	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: fgenesh4_pg.C_LG_I002524 hypothetical protein (225 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	203
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	1e-14
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	1e-11
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	3e-10
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	8e-10
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	2e-07
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	2e-06
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	2e-06
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	3e-06
smart00184	40	smart00184, RING, Ring finger	2e-05
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	1e-04
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	4e-04
pfam11793	70	pfam11793, FANCL_C, FANCL C-terminal domain	9e-04
pfam00097	40	pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING	0.001
COG5432	391	COG5432, RAD18, RING-finger-containing E3 ubiquiti	0.004

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

 Score = 65.1 bits (159), Expect = 1e-14
 Identities = 27/46 (58%), Positives = 34/46 (73%), Gaps = 1/46 (2%)

Query: 110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRH 155
           +EC ICL +F PGE V +LP C H FH  C+DKWLRS+++CP CR 
Sbjct: 1   DECPICLDEFEPGEEVVVLP-CGHVFHKECLDKWLRSSNTCPLCRA 45

Length = 46

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

 Score = 62.3 bits (151), Expect = 1e-11
 Identities = 25/45 (55%), Positives = 32/45 (71%), Gaps = 2/45 (4%)

Query: 111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS-SCPKCR 154
           EC IC+S+F   +R+R+LP C+H FHV C+DKWL   S  CP CR
Sbjct: 325 ECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCR 368

Length = 374

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

 Score = 54.0 bits (130), Expect = 3e-10
 Identities = 19/55 (34%), Positives = 30/55 (54%), Gaps = 9/55 (16%)

Query: 109 DNECVICLSDFA--------PGERVRI-LPKCNHGFHVRCIDKWLRSNSSCPKCR 154
           D+ C IC + F         PG+   +   +C H FH+ CI +WL++ ++CP CR
Sbjct: 19  DDVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 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|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 = 52.1 bits (125), Expect = 8e-10
 Identities = 21/48 (43%), Positives = 27/48 (56%), Gaps = 4/48 (8%)

Query: 111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS-NSSCPKCRHCL 157
           EC ICL +F       +L  C H F   CIDKWL+S  ++CP CR  +
Sbjct: 1   ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 49.4 bits (118), Expect = 2e-07
 Identities = 21/56 (37%), Positives = 27/56 (48%), Gaps = 16/56 (28%)

Query: 109 DNECVICLSDFAPGERVR----------ILPKCNHGFHVRCIDKWLRSNSSCPKCR 154
           D EC IC+      E+V           IL  CNH F + CID W +  ++CP CR
Sbjct: 174 DKECAICM------EKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCR 223

Length = 238

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

 Score = 47.4 bits (112), Expect = 2e-06
 Identities = 22/76 (28%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 84   TGIKKKALKAFTIVKYSGELKLPGLDNECVICLSDFAPGERV---RILPKCNHGFHVRCI 140
                   +    + K + + K  G + EC IC S     +R    +    C + FH RC+
Sbjct: 1445 IKKNGSFMDLLGLWKKNIDEKFSGHE-ECAICYSVLDMVDRSLPSKRCATCKNKFHTRCL 1503

Query: 141  DKWLRS--NSSCPKCR 154
             KW  S   S+CP CR
Sbjct: 1504 YKWFASSARSNCPLCR 1519

Length = 1525

>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 = 43.7 bits (103), Expect = 2e-06
 Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 108 LDNECVICLSDFAPGERVRIL-PKCNHGFHVRCIDKWLRSNSSCPKCR 154
           +   C  C     PG+   ++   CNH FH  CI +WL +   CP  R
Sbjct: 30  IMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDR 77

Length = 88

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

 Score = 42.5 bits (100), Expect = 3e-06
 Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 3/47 (6%)

Query: 109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRH 155
           + EC ICL          +L  C H F   CI ++L+  S CP CR 
Sbjct: 2   ELECPICLDLLR---DPVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 39.8 bits (93), Expect = 2e-05
 Identities = 20/43 (46%), Positives = 25/43 (58%), Gaps = 4/43 (9%)

Query: 112 CVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS-NSSCPKC 153
           C ICL ++   +   ILP C H F   CI KWL S N++CP C
Sbjct: 1   CPICLEEYL--KDPVILP-CGHTFCRSCIRKWLESGNNTCPIC 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|193335 pfam12861, zf-Apc11, Anaphase-promoting complex subunit 11 RING-H2 finger

 Score = 39.0 bits (91), Expect = 1e-04
 Identities = 22/58 (37%), Positives = 28/58 (48%), Gaps = 12/58 (20%)

Query: 109 DNECVICLSDF--------APGERVRI-LPKCNHGFHVRCIDKWLRSNSS---CPKCR 154
           D+ C IC   F         PG+   +   KC H FH+ CI KWL + +S   CP CR
Sbjct: 21  DDVCGICRVSFDGTCPQCKFPGDDCPLVWGKCKHNFHMHCILKWLATETSKGLCPMCR 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|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]

 Score = 40.3 bits (94), Expect = 4e-04
 Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 9/81 (11%)

Query: 109 DNECVICL-----SDFAPGER-VRILPK---CNHGFHVRCIDKWLRSNSSCPKCRHCLIE 159
           D  C IC+      D  P  R + + PK   C H  H+ C+  WL    +CP CR  +I 
Sbjct: 287 DRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVIF 346

Query: 160 SCKKIEGSTQPSSLSGISTPV 180
                  ++     + I+T V
Sbjct: 347 DQSSPTPASPNVRNTQIATQV 367

Length = 491

>gnl|CDD|204746 pfam11793, FANCL_C, FANCL C-terminal domain

 Score = 36.2 bits (84), Expect = 9e-04
 Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 4/55 (7%)

Query: 111 ECVICLSDFAPGERVRIL----PKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESC 161
           EC IC +    G  +  +    PKC   FH+ C+ +WLR+     +  +    +C
Sbjct: 4   ECGICYAYRLDGGEIPDISCDNPKCGLPFHIACLYEWLRTLRDSRQSFNVSFGTC 58

This domain is found at the C-terminus of the Fancl protein in humans which is the putative E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2. Length = 70

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

 Score = 34.8 bits (80), Expect = 0.001
 Identities = 19/43 (44%), Positives = 23/43 (53%), Gaps = 4/43 (9%)

Query: 112 CVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS-SCPKC 153
           C ICL +      V ILP C H F  +CI  WL S + +CP C
Sbjct: 1   CPICLEEPKDP--VTILP-CGHLFCSKCILSWLESGNVTCPLC 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|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

 Score = 37.0 bits (85), Expect = 0.004
 Identities = 17/52 (32%), Positives = 21/52 (40%), Gaps = 6/52 (11%)

Query: 105 LPGLDN--ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCR 154
           L GLD+   C IC         +     C H F   CI + L +   CP CR
Sbjct: 19  LKGLDSMLRCRICDCRI----SIPCETTCGHTFCSLCIRRHLGTQPFCPVCR 66

Length = 391

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	203
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.85
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.65
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.44
PHA02929	238	N1R/p28-like protein; Provisional	99.43
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.41
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.37
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.17
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.17
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.17
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.13
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.13
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.11
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.1
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.09
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.03
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	98.98
PHA02926	242	zinc finger-like protein; Provisional	98.94
PF14634	44	zf-RING_5: zinc-RING finger domain	98.9
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.85
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.84
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.82
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.79
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.78
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.72
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.68
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.63
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.6
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.58
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.46
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.43
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.38
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.35
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.34
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.32
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.21
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.17
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.07
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.07
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.06
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.01
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.92
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	97.91
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.85
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.79
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.75
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.7
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	97.61
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.57
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.49
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.49
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.41
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	97.37
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.37
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.33
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.22
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.04
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.02
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	96.98
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	96.94
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	96.78
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	96.69
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	96.67
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.6
PHA02862	156	5L protein; Provisional	96.5
PHA02825	162	LAP/PHD finger-like protein; Provisional	96.4
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	96.08
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	96.06
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	96.03
COG5152	259	Uncharacterized conserved protein, contains RING a	96.03
KOG2660	331	consensus Locus-specific chromosome binding protei	96.01
PHA03096	284	p28-like protein; Provisional	95.98
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	95.93
KOG3039	303	consensus Uncharacterized conserved protein [Funct	95.89
KOG1002	791	consensus Nucleotide excision repair protein RAD16	95.81
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	95.76
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	95.74
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	95.63
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	95.17
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	95.15
KOG4739	233	consensus Uncharacterized protein involved in syna	95.13
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	94.81
COG5236	493	Uncharacterized conserved protein, contains RING Z	94.65
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	94.27
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	93.96
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	93.86
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	93.81
COG5222	427	Uncharacterized conserved protein, contains RING Z	93.66
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	93.61
PF02439	38	Adeno_E3_CR2: Adenovirus E3 region protein CR2; In	93.56
PF04641	260	Rtf2: Rtf2 RING-finger	93.38
KOG1001	674	consensus Helicase-like transcription factor HLTF/	93.17
KOG0298	1394	consensus DEAD box-containing helicase-like transc	93.02
COG5175	480	MOT2 Transcriptional repressor [Transcription]	92.93
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	92.88
KOG1940	276	consensus Zn-finger protein [General function pred	92.45
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	92.31
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	92.3
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	91.5
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	91.0
PF01102	122	Glycophorin_A: Glycophorin A; InterPro: IPR001195	90.22
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	90.12
PF15050	133	SCIMP: SCIMP protein	89.96
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	89.39
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	88.62
KOG1829	580	consensus Uncharacterized conserved protein, conta	88.56
KOG3002	299	consensus Zn finger protein [General function pred	88.53
KOG3053	293	consensus Uncharacterized conserved protein [Funct	88.03
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	87.93
KOG0269	839	consensus WD40 repeat-containing protein [Function	87.88
KOG1609	323	consensus Protein involved in mRNA turnover and st	87.88
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	87.71
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	87.26
PF01708	91	Gemini_mov: Geminivirus putative movement protein	86.27
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	86.17
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	85.93
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	85.62
KOG3899	381	consensus Uncharacterized conserved protein [Funct	85.59
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	85.01
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	84.9
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	84.14
PF08374	221	Protocadherin: Protocadherin; InterPro: IPR013585	84.02
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	83.29
KOG0825	1134	consensus PHD Zn-finger protein [General function	82.78
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	81.39

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

Probab=99.85  E-value=3.4e-21  Score=164.46  Aligned_cols=81  Identities=33%  Similarity=0.811  Sum_probs=68.4

Q ss_pred             hhhcCCCHHHHhhcCeEEccCCCCCCCCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCC-Cccccccccc
Q 042698           81 LAKTGIKKKALKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSS-CPKCRHCLIE  159 (203)
Q Consensus        81 ~~~~~~~~~~~~~lp~~~~~~~~~~~~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~-CP~CR~~l~~  159 (203)
                      .....+.++.++++|...|......... .+|+||||+|+++|+++.|| |+|.||..||+.||..+++ ||+||+++..
T Consensus       202 ~~~~r~~k~~l~~~p~~~f~~~~~~~~~-~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~~  279 (348)
T KOG4628|consen  202 LRRNRLIKRLLKKLPVRTFTKGDDEDAT-DTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIRT  279 (348)
T ss_pred             hhhhhhHHHHHhhCCcEEeccccccCCC-ceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence            3466788999999999999886554433 68999999999999999999 9999999999999977654 9999998775


Q ss_pred             cccc
Q 042698          160 SCKK  163 (203)
Q Consensus       160 ~~~~  163 (203)
                      ....
T Consensus       280 ~~~~  283 (348)
T KOG4628|consen  280 DSGS  283 (348)
T ss_pred             CCCC
Confidence            5433

>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=99.65  E-value=5.9e-17  Score=99.68  Aligned_cols=44  Identities=57%  Similarity=1.300  Sum_probs=40.4

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCR  154 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR  154 (203)
                      ++|+||+++|..++.+..++ |+|.||.+||..|++.+.+||+||
T Consensus         1 d~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~~~~CP~CR   44 (44)
T PF13639_consen    1 DECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKRNNSCPVCR   44 (44)
T ss_dssp             -CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred             CCCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHhCCcCCccC
Confidence            37999999999999999999 999999999999999999999998

...

>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=99.44  E-value=8.4e-14  Score=94.77  Aligned_cols=45  Identities=40%  Similarity=1.004  Sum_probs=35.7

Q ss_pred             CCcCccccCcccCC----------CceeecCCCCccccHhhHHHHHhcCCCCcccc
Q 042698          109 DNECVICLSDFAPG----------ERVRILPKCNHGFHVRCIDKWLRSNSSCPKCR  154 (203)
Q Consensus       109 ~~~CaICl~~~~~~----------~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR  154 (203)
                      ++.|+||++++.+.          -.+...+ |||.||..||.+|++.+.+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGP-CGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEET-TSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecc-cCCCEEHHHHHHHHhcCCcCCCCC
Confidence            45699999999422          2344455 999999999999999999999998

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 ....

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.43  E-value=1.2e-13  Score=113.43  Aligned_cols=75  Identities=36%  Similarity=0.619  Sum_probs=55.9

Q ss_pred             cCCCHHHHhhcCeEEccCCCC-CCCCCCcCccccCcccCCC----ceeecCCCCccccHhhHHHHHhcCCCCcccccccc
Q 042698           84 TGIKKKALKAFTIVKYSGELK-LPGLDNECVICLSDFAPGE----RVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  158 (203)
Q Consensus        84 ~~~~~~~~~~lp~~~~~~~~~-~~~~~~~CaICl~~~~~~~----~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  158 (203)
                      .+..+..++.+|.+....... ....+.+|+||++++..++    .+.+++.|+|.||..||..|++.+.+||+||..+.
T Consensus       148 ~~~~~~~i~~lp~vl~~~e~~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~  227 (238)
T PHA02929        148 GKNYKKFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI  227 (238)
T ss_pred             cchhHHHHHhcchhhhhhhhhhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence            455677788888886553221 2234578999999987653    12344459999999999999999999999999776

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

Probab=99.41  E-value=1e-13  Score=115.29  Aligned_cols=51  Identities=47%  Similarity=1.138  Sum_probs=46.6

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHh-cCCCCccccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR-SNSSCPKCRHCLIE  159 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~l~~  159 (203)
                      .+.+|+|||+.|..+|+++++| |+|.||..|++.|+. .+..||+||..+++
T Consensus       322 ~GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         322 KGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            3478999999999999999999 999999999999997 56679999999876

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

Probab=99.37  E-value=3.1e-12  Score=109.13  Aligned_cols=55  Identities=31%  Similarity=0.826  Sum_probs=44.8

Q ss_pred             CCCCCcCccccCcccCCC----------ceeecCCCCccccHhhHHHHHhcCCCCccccccccccc
Q 042698          106 PGLDNECVICLSDFAPGE----------RVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESC  161 (203)
Q Consensus       106 ~~~~~~CaICl~~~~~~~----------~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  161 (203)
                      ..+|..|.||+|++-+.+          +-+.+| |||+||-+|+..|+.++++||+||.++.-..
T Consensus       284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~ifd~  348 (491)
T COG5243         284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPVIFDQ  348 (491)
T ss_pred             cCCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCcccccc
Confidence            346789999999954332          346788 9999999999999999999999999965443

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

Probab=99.17  E-value=3.5e-11  Score=97.11  Aligned_cols=76  Identities=22%  Similarity=0.339  Sum_probs=53.1

Q ss_pred             CCCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC---CCcccccccccccccccCCCCCCCCC------CC
Q 042698          106 PGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS---SCPKCRHCLIESCKKIEGSTQPSSLS------GI  176 (203)
Q Consensus       106 ~~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~---~CP~CR~~l~~~~~~~~~~~~~~~~~------~~  176 (203)
                      .....+|-||||.-+++  |. +. |||.||+.||.+|++.+.   .||+||..+....--..++......+      -+
T Consensus        44 ~~~~FdCNICLd~akdP--Vv-Tl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvPlYGrG~~~~~~~~~~~vP  119 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKDP--VV-TL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVPLYGRGSKKPSDPRKKDVP  119 (230)
T ss_pred             CCCceeeeeeccccCCC--EE-ee-cccceehHHHHHHHhhcCCCeeCCccccccccceEEeeeccCCCCCCCcccccCC
Confidence            35567899999996654  44 43 999999999999997543   59999998887765555555332222      35


Q ss_pred             CCCcccccc
Q 042698          177 STPVQETVV  185 (203)
Q Consensus       177 ~~~~~~~~~  185 (203)
                      .+|++...-
T Consensus       120 ~RP~~~R~e  128 (230)
T KOG0823|consen  120 PRPAGQRYE  128 (230)
T ss_pred             CCCCCcccc
Confidence            556554443

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.17  E-value=7.3e-11  Score=93.59  Aligned_cols=51  Identities=33%  Similarity=0.722  Sum_probs=40.9

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc----------------CCCCccccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS----------------NSSCPKCRHCLIESC  161 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~----------------~~~CP~CR~~l~~~~  161 (203)
                      +.+.+|+||++.+++.   .+++ |||.||+.||..|+..                +..||+||..+....
T Consensus        16 ~~~~~CpICld~~~dP---VvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~   82 (193)
T PLN03208         16 GGDFDCNICLDQVRDP---VVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT   82 (193)
T ss_pred             CCccCCccCCCcCCCc---EEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence            3457899999998764   4566 9999999999999842                246999999887644

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

Probab=99.17  E-value=1.6e-11  Score=101.83  Aligned_cols=52  Identities=31%  Similarity=0.722  Sum_probs=44.9

Q ss_pred             CCCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccccccccc
Q 042698          106 PGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESC  161 (203)
Q Consensus       106 ~~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  161 (203)
                      ......|.+||+..+++   ..+| |||+||+.||..|...+..||+||....+..
T Consensus       236 ~~a~~kC~LCLe~~~~p---SaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~psk  287 (293)
T KOG0317|consen  236 PEATRKCSLCLENRSNP---SATP-CGHIFCWSCILEWCSEKAECPLCREKFQPSK  287 (293)
T ss_pred             CCCCCceEEEecCCCCC---CcCc-CcchHHHHHHHHHHccccCCCcccccCCCcc
Confidence            34557899999998775   6777 9999999999999999999999999887653

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

Probab=99.13  E-value=3.3e-11  Score=110.58  Aligned_cols=54  Identities=35%  Similarity=0.925  Sum_probs=46.4

Q ss_pred             CCCcCccccCcccCCCc--eeecCCCCccccHhhHHHHHhcCCCCcccccccccccc
Q 042698          108 LDNECVICLSDFAPGER--VRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCK  162 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~--v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~  162 (203)
                      .+..|+||+|++...+.  .+.++ |+|+||..|+..|++++++||+||..+.....
T Consensus       290 ~~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~~~~~~~  345 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTVLYDYVL  345 (543)
T ss_pred             cCCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhhhhcccc
Confidence            46789999999988655  67788 99999999999999999999999995555443

>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=99.13  E-value=5.3e-11  Score=72.14  Aligned_cols=44  Identities=55%  Similarity=1.215  Sum_probs=36.7

Q ss_pred             cCccccCcccCCCceeecCCCCccccHhhHHHHHhc-CCCCccccccc
Q 042698          111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS-NSSCPKCRHCL  157 (203)
Q Consensus       111 ~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l  157 (203)
                      +|+||++.+  .+.+...+ |+|.||..|+..|++. +..||+||..+
T Consensus         1 ~C~iC~~~~--~~~~~~~~-C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEF--REPVVLLP-CGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhh--hCceEecC-CCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            599999998  33455666 9999999999999987 67799999764

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

Probab=99.11  E-value=5e-11  Score=82.37  Aligned_cols=52  Identities=40%  Similarity=0.894  Sum_probs=39.2

Q ss_pred             CCCcCccccCccc--------CCCc-eeecCCCCccccHhhHHHHHhc---CCCCccccccccc
Q 042698          108 LDNECVICLSDFA--------PGER-VRILPKCNHGFHVRCIDKWLRS---NSSCPKCRHCLIE  159 (203)
Q Consensus       108 ~~~~CaICl~~~~--------~~~~-v~~l~~C~H~FH~~Ci~~Wl~~---~~~CP~CR~~l~~  159 (203)
                      .++.|.||+..|.        +++. -.+...|+|.||..||..|+..   +..||+||+...-
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            3678999999987        2222 2234459999999999999975   4579999997653

>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=99.10  E-value=8.3e-11  Score=74.07  Aligned_cols=46  Identities=37%  Similarity=0.880  Sum_probs=38.9

Q ss_pred             CCcCccccCcccCCCceeecCCCCcc-ccHhhHHHHHhcCCCCcccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHG-FHVRCIDKWLRSNSSCPKCRHCLI  158 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~  158 (203)
                      +..|.||++....   +..+| |||. |+..|+..|++.+..||+||+.+.
T Consensus         2 ~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPRD---VVLLP-CGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBSS---EEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCCc---eEEeC-CCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            4679999998654   67778 9999 999999999999999999999875

...

>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=99.09  E-value=8.4e-11  Score=70.24  Aligned_cols=39  Identities=44%  Similarity=1.100  Sum_probs=32.9

Q ss_pred             CccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccc
Q 042698          112 CVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKC  153 (203)
Q Consensus       112 CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~C  153 (203)
                      |+||++.+.+  .+..++ |||.|+.+|+..|++.+..||+|
T Consensus         1 C~iC~~~~~~--~~~~~~-CGH~fC~~C~~~~~~~~~~CP~C   39 (39)
T PF13923_consen    1 CPICLDELRD--PVVVTP-CGHSFCKECIEKYLEKNPKCPVC   39 (39)
T ss_dssp             ETTTTSB-SS--EEEECT-TSEEEEHHHHHHHHHCTSB-TTT
T ss_pred             CCCCCCcccC--cCEECC-CCCchhHHHHHHHHHCcCCCcCC
Confidence            8999999877  456777 99999999999999998899998

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

Probab=99.03  E-value=1.6e-10  Score=89.80  Aligned_cols=54  Identities=28%  Similarity=0.600  Sum_probs=44.2

Q ss_pred             CCCCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          105 LPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       105 ~~~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      .+..-..|+|||+.+.+...+ .+. |||+|++.||..-++....||+||..|..+
T Consensus       127 ~~~~~~~CPiCl~~~sek~~v-sTk-CGHvFC~~Cik~alk~~~~CP~C~kkIt~k  180 (187)
T KOG0320|consen  127 RKEGTYKCPICLDSVSEKVPV-STK-CGHVFCSQCIKDALKNTNKCPTCRKKITHK  180 (187)
T ss_pred             ccccccCCCceecchhhcccc-ccc-cchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence            344457899999999876433 244 999999999999999999999999988765

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

Probab=98.98  E-value=2.5e-10  Score=77.14  Aligned_cols=51  Identities=33%  Similarity=0.840  Sum_probs=38.7

Q ss_pred             CcCccccCccc-----------CCCce-eecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          110 NECVICLSDFA-----------PGERV-RILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       110 ~~CaICl~~~~-----------~~~~v-~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      +.|+||...|.           ++++. ..-..|+|.||..||.+||..+..||++|+...-.
T Consensus        21 d~CaICRnhim~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~   83 (88)
T COG5194          21 DVCAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLA   83 (88)
T ss_pred             chhhhhhccccCcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEe
Confidence            56888877763           33322 23334999999999999999999999999877644

>PHA02926 zinc finger-like protein; Provisional

Probab=98.94  E-value=6e-10  Score=89.62  Aligned_cols=51  Identities=33%  Similarity=0.775  Sum_probs=38.3

Q ss_pred             CCCcCccccCcccCC-----CceeecCCCCccccHhhHHHHHhcC------CCCcccccccc
Q 042698          108 LDNECVICLSDFAPG-----ERVRILPKCNHGFHVRCIDKWLRSN------SSCPKCRHCLI  158 (203)
Q Consensus       108 ~~~~CaICl~~~~~~-----~~v~~l~~C~H~FH~~Ci~~Wl~~~------~~CP~CR~~l~  158 (203)
                      .+.+|+||+|..-+.     ..-.+++.|+|.||..||..|.+.+      .+||+||..+.
T Consensus       169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            347899999986432     1223565699999999999999753      35999998654

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.90  E-value=1.3e-09  Score=66.77  Aligned_cols=44  Identities=32%  Similarity=0.838  Sum_probs=37.9

Q ss_pred             cCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccc
Q 042698          111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRH  155 (203)
Q Consensus       111 ~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~  155 (203)
                      .|.||+++|.+.....+++ |||+|+..|+..+......||+||+
T Consensus         1 ~C~~C~~~~~~~~~~~l~~-CgH~~C~~C~~~~~~~~~~CP~C~k   44 (44)
T PF14634_consen    1 HCNICFEKYSEERRPRLTS-CGHIFCEKCLKKLKGKSVKCPICRK   44 (44)
T ss_pred             CCcCcCccccCCCCeEEcc-cCCHHHHHHHHhhcCCCCCCcCCCC
Confidence            4999999996666778887 9999999999998856678999984

>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=98.85  E-value=1.7e-09  Score=65.05  Aligned_cols=39  Identities=46%  Similarity=1.154  Sum_probs=33.2

Q ss_pred             CccccCcccCCCceeecCCCCccccHhhHHHHHh--cCCCCccc
Q 042698          112 CVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR--SNSSCPKC  153 (203)
Q Consensus       112 CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~--~~~~CP~C  153 (203)
                      |+||++.+...  +..++ |+|.|+..||..|++  ....||+|
T Consensus         1 C~iC~~~~~~~--~~~~~-C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDP--VILLP-CGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSE--EEETT-TSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCC--CEEec-CCCcchHHHHHHHHHhcCCccCCcC
Confidence            89999998775  35777 999999999999998  45569998

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 ....

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

Probab=98.84  E-value=4.1e-09  Score=93.09  Aligned_cols=50  Identities=36%  Similarity=0.856  Sum_probs=38.9

Q ss_pred             CCcCccccCcccC---C-------Cc----eeecCCCCccccHhhHHHHHh-cCCCCccccccccc
Q 042698          109 DNECVICLSDFAP---G-------ER----VRILPKCNHGFHVRCIDKWLR-SNSSCPKCRHCLIE  159 (203)
Q Consensus       109 ~~~CaICl~~~~~---~-------~~----v~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~l~~  159 (203)
                      ...|+||+.++.-   +       +.    -..+| |+|+||..|+..|+. .+-.||+||..+++
T Consensus       571 t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tP-C~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  571 TNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTP-CHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             cccceEeccccceeeccCcchhhhhhhhccccccc-hHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            3579999998751   1       11    23467 999999999999998 55589999998865

>smart00184 RING Ring finger

Probab=98.82  E-value=3.7e-09  Score=61.68  Aligned_cols=38  Identities=47%  Similarity=1.232  Sum_probs=31.8

Q ss_pred             CccccCcccCCCceeecCCCCccccHhhHHHHHh-cCCCCccc
Q 042698          112 CVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR-SNSSCPKC  153 (203)
Q Consensus       112 CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~C  153 (203)
                      |+||++..   .....++ |+|.||..|+..|++ .+..||+|
T Consensus         1 C~iC~~~~---~~~~~~~-C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEEL---KDPVVLP-CGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCC---CCcEEec-CCChHHHHHHHHHHHhCcCCCCCC
Confidence            78999883   3456777 999999999999998 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)

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

Probab=98.79  E-value=3.5e-09  Score=64.24  Aligned_cols=38  Identities=39%  Similarity=0.974  Sum_probs=29.2

Q ss_pred             CccccCcccCCCceeecCCCCccccHhhHHHHHhcC----CCCccc
Q 042698          112 CVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN----SSCPKC  153 (203)
Q Consensus       112 CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~----~~CP~C  153 (203)
                      |+||++-|.++   ..++ |||.|+..||..|++..    ..||.|
T Consensus         1 CpiC~~~~~~P---v~l~-CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDP---VSLP-CGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSE---EE-S-SSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCc---cccC-CcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999886   6677 99999999999999653    359987

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

Probab=98.78  E-value=1.1e-09  Score=73.41  Aligned_cols=50  Identities=40%  Similarity=0.907  Sum_probs=37.4

Q ss_pred             CCcCccccCccc--------CCC-ceeecCCCCccccHhhHHHHHhcC---CCCcccccccc
Q 042698          109 DNECVICLSDFA--------PGE-RVRILPKCNHGFHVRCIDKWLRSN---SSCPKCRHCLI  158 (203)
Q Consensus       109 ~~~CaICl~~~~--------~~~-~v~~l~~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~l~  158 (203)
                      +++|.||.-+|.        ++| --.++..|.|.||..||..|+..+   ..||+||+...
T Consensus        20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            458999999986        223 222344599999999999999643   45999998764

>smart00504 Ubox Modified RING finger domain

Probab=98.72  E-value=1.6e-08  Score=66.26  Aligned_cols=45  Identities=31%  Similarity=0.482  Sum_probs=39.2

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  158 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  158 (203)
                      ..|+||++.+.++   .+++ |||+|...||..|++.+..||+|+..+.
T Consensus         2 ~~Cpi~~~~~~~P---v~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~   46 (63)
T smart00504        2 FLCPISLEVMKDP---VILP-SGQTYERRAIEKWLLSHGTDPVTGQPLT   46 (63)
T ss_pred             cCCcCCCCcCCCC---EECC-CCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence            3699999999875   4566 9999999999999998889999998774

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

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

Probab=98.68  E-value=5.9e-09  Score=73.87  Aligned_cols=49  Identities=31%  Similarity=0.780  Sum_probs=37.5

Q ss_pred             CcCccccCccc-------------CCCceeecCCCCccccHhhHHHHHhcCCCCcccccccc
Q 042698          110 NECVICLSDFA-------------PGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  158 (203)
Q Consensus       110 ~~CaICl~~~~-------------~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  158 (203)
                      +.|+||...+-             .++-...-..|+|.||..||.+||+++..||+|.++..
T Consensus        47 DnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~  108 (114)
T KOG2930|consen   47 DNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWV  108 (114)
T ss_pred             chhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCccee
Confidence            57999987752             12223334459999999999999999999999977644

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

Probab=98.63  E-value=7.5e-09  Score=85.26  Aligned_cols=51  Identities=29%  Similarity=0.650  Sum_probs=41.6

Q ss_pred             CCCCcCccccCcccCCC-------ceeecCCCCccccHhhHHHHH--hcCCCCcccccccc
Q 042698          107 GLDNECVICLSDFAPGE-------RVRILPKCNHGFHVRCIDKWL--RSNSSCPKCRHCLI  158 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~-------~v~~l~~C~H~FH~~Ci~~Wl--~~~~~CP~CR~~l~  158 (203)
                      .++..|+||-..+....       ....+. |+|+||..||.-|-  .++++||.|+..+.
T Consensus       222 l~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVd  281 (328)
T KOG1734|consen  222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVD  281 (328)
T ss_pred             CCcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhh
Confidence            45678999998876543       566787 99999999999995  57789999987654

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.60  E-value=2.9e-08  Score=87.30  Aligned_cols=48  Identities=29%  Similarity=0.590  Sum_probs=40.9

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  158 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  158 (203)
                      +....|+||++.|...   .+++ |+|.||..||..|+.....||+||..+.
T Consensus        24 e~~l~C~IC~d~~~~P---vitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~   71 (397)
T TIGR00599        24 DTSLRCHICKDFFDVP---VLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQ   71 (397)
T ss_pred             ccccCCCcCchhhhCc---cCCC-CCCchhHHHHHHHHhCCCCCCCCCCccc
Confidence            3456899999999765   3567 9999999999999998888999998665

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

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

Probab=98.58  E-value=2.6e-08  Score=82.01  Aligned_cols=51  Identities=27%  Similarity=0.659  Sum_probs=41.6

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHH-HHhcCCC-Cccccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDK-WLRSNSS-CPKCRHCLIESC  161 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~-Wl~~~~~-CP~CR~~l~~~~  161 (203)
                      ..+..|+||++.....   ..++ |||+|+..||.. |=+++.. ||+||+...+..
T Consensus       213 ~~d~kC~lC~e~~~~p---s~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~  265 (271)
T COG5574         213 LADYKCFLCLEEPEVP---SCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKK  265 (271)
T ss_pred             ccccceeeeecccCCc---cccc-ccchhhHHHHHHHHHhhccccCchhhhhccchh
Confidence            4467899999997664   5566 999999999999 8766554 999999887664

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

Probab=98.46  E-value=1.6e-07  Score=58.81  Aligned_cols=42  Identities=24%  Similarity=0.772  Sum_probs=31.7

Q ss_pred             cCccccCcccCCCceeecCCCC-----ccccHhhHHHHHhcC--CCCcccc
Q 042698          111 ECVICLSDFAPGERVRILPKCN-----HGFHVRCIDKWLRSN--SSCPKCR  154 (203)
Q Consensus       111 ~CaICl~~~~~~~~v~~l~~C~-----H~FH~~Ci~~Wl~~~--~~CP~CR  154 (203)
                      .|.||++...+ +...+.| |.     |.+|..|+..|+..+  .+||+|+
T Consensus         1 ~CrIC~~~~~~-~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHDEGDE-GDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCCCCCC-CCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            48999994334 3444677 74     999999999999544  4799995

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

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

Probab=98.43  E-value=1.2e-07  Score=84.40  Aligned_cols=49  Identities=31%  Similarity=0.558  Sum_probs=38.9

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC-----CCCccccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN-----SSCPKCRHCLIESC  161 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~-----~~CP~CR~~l~~~~  161 (203)
                      +..|+|||++...+   ..+. |||+||..||..++...     ..||+||..|...+
T Consensus       186 ~~~CPICL~~~~~p---~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kd  239 (513)
T KOG2164|consen  186 DMQCPICLEPPSVP---VRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKD  239 (513)
T ss_pred             CCcCCcccCCCCcc---cccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhccccc
Confidence            57899999996654   2333 99999999999998543     46999999888744

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

Probab=98.38  E-value=6.5e-08  Score=91.15  Aligned_cols=52  Identities=35%  Similarity=0.789  Sum_probs=39.5

Q ss_pred             CCCCcCccccCcccC-CC--ceeecCCCCccccHhhHHHHHhcC--CCCcccccccc
Q 042698          107 GLDNECVICLSDFAP-GE--RVRILPKCNHGFHVRCIDKWLRSN--SSCPKCRHCLI  158 (203)
Q Consensus       107 ~~~~~CaICl~~~~~-~~--~v~~l~~C~H~FH~~Ci~~Wl~~~--~~CP~CR~~l~  158 (203)
                      ...++||||..-... +.  .-..+++|+|-||..|+..|++..  .+||+||.+++
T Consensus      1467 sG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219        1467 SGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred             CCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence            446789999887651 11  224566799999999999999754  46999998775

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

Probab=98.35  E-value=3.7e-07  Score=55.54  Aligned_cols=34  Identities=35%  Similarity=0.806  Sum_probs=21.3

Q ss_pred             CccccCcccCCC-ceeecCCCCccccHhhHHHHHhcC
Q 042698          112 CVICLSDFAPGE-RVRILPKCNHGFHVRCIDKWLRSN  147 (203)
Q Consensus       112 CaICl~~~~~~~-~v~~l~~C~H~FH~~Ci~~Wl~~~  147 (203)
                      |+||.+ |..++ .-.+|+ |||+|..+||+.++++.
T Consensus         1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~   35 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKS   35 (43)
T ss_dssp             -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-
T ss_pred             CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcC
Confidence            899999 76544 456788 99999999999999743

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

Probab=98.34  E-value=1.3e-07  Score=63.71  Aligned_cols=50  Identities=30%  Similarity=0.668  Sum_probs=24.2

Q ss_pred             CcCccccCcccCCC--ceeecC--CCCccccHhhHHHHHhc----C-------CCCccccccccc
Q 042698          110 NECVICLSDFAPGE--RVRILP--KCNHGFHVRCIDKWLRS----N-------SSCPKCRHCLIE  159 (203)
Q Consensus       110 ~~CaICl~~~~~~~--~v~~l~--~C~H~FH~~Ci~~Wl~~----~-------~~CP~CR~~l~~  159 (203)
                      .+|.||.+.+..++  ...+.+  .|++.||..||..||+.    +       ..||.|+..|.-
T Consensus         3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~   67 (70)
T PF11793_consen    3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW   67 (70)
T ss_dssp             -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred             CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence            57999999876333  233443  69999999999999962    1       139999988753

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

Probab=98.32  E-value=2e-07  Score=81.73  Aligned_cols=49  Identities=37%  Similarity=0.864  Sum_probs=39.7

Q ss_pred             CCCCcCccccCcccCCC-ceeecCCCCccccHhhHHHHHhcCCCCcccccccc
Q 042698          107 GLDNECVICLSDFAPGE-RVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  158 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~-~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  158 (203)
                      -+.++|+||||.+...- .++... |+|.||..|+..|  ...+||+||....
T Consensus       173 tELPTCpVCLERMD~s~~gi~t~~-c~Hsfh~~cl~~w--~~~scpvcR~~q~  222 (493)
T KOG0804|consen  173 TELPTCPVCLERMDSSTTGILTIL-CNHSFHCSCLMKW--WDSSCPVCRYCQS  222 (493)
T ss_pred             ccCCCcchhHhhcCccccceeeee-cccccchHHHhhc--ccCcChhhhhhcC
Confidence            34578999999997654 455555 9999999999999  5668999998766

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

Probab=98.21  E-value=5.9e-07  Score=77.59  Aligned_cols=48  Identities=35%  Similarity=0.859  Sum_probs=35.7

Q ss_pred             CcCccccCcccCC-CceeecCCCCccccHhhHHHHHhc---CCCCcccccccc
Q 042698          110 NECVICLSDFAPG-ERVRILPKCNHGFHVRCIDKWLRS---NSSCPKCRHCLI  158 (203)
Q Consensus       110 ~~CaICl~~~~~~-~~v~~l~~C~H~FH~~Ci~~Wl~~---~~~CP~CR~~l~  158 (203)
                      ..|.|| .++.+. ..+.-..+|||+||..|+..|+..   +++||+||-.+.
T Consensus         5 A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~   56 (465)
T KOG0827|consen    5 AECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQ   56 (465)
T ss_pred             ceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeeccc
Confidence            579999 555544 345444469999999999999975   357999994443

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.17  E-value=1.7e-06  Score=73.58  Aligned_cols=52  Identities=25%  Similarity=0.632  Sum_probs=37.7

Q ss_pred             CCcCccccCc-ccCCC-ceeecCCCCccccHhhHHHHH-hcCCCCccccccccccc
Q 042698          109 DNECVICLSD-FAPGE-RVRILPKCNHGFHVRCIDKWL-RSNSSCPKCRHCLIESC  161 (203)
Q Consensus       109 ~~~CaICl~~-~~~~~-~v~~l~~C~H~FH~~Ci~~Wl-~~~~~CP~CR~~l~~~~  161 (203)
                      +..|++|... |..++ .+.+.+ |||.||..||+..+ .....||.|+..+....
T Consensus         3 ~~~CP~Ck~~~y~np~~kl~i~~-CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~   57 (309)
T TIGR00570         3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGSGSCPECDTPLRKNN   57 (309)
T ss_pred             CCCCCcCCCCCccCcccccccCC-CCCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence            3579999996 33443 233335 99999999999966 44557999998776553

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).

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

Probab=98.07  E-value=3.2e-06  Score=57.29  Aligned_cols=48  Identities=29%  Similarity=0.454  Sum_probs=36.6

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc-CCCCcccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~  160 (203)
                      ...|+|+.+-|.++   .+++ +||.|-+.||..|++. +..||+|+..+...
T Consensus         4 ~f~CpIt~~lM~dP---Vi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~   52 (73)
T PF04564_consen    4 EFLCPITGELMRDP---VILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSES   52 (73)
T ss_dssp             GGB-TTTSSB-SSE---EEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SGG
T ss_pred             ccCCcCcCcHhhCc---eeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCcc
Confidence            45799999999886   4567 9999999999999988 77899999887654

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 ....

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

Probab=98.07  E-value=1.3e-06  Score=74.38  Aligned_cols=48  Identities=38%  Similarity=0.734  Sum_probs=41.9

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      -..|-||.+=|..+   ..+| |+|.||.-||..+|..+..||.|+..+.+.
T Consensus        23 lLRC~IC~eyf~ip---~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~Es   70 (442)
T KOG0287|consen   23 LLRCGICFEYFNIP---MITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVTES   70 (442)
T ss_pred             HHHHhHHHHHhcCc---eecc-ccchHHHHHHHHHhccCCCCCceecccchh
Confidence            35799999998876   5677 999999999999999999999999877654

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

Probab=98.06  E-value=2e-06  Score=71.91  Aligned_cols=49  Identities=31%  Similarity=0.527  Sum_probs=40.6

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      ....|-||-+-|..+   ..++ |||.||.-||...|..+..||+||.+.-+.
T Consensus        24 s~lrC~IC~~~i~ip---~~Tt-CgHtFCslCIR~hL~~qp~CP~Cr~~~~es   72 (391)
T COG5432          24 SMLRCRICDCRISIP---CETT-CGHTFCSLCIRRHLGTQPFCPVCREDPCES   72 (391)
T ss_pred             hHHHhhhhhheeecc---eecc-cccchhHHHHHHHhcCCCCCccccccHHhh
Confidence            345799998887764   3455 999999999999999999999999866544

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

Probab=98.01  E-value=2.2e-06  Score=71.22  Aligned_cols=43  Identities=37%  Similarity=0.838  Sum_probs=38.1

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCR  154 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR  154 (203)
                      ....|+||++.|...   .+++ |+|.|+..|+..++.....||.||
T Consensus        12 ~~~~C~iC~~~~~~p---~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr   54 (386)
T KOG2177|consen   12 EELTCPICLEYFREP---VLLP-CGHNFCRACLTRSWEGPLSCPVCR   54 (386)
T ss_pred             ccccChhhHHHhhcC---cccc-ccchHhHHHHHHhcCCCcCCcccC
Confidence            456899999999998   7788 999999999999988555799999

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

Probab=97.92  E-value=8e-06  Score=70.12  Aligned_cols=52  Identities=33%  Similarity=0.662  Sum_probs=41.6

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCcc-ccHhhHHHHHhcCCCCcccccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHG-FHVRCIDKWLRSNSSCPKCRHCLIESCK  162 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~  162 (203)
                      ++..+|.||+++-++   ..++| |.|. .|..|.+.-.-.+.+||+||+.+.+.-+
T Consensus       288 ~~gkeCVIClse~rd---t~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~ll~  340 (349)
T KOG4265|consen  288 ESGKECVICLSESRD---TVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIEELLE  340 (349)
T ss_pred             cCCCeeEEEecCCcc---eEEec-chhhehhHhHHHHHHHhhcCCCccccchHhhhe
Confidence            346789999999766   47899 9995 6788999865567789999999886643

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

Probab=97.91  E-value=7.6e-06  Score=71.27  Aligned_cols=49  Identities=31%  Similarity=0.781  Sum_probs=37.2

Q ss_pred             CCCcCccccCcccCC-CceeecCCCCccccHhhHHHHHhc--CCCCcccccc
Q 042698          108 LDNECVICLSDFAPG-ERVRILPKCNHGFHVRCIDKWLRS--NSSCPKCRHC  156 (203)
Q Consensus       108 ~~~~CaICl~~~~~~-~~v~~l~~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~  156 (203)
                      ...+|+|||+++... +...+.+.|+|.|-.+||+.|+.+  ...||.|...
T Consensus         3 ~g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~k   54 (463)
T KOG1645|consen    3 CGTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGK   54 (463)
T ss_pred             ccccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCCh
Confidence            346899999999743 444444469999999999999952  2359999753

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

Probab=97.85  E-value=6.9e-06  Score=68.97  Aligned_cols=52  Identities=31%  Similarity=0.784  Sum_probs=43.1

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHh-----------------------cCCCCccccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR-----------------------SNSSCPKCRHCLIESC  161 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~-----------------------~~~~CP~CR~~l~~~~  161 (203)
                      ...|+|||.-|...+...++. |.|.||..|+.++|.                       .+..||+||..|....
T Consensus       115 ~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~  189 (368)
T KOG4445|consen  115 NGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEE  189 (368)
T ss_pred             CCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccc
Confidence            457999999999999899998 999999999988874                       1124999998887543

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

Probab=97.79  E-value=2.7e-06  Score=72.81  Aligned_cols=57  Identities=35%  Similarity=0.581  Sum_probs=45.0

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc-CCCCcccccccccccccccC
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIESCKKIEG  166 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~~~~~~~  166 (203)
                      ..+..|+|||+-++..   +.++.|.|.|+.+||..-++. +..||.||..+........+
T Consensus        41 ~~~v~c~icl~llk~t---mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr~D   98 (381)
T KOG0311|consen   41 DIQVICPICLSLLKKT---MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLRID   98 (381)
T ss_pred             hhhhccHHHHHHHHhh---cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCCCC
Confidence            4467899999988775   455569999999999998865 56799999998876555433

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

Probab=97.75  E-value=1.4e-05  Score=64.68  Aligned_cols=53  Identities=25%  Similarity=0.718  Sum_probs=44.5

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc--------CCCCccccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS--------NSSCPKCRHCLIESC  161 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~--------~~~CP~CR~~l~~~~  161 (203)
                      +....|..|-..+..+|.+|..  |-|+||++|+++|-..        ...||.|...|++.-
T Consensus        48 DY~pNC~LC~t~La~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~  108 (299)
T KOG3970|consen   48 DYNPNCRLCNTPLASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPI  108 (299)
T ss_pred             CCCCCCceeCCccccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCc
Confidence            4567799999999999999876  9999999999999742        235999999988654

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

Probab=97.70  E-value=7.3e-06  Score=76.35  Aligned_cols=51  Identities=25%  Similarity=0.466  Sum_probs=40.6

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      ...|++|+..+.++......+ |+|.||..||+.|-+.-.+||+||..+...
T Consensus       123 ~~~CP~Ci~s~~DqL~~~~k~-c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~v  173 (1134)
T KOG0825|consen  123 ENQCPNCLKSCNDQLEESEKH-TAHYFCEECVGSWSRCAQTCPVDRGEFGEV  173 (1134)
T ss_pred             hhhhhHHHHHHHHHhhccccc-cccccHHHHhhhhhhhcccCchhhhhhhee
Confidence            346888887776665444455 999999999999999999999999876643

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

Probab=97.61  E-value=1.4e-05  Score=52.24  Aligned_cols=46  Identities=28%  Similarity=0.566  Sum_probs=22.7

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      -.|++|.+-++.+  +... .|.|+|+..||..-+..  .||+|+.+-...
T Consensus         8 LrCs~C~~~l~~p--v~l~-~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~q   53 (65)
T PF14835_consen    8 LRCSICFDILKEP--VCLG-GCEHIFCSSCIRDCIGS--ECPVCHTPAWIQ   53 (65)
T ss_dssp             TS-SSS-S--SS---B----SSS--B-TTTGGGGTTT--B-SSS--B-S-S
T ss_pred             cCCcHHHHHhcCC--ceec-cCccHHHHHHhHHhcCC--CCCCcCChHHHH
Confidence            4699999988775  4344 49999999999885443  499998766544

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

Probab=97.57  E-value=3.4e-05  Score=66.86  Aligned_cols=50  Identities=42%  Similarity=0.937  Sum_probs=37.7

Q ss_pred             CCCcCccccCcccCCC----ceeecCCCCccccHhhHHHHHh--c-----CCCCccccccc
Q 042698          108 LDNECVICLSDFAPGE----RVRILPKCNHGFHVRCIDKWLR--S-----NSSCPKCRHCL  157 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~----~v~~l~~C~H~FH~~Ci~~Wl~--~-----~~~CP~CR~~l  157 (203)
                      .+.+|.||++...+..    -...+|.|.|.|+..||..|-+  +     .+.||.||...
T Consensus       160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s  220 (344)
T KOG1039|consen  160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPS  220 (344)
T ss_pred             ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcc
Confidence            4678999999876543    1233567999999999999984  3     35699999743

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

Probab=97.49  E-value=8.7e-05  Score=47.85  Aligned_cols=41  Identities=29%  Similarity=0.620  Sum_probs=28.6

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC--CCcc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS--SCPK  152 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~--~CP~  152 (203)
                      ...|+|.+..|+++  ++... |+|+|-++.|..|++++.  .||+
T Consensus        11 ~~~CPiT~~~~~~P--V~s~~-C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   11 SLKCPITLQPFEDP--VKSKK-CGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             -SB-TTTSSB-SSE--EEESS-S--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             ccCCCCcCChhhCC--cCcCC-CCCeecHHHHHHHHHhcCCCCCCC
Confidence            46799999998865  66666 999999999999995433  5998

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

Probab=97.49  E-value=3.3e-05  Score=71.99  Aligned_cols=47  Identities=28%  Similarity=0.699  Sum_probs=36.7

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHh-cCCCCcccccccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR-SNSSCPKCRHCLIES  160 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~l~~~  160 (203)
                      -.|++|-+.+.+  .+ .. .|+|+||..|+..-+. +++.||.|...+.+.
T Consensus       644 LkCs~Cn~R~Kd--~v-I~-kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan  691 (698)
T KOG0978|consen  644 LKCSVCNTRWKD--AV-IT-KCGHVFCEECVQTRYETRQRKCPKCNAAFGAN  691 (698)
T ss_pred             eeCCCccCchhh--HH-HH-hcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence            479999866554  23 33 3999999999999885 567899999887765

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

Probab=97.41  E-value=0.0001  Score=64.32  Aligned_cols=53  Identities=30%  Similarity=0.691  Sum_probs=40.0

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhc--CCCCcccccccccccccccC
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS--NSSCPKCRHCLIESCKKIEG  166 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~l~~~~~~~~~  166 (203)
                      .-|-||-|.   +..|++-| |||..|..|+..|-..  .+.||.||..|-..+..+.+
T Consensus       370 eLCKICaen---dKdvkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~viid  424 (563)
T KOG1785|consen  370 ELCKICAEN---DKDVKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPVIID  424 (563)
T ss_pred             HHHHHhhcc---CCCccccc-ccchHHHHHHHhhcccCCCCCCCceeeEeccccceeee
Confidence            359999765   33477788 9999999999999633  56799999988755544433

>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=97.37  E-value=6.5e-05  Score=56.35  Aligned_cols=35  Identities=23%  Similarity=0.537  Sum_probs=30.0

Q ss_pred             CCcCccccCcccCCCceeecCCCC------ccccHhhHHHHH
Q 042698          109 DNECVICLSDFAPGERVRILPKCN------HGFHVRCIDKWL  144 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~------H~FH~~Ci~~Wl  144 (203)
                      ..+|+||++.+..++.+..++ |+      |.||.+|+.+|-
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt-~~g~lnLEkmfc~~C~~rw~   66 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVT-DGGTLNLEKMFCADCDKRWR   66 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEe-cCCeehHHHHHHHHHHHHHH
Confidence            468999999999866777776 65      999999999994

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.

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

Probab=97.37  E-value=4.6e-05  Score=48.06  Aligned_cols=47  Identities=28%  Similarity=0.581  Sum_probs=31.7

Q ss_pred             CCcCccccCcccCCCceeecCCCCcc-ccHhhHHHHH-hcCCCCccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHG-FHVRCIDKWL-RSNSSCPKCRHCLIE  159 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~-FH~~Ci~~Wl-~~~~~CP~CR~~l~~  159 (203)
                      +++|.||+|.-.+.  +  +-.|||. .+.+|-.+-+ ..+..||+||+.+-.
T Consensus         7 ~dECTICye~pvds--V--lYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~d   55 (62)
T KOG4172|consen    7 SDECTICYEHPVDS--V--LYTCGHMCMCYACGLRLKKALHGCCPICRAPIKD   55 (62)
T ss_pred             ccceeeeccCcchH--H--HHHcchHHhHHHHHHHHHHccCCcCcchhhHHHH
Confidence            37899999885442  3  2239996 4456654433 367789999998753

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

Probab=97.33  E-value=0.0001  Score=62.04  Aligned_cols=48  Identities=27%  Similarity=0.538  Sum_probs=38.3

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc-CCCCcccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~  160 (203)
                      ..+|+||+.....+   ..++ |+|.|+.-||.--.+. +.+|++||..+...
T Consensus         7 ~~eC~IC~nt~n~P---v~l~-C~HkFCyiCiKGsy~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    7 KKECLICYNTGNCP---VNLY-CFHKFCYICIKGSYKNDKKTCAVCRFPIDST   55 (324)
T ss_pred             CCcceeeeccCCcC---cccc-ccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence            35899999987665   4566 9999999999876654 55799999988743

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

Probab=97.22  E-value=0.00022  Score=70.56  Aligned_cols=53  Identities=28%  Similarity=0.679  Sum_probs=42.7

Q ss_pred             CCCCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC----------CCCcccccccc
Q 042698          105 LPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN----------SSCPKCRHCLI  158 (203)
Q Consensus       105 ~~~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~----------~~CP~CR~~l~  158 (203)
                      ..+.++.|.||+.|--.....+.+. |+|+||.+|...-|.+.          -+||+|+.+|.
T Consensus      3482 kQD~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             hcccCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            3466789999999988778889998 99999999997765432          15999998765

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

Probab=97.04  E-value=0.00032  Score=62.25  Aligned_cols=54  Identities=28%  Similarity=0.577  Sum_probs=44.0

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKK  163 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  163 (203)
                      +.+..|++|...+.++  +..+. |||.|+..|+..|+..+..||.|+..+......
T Consensus        19 ~~~l~C~~C~~vl~~p--~~~~~-cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~   72 (391)
T KOG0297|consen   19 DENLLCPICMSVLRDP--VQTTT-CGHRFCAGCLLESLSNHQKCPVCRQELTQAEEL   72 (391)
T ss_pred             cccccCccccccccCC--CCCCC-CCCcccccccchhhccCcCCcccccccchhhcc
Confidence            4557899999998876  22234 999999999999999999999999888766544

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

Probab=97.02  E-value=0.00024  Score=61.90  Aligned_cols=45  Identities=42%  Similarity=0.973  Sum_probs=37.0

Q ss_pred             CCcCccccCcccCC-CceeecCCCCccccHhhHHHHHhcC--CCCcccc
Q 042698          109 DNECVICLSDFAPG-ERVRILPKCNHGFHVRCIDKWLRSN--SSCPKCR  154 (203)
Q Consensus       109 ~~~CaICl~~~~~~-~~v~~l~~C~H~FH~~Ci~~Wl~~~--~~CP~CR  154 (203)
                      +--|-.|-+.+... +.+..+| |.|+||..|+...|.++  ++||.||
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~Cr  412 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCR  412 (518)
T ss_pred             hhhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHH
Confidence            34699999888644 4677898 99999999999999654  4799998

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

Probab=96.98  E-value=0.00048  Score=60.93  Aligned_cols=50  Identities=34%  Similarity=0.847  Sum_probs=42.0

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      ..+.+|.||..-+.+.   .++| |||.|+..||++-+-....||.||..+.+.
T Consensus        82 ~sef~c~vc~~~l~~p---v~tp-cghs~c~~Cl~r~ld~~~~cp~Cr~~l~e~  131 (398)
T KOG4159|consen   82 RSEFECCVCSRALYPP---VVTP-CGHSFCLECLDRSLDQETECPLCRDELVEL  131 (398)
T ss_pred             cchhhhhhhHhhcCCC---cccc-ccccccHHHHHHHhccCCCCcccccccccc
Confidence            4567899998888775   5667 999999999999777677799999998863

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

Probab=96.94  E-value=0.00036  Score=65.91  Aligned_cols=51  Identities=35%  Similarity=0.791  Sum_probs=40.6

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC-------CCccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS-------SCPKCRHCL  157 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~-------~CP~CR~~l  157 (203)
                      ....+|.||.+.+...+.+-....|.|+||..||..|.+...       .||.|....
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~  246 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVS  246 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchh
Confidence            345689999999998887766667999999999999986421       499998433

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

Probab=96.78  E-value=0.00042  Score=53.50  Aligned_cols=42  Identities=33%  Similarity=0.737  Sum_probs=31.7

Q ss_pred             CeEEccCCCCCCCCCCcCccccCcccCCCceeecCCCCccccHh
Q 042698           95 TIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVR  138 (203)
Q Consensus        95 p~~~~~~~~~~~~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~  138 (203)
                      |...|.++. ..+...+|.||||++..++.+..|| |-.+||+.
T Consensus       164 PrlsYNdDV-L~ddkGECvICLEdL~~GdtIARLP-CLCIYHK~  205 (205)
T KOG0801|consen  164 PRLSYNDDV-LKDDKGECVICLEDLEAGDTIARLP-CLCIYHKQ  205 (205)
T ss_pred             cccccccch-hcccCCcEEEEhhhccCCCceeccc-eEEEeecC
Confidence            444444422 2234568999999999999999999 99999973

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

Probab=96.69  E-value=0.00021  Score=61.62  Aligned_cols=45  Identities=27%  Similarity=0.578  Sum_probs=33.4

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      .+-|.||+++..+   ...+| |||.=+  |...-. ...+||+||..+.-.
T Consensus       305 p~lcVVcl~e~~~---~~fvp-cGh~cc--ct~cs~-~l~~CPvCR~rI~~~  349 (355)
T KOG1571|consen  305 PDLCVVCLDEPKS---AVFVP-CGHVCC--CTLCSK-HLPQCPVCRQRIRLV  349 (355)
T ss_pred             CCceEEecCCccc---eeeec-CCcEEE--chHHHh-hCCCCchhHHHHHHH
Confidence            3569999999877   46778 999954  777643 334599999987543

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

Probab=96.67  E-value=0.0046  Score=52.88  Aligned_cols=45  Identities=20%  Similarity=0.425  Sum_probs=36.1

Q ss_pred             CCCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccc
Q 042698          106 PGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKC  153 (203)
Q Consensus       106 ~~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~C  153 (203)
                      +.....|++|+...+++-.+.+   -|-+||..||..++.++..||+=
T Consensus       297 ~~~~~~CpvClk~r~Nptvl~v---SGyVfCY~Ci~~Yv~~~~~CPVT  341 (357)
T KOG0826|consen  297 PPDREVCPVCLKKRQNPTVLEV---SGYVFCYPCIFSYVVNYGHCPVT  341 (357)
T ss_pred             CCccccChhHHhccCCCceEEe---cceEEeHHHHHHHHHhcCCCCcc
Confidence            3455789999999877633322   69999999999999999999974

>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=96.60  E-value=0.00092  Score=47.96  Aligned_cols=32  Identities=25%  Similarity=0.682  Sum_probs=26.7

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHH
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCID  141 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~  141 (203)
                      .+..|++|-..+.. ....+.| |||+||..|+.
T Consensus        77 ~~~~C~vC~k~l~~-~~f~~~p-~~~v~H~~C~~  108 (109)
T PF10367_consen   77 ESTKCSVCGKPLGN-SVFVVFP-CGHVVHYSCIK  108 (109)
T ss_pred             CCCCccCcCCcCCC-ceEEEeC-CCeEEeccccc
Confidence            35679999999977 5667778 99999999975

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 [].

>PHA02862 5L protein; Provisional

Probab=96.50  E-value=0.0023  Score=48.56  Aligned_cols=48  Identities=21%  Similarity=0.562  Sum_probs=34.3

Q ss_pred             CCcCccccCcccCCCceeecCCC---CccccHhhHHHHHhc--CCCCccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKC---NHGFHVRCIDKWLRS--NSSCPKCRHCLIE  159 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C---~H~FH~~Ci~~Wl~~--~~~CP~CR~~l~~  159 (203)
                      ++.|=||+++-.+  .+.-+. |   ...-|.+|+.+|+..  +..|++|+....-
T Consensus         2 ~diCWIC~~~~~e--~~~PC~-C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I   54 (156)
T PHA02862          2 SDICWICNDVCDE--RNNFCG-CNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI   54 (156)
T ss_pred             CCEEEEecCcCCC--Cccccc-ccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence            3579999998533  233222 4   377899999999964  4469999987653

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=96.40  E-value=0.0038  Score=48.21  Aligned_cols=50  Identities=22%  Similarity=0.624  Sum_probs=34.7

Q ss_pred             CCCcCccccCcccCCCceeecCCCCc---cccHhhHHHHHhcC--CCCcccccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNH---GFHVRCIDKWLRSN--SSCPKCRHCLIES  160 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H---~FH~~Ci~~Wl~~~--~~CP~CR~~l~~~  160 (203)
                      .+..|=||.++-.  +...-.. |..   .-|.+|+..|+...  ..|++|+....-.
T Consensus         7 ~~~~CRIC~~~~~--~~~~PC~-CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          7 MDKCCWICKDEYD--VVTNYCN-CKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCCeeEecCCCCC--CccCCcc-cCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            4568999998853  2233232 544   55999999999644  4699999876543

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

Probab=96.08  E-value=0.0041  Score=38.39  Aligned_cols=41  Identities=37%  Similarity=0.978  Sum_probs=25.9

Q ss_pred             CccccCcccCCCceeecC-CCC---ccccHhhHHHHHh--cCCCCccc
Q 042698          112 CVICLSDFAPGERVRILP-KCN---HGFHVRCIDKWLR--SNSSCPKC  153 (203)
Q Consensus       112 CaICl~~~~~~~~v~~l~-~C~---H~FH~~Ci~~Wl~--~~~~CP~C  153 (203)
                      |-||+++-..++.+ +.| .|+   -..|..|+..|+.  .+.+|++|
T Consensus         1 CrIC~~~~~~~~~l-i~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDEPL-ISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS-E-E-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCCce-ecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            67899887766533 344 133   4789999999996  44569887

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

Probab=96.06  E-value=0.0036  Score=55.00  Aligned_cols=46  Identities=24%  Similarity=0.635  Sum_probs=37.4

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc--------CCCCccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS--------NSSCPKCRH  155 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~--------~~~CP~CR~  155 (203)
                      -..|.||+++......+..+| |+|+|++.|+..++..        .-+||-+..
T Consensus       184 lf~C~ICf~e~~G~~c~~~lp-C~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~~C  237 (445)
T KOG1814|consen  184 LFDCCICFEEQMGQHCFKFLP-CSHVFCKSCLKDYFTIQIQEGQVSCLKCPDPKC  237 (445)
T ss_pred             cccceeeehhhcCcceeeecc-cchHHHHHHHHHHHHHhhhcceeeeecCCCCCC
Confidence            357999999988888889999 9999999999999842        124876654

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

Probab=96.03  E-value=0.027  Score=47.22  Aligned_cols=51  Identities=24%  Similarity=0.359  Sum_probs=37.6

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC--CCCcccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN--SSCPKCRHCLIES  160 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~--~~CP~CR~~l~~~  160 (203)
                      .++.+|++|-+.-..+  ....+ |+|+||.-||..-+...  -+||.|-.+..+.
T Consensus       237 t~~~~C~~Cg~~PtiP--~~~~~-C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~l  289 (298)
T KOG2879|consen  237 TSDTECPVCGEPPTIP--HVIGK-CGHIYCYYCIATSRLWDASFTCPLCGENVEPL  289 (298)
T ss_pred             cCCceeeccCCCCCCC--eeecc-ccceeehhhhhhhhcchhhcccCccCCCCcch
Confidence            4567899998775443  34444 99999999999876544  5799997766543

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

Probab=96.03  E-value=0.0025  Score=50.83  Aligned_cols=43  Identities=23%  Similarity=0.567  Sum_probs=36.7

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHC  156 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~  156 (203)
                      ..|.||-.+|+.+   .++. |||.|+..|...=++....|-+|-..
T Consensus       197 F~C~iCKkdy~sp---vvt~-CGH~FC~~Cai~~y~kg~~C~~Cgk~  239 (259)
T COG5152         197 FLCGICKKDYESP---VVTE-CGHSFCSLCAIRKYQKGDECGVCGKA  239 (259)
T ss_pred             eeehhchhhccch---hhhh-cchhHHHHHHHHHhccCCcceecchh
Confidence            4799999999886   4554 99999999999988888899999654

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

Probab=96.01  E-value=0.0016  Score=55.66  Aligned_cols=48  Identities=25%  Similarity=0.602  Sum_probs=38.2

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  158 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  158 (203)
                      ..-+|.+|-.=|.+...+.   .|-|.||+.||...+.....||.|...+-
T Consensus        14 ~~itC~LC~GYliDATTI~---eCLHTFCkSCivk~l~~~~~CP~C~i~ih   61 (331)
T KOG2660|consen   14 PHITCRLCGGYLIDATTIT---ECLHTFCKSCIVKYLEESKYCPTCDIVIH   61 (331)
T ss_pred             cceehhhccceeecchhHH---HHHHHHHHHHHHHHHHHhccCCccceecc
Confidence            4568999977766653332   39999999999999999999999986554

>PHA03096 p28-like protein; Provisional

Probab=95.98  E-value=0.0034  Score=53.31  Aligned_cols=37  Identities=30%  Similarity=0.675  Sum_probs=29.0

Q ss_pred             CcCccccCcccCCC----ceeecCCCCccccHhhHHHHHhc
Q 042698          110 NECVICLSDFAPGE----RVRILPKCNHGFHVRCIDKWLRS  146 (203)
Q Consensus       110 ~~CaICl~~~~~~~----~v~~l~~C~H~FH~~Ci~~Wl~~  146 (203)
                      -.|.||++......    .-..++.|.|.|+..|+..|...
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~  219 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTE  219 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHh
Confidence            47999999876542    22356789999999999999853

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=95.93  E-value=0.012  Score=37.37  Aligned_cols=34  Identities=26%  Similarity=0.787  Sum_probs=30.5

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHH
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDK  142 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~  142 (203)
                      ...|.+|-+.|.+++.+.+.+.|+-.||..|.+.
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            4579999999998888999999999999999765

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.89  E-value=0.0075  Score=49.73  Aligned_cols=53  Identities=15%  Similarity=0.255  Sum_probs=46.3

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESC  161 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  161 (203)
                      ...|+||.+.+.+.-.+.+|..|||+|..+|++..++....||+|-.++.+..
T Consensus       221 ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrd  273 (303)
T KOG3039|consen  221 RYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRD  273 (303)
T ss_pred             ceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccc
Confidence            35699999999998888888779999999999999999999999987776553

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

Probab=95.81  E-value=0.0038  Score=56.52  Aligned_cols=48  Identities=27%  Similarity=0.560  Sum_probs=36.4

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHh-----cCCCCcccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR-----SNSSCPKCRHCLI  158 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~-----~~~~CP~CR~~l~  158 (203)
                      .+..+|.+|-++-++.   +... |.|.||+-||.+++.     .+-+||.|...+.
T Consensus       534 k~~~~C~lc~d~aed~---i~s~-ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls  586 (791)
T KOG1002|consen  534 KGEVECGLCHDPAEDY---IESS-CHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS  586 (791)
T ss_pred             cCceeecccCChhhhh---Hhhh-hhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence            3456899999885553   4555 999999999988874     3457999976554

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

Probab=95.76  E-value=0.0005  Score=59.81  Aligned_cols=50  Identities=24%  Similarity=0.609  Sum_probs=44.0

Q ss_pred             CCcCccccCcccCC-CceeecCCCCccccHhhHHHHHhcCCCCccccccccc
Q 042698          109 DNECVICLSDFAPG-ERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  159 (203)
Q Consensus       109 ~~~CaICl~~~~~~-~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  159 (203)
                      ...|+||.+.+... +.+..+. |||++|..||..||.....||.||+.+..
T Consensus       196 v~sl~I~~~slK~~y~k~~~~~-~g~~~~~~kL~k~L~~~~kl~~~~rel~~  246 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAIV-CGHIYHHGKLSKWLATKRKLPSCRRELPK  246 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHHh-hcccchhhHHHHHHHHHHHhHHHHhhhhh
Confidence            35799999999877 6777777 99999999999999988899999998773

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

Probab=95.74  E-value=0.011  Score=36.69  Aligned_cols=44  Identities=20%  Similarity=0.538  Sum_probs=21.6

Q ss_pred             CccccCcccCCC-ceeecCCCCccccHhhHHHHHh-cCCCCcccccc
Q 042698          112 CVICLSDFAPGE-RVRILPKCNHGFHVRCIDKWLR-SNSSCPKCRHC  156 (203)
Q Consensus       112 CaICl~~~~~~~-~v~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~  156 (203)
                      |++|.+++...+ ...-.+ |++..+..|...-+. ....||-||..
T Consensus         1 cp~C~e~~d~~d~~~~PC~-Cgf~IC~~C~~~i~~~~~g~CPgCr~~   46 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCE-CGFQICRFCYHDILENEGGRCPGCREP   46 (48)
T ss_dssp             -TTTS-B--CCCTT--SST-TS----HHHHHHHTTSS-SB-TTT--B
T ss_pred             CCCcccccccCCCccccCc-CCCcHHHHHHHHHHhccCCCCCCCCCC
Confidence            789999984443 334444 889888888888665 36679999975

>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=95.63  E-value=0.007  Score=36.65  Aligned_cols=41  Identities=34%  Similarity=0.814  Sum_probs=23.0

Q ss_pred             CccccCcccCCCceeecCCCCccccHhhHHHHHhcCC--CCccc
Q 042698          112 CVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS--SCPKC  153 (203)
Q Consensus       112 CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~--~CP~C  153 (203)
                      |.+|-+-...+....... |+=.+|..|+..+++...  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~~-C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNRD-CNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS---S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCCc-cCchHHHHHHHHHHhcCCCCCCcCC
Confidence            667777666664333333 888999999999997665  69987

; PDB: 3NW0_A 2CT0_A.

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

Probab=95.17  E-value=0.0074  Score=50.94  Aligned_cols=44  Identities=25%  Similarity=0.457  Sum_probs=37.4

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCL  157 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l  157 (203)
                      ..|-||...|..+   .++. |+|.|+..|...=+++...|.+|-+..
T Consensus       242 f~c~icr~~f~~p---Vvt~-c~h~fc~~ca~~~~qk~~~c~vC~~~t  285 (313)
T KOG1813|consen  242 FKCFICRKYFYRP---VVTK-CGHYFCEVCALKPYQKGEKCYVCSQQT  285 (313)
T ss_pred             ccccccccccccc---hhhc-CCceeehhhhccccccCCcceeccccc
Confidence            4599999999886   4555 999999999999888889999997644

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

Probab=95.15  E-value=0.014  Score=45.95  Aligned_cols=30  Identities=33%  Similarity=0.947  Sum_probs=23.9

Q ss_pred             CCCccccHhhHHHHHhc----C-------CCCccccccccc
Q 042698          130 KCNHGFHVRCIDKWLRS----N-------SSCPKCRHCLIE  159 (203)
Q Consensus       130 ~C~H~FH~~Ci~~Wl~~----~-------~~CP~CR~~l~~  159 (203)
                      +||.-||.-|+..||+.    +       ..||.|..++.-
T Consensus       189 qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pial  229 (234)
T KOG3268|consen  189 QCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIAL  229 (234)
T ss_pred             ccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCccee
Confidence            49999999999999963    1       149999877653

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

Probab=95.13  E-value=0.0075  Score=49.52  Aligned_cols=43  Identities=23%  Similarity=0.593  Sum_probs=31.5

Q ss_pred             cCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccccc
Q 042698          111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCL  157 (203)
Q Consensus       111 ~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l  157 (203)
                      -|-.|.--- .++....+. |.|+||..|...-  ....||+||..+
T Consensus         5 hCn~C~~~~-~~~~f~LTa-C~HvfC~~C~k~~--~~~~C~lCkk~i   47 (233)
T KOG4739|consen    5 HCNKCFRFP-SQDPFFLTA-CRHVFCEPCLKAS--SPDVCPLCKKSI   47 (233)
T ss_pred             EeccccccC-CCCceeeee-chhhhhhhhcccC--Ccccccccccee
Confidence            366665433 377788887 9999999998773  222899999874

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

Probab=94.81  E-value=0.015  Score=55.45  Aligned_cols=40  Identities=25%  Similarity=0.763  Sum_probs=31.2

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRH  155 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~  155 (203)
                      ..|..|-....-+  ..-.. |+|.||.+|++   .+...||-|+.
T Consensus       841 skCs~C~~~LdlP--~VhF~-CgHsyHqhC~e---~~~~~CP~C~~  880 (933)
T KOG2114|consen  841 SKCSACEGTLDLP--FVHFL-CGHSYHQHCLE---DKEDKCPKCLP  880 (933)
T ss_pred             eeecccCCccccc--eeeee-cccHHHHHhhc---cCcccCCccch
Confidence            5799998776654  33343 99999999999   45567999987

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

Probab=94.65  E-value=0.044  Score=47.45  Aligned_cols=62  Identities=23%  Similarity=0.356  Sum_probs=41.9

Q ss_pred             hcCeEEccCCCCCCCCCCcCccccCcccCCCceeecCCCCccccHhhHHHH--HhcCCCCcccccccc
Q 042698           93 AFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKW--LRSNSSCPKCRHCLI  158 (203)
Q Consensus        93 ~lp~~~~~~~~~~~~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~W--l~~~~~CP~CR~~l~  158 (203)
                      ..|...-++.+...++..-|.||-+.+.-   ..++| |+|..+.-|-.+-  |-.++.||+||....
T Consensus        45 aEPnlttsSaddtDEen~~C~ICA~~~TY---s~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE~e  108 (493)
T COG5236          45 AEPNLTTSSADDTDEENMNCQICAGSTTY---SARYP-CGHQICHACAVRLRALYMQKGCPLCRTETE  108 (493)
T ss_pred             cCCccccccccccccccceeEEecCCceE---EEecc-CCchHHHHHHHHHHHHHhccCCCccccccc
Confidence            34554444444444445679999877543   46788 9999999998663  345778999997543

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

Probab=94.27  E-value=0.048  Score=47.31  Aligned_cols=49  Identities=29%  Similarity=0.577  Sum_probs=40.1

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  159 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  159 (203)
                      .++..|+||.-.-..   ....| |+|.=+..||.+-+.+.+.|=.|+..+..
T Consensus       420 sEd~lCpICyA~pi~---Avf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~~  468 (489)
T KOG4692|consen  420 SEDNLCPICYAGPIN---AVFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVID  468 (489)
T ss_pred             cccccCcceecccch---hhccC-CCCchHHHHHHHHHhcCCeeeEecceeee
Confidence            456789999755322   35667 99999999999999999999999988774

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

Probab=93.96  E-value=0.011  Score=49.84  Aligned_cols=43  Identities=26%  Similarity=0.697  Sum_probs=30.0

Q ss_pred             CCcCccccCcccCCCceeecCCCCccc-cHhhHHHHHhcCCCCccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGF-HVRCIDKWLRSNSSCPKCRHCLIE  159 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~F-H~~Ci~~Wl~~~~~CP~CR~~l~~  159 (203)
                      ..-|+||++...+   +..|+ |||.- +.+|-..    -..||+||+.+.-
T Consensus       300 ~~LC~ICmDaP~D---CvfLe-CGHmVtCt~CGkr----m~eCPICRqyi~r  343 (350)
T KOG4275|consen  300 RRLCAICMDAPRD---CVFLE-CGHMVTCTKCGKR----MNECPICRQYIVR  343 (350)
T ss_pred             HHHHHHHhcCCcc---eEEee-cCcEEeehhhccc----cccCchHHHHHHH
Confidence            4569999988544   57788 99963 3344433    3479999987653

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

Probab=93.86  E-value=0.028  Score=53.87  Aligned_cols=36  Identities=22%  Similarity=0.564  Sum_probs=28.5

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHH
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWL  144 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl  144 (203)
                      +.+++|.+|.-.+... .-.+.+ |||.||++||..-.
T Consensus       815 ep~d~C~~C~~~ll~~-pF~vf~-CgH~FH~~Cl~~~v  850 (911)
T KOG2034|consen  815 EPQDSCDHCGRPLLIK-PFYVFP-CGHCFHRDCLIRHV  850 (911)
T ss_pred             cCccchHHhcchhhcC-cceeee-ccchHHHHHHHHHH
Confidence            4567899998887665 345667 99999999998765

>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=93.81  E-value=0.073  Score=41.15  Aligned_cols=36  Identities=25%  Similarity=0.536  Sum_probs=22.6

Q ss_pred             CCcCccccCcccCCCc---------eeecCCCCc-cccHhhHHHHHh
Q 042698          109 DNECVICLSDFAPGER---------VRILPKCNH-GFHVRCIDKWLR  145 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~---------v~~l~~C~H-~FH~~Ci~~Wl~  145 (203)
                      +..|+||||--.+.-.         .|-.- |+- .-|..|++++-+
T Consensus         2 d~~CpICme~PHNAVLLlCSS~~kgcRpym-c~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    2 DVTCPICMEHPHNAVLLLCSSHEKGCRPYM-CDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CccCceeccCCCceEEEEeccccCCccccc-cCCccchhHHHHHHHH
Confidence            4689999988654421         22222 543 347899999864

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.

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

Probab=93.66  E-value=0.045  Score=46.49  Aligned_cols=43  Identities=30%  Similarity=0.702  Sum_probs=33.1

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHh-cCCCCccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR-SNSSCPKCRH  155 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~  155 (203)
                      ..|+.|..-....  ++ ++.|+|.|+.+||..-|. ....||.|..
T Consensus       275 LkCplc~~Llrnp--~k-T~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRNP--MK-TPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhCc--cc-CccccchHHHHHHhhhhhhccccCCCccc
Confidence            5799987766654  33 366999999999998875 4567999944

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

Probab=93.61  E-value=0.037  Score=52.30  Aligned_cols=25  Identities=32%  Similarity=0.878  Sum_probs=22.1

Q ss_pred             cCCCCccccHhhHHHHHhcCCCCcc
Q 042698          128 LPKCNHGFHVRCIDKWLRSNSSCPK  152 (203)
Q Consensus       128 l~~C~H~FH~~Ci~~Wl~~~~~CP~  152 (203)
                      +..|+|+.|..|...|+.....||.
T Consensus      1045 Cg~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1045 CGTCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             hccccccccHHHHHHHHhcCCcCCC
Confidence            3359999999999999999999984

>PF02439 Adeno_E3_CR2: Adenovirus E3 region protein CR2; InterPro: IPR003470 Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host []

Probab=93.56  E-value=0.22  Score=29.11  Aligned_cols=30  Identities=13%  Similarity=0.307  Sum_probs=15.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 042698           37 AVIVLSVLVCGIICSLGLHFLIRCILVSWS   66 (203)
Q Consensus        37 ~iiii~il~~~~i~~l~~~~~~~~~~rr~~   66 (203)
                      ++-+++.+++++++.++.++++.|++||.+
T Consensus         5 ~IaIIv~V~vg~~iiii~~~~YaCcykk~~   34 (38)
T PF02439_consen    5 TIAIIVAVVVGMAIIIICMFYYACCYKKHR   34 (38)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHHcccc
Confidence            444444444454444555555566666633

This region called CR1 (conserved region 1) [] is found three times in Human adenovirus 19 (a subgroup D adenovirus) 49 kDa protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain.

>PF04641 Rtf2: Rtf2 RING-finger

Probab=93.38  E-value=0.1  Score=43.72  Aligned_cols=53  Identities=17%  Similarity=0.379  Sum_probs=40.0

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      .....|+|...+|........+-.|||+|-..+|..- +....||+|-.++...
T Consensus       111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~f~~~  163 (260)
T PF04641_consen  111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKPFTEE  163 (260)
T ss_pred             CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-cccccccccCCccccC
Confidence            4456799999999665555555449999999999995 3355799998776633

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

Probab=93.17  E-value=0.036  Score=52.49  Aligned_cols=47  Identities=36%  Similarity=0.758  Sum_probs=36.6

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhc--CCCCccccccccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS--NSSCPKCRHCLIESC  161 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~l~~~~  161 (203)
                      ..|.||++    .+...... |+|.|+.+|+..-+..  ...||+||..+.+..
T Consensus       455 ~~c~ic~~----~~~~~it~-c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~  503 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITR-CGHDFCVECLKKSIQQSENAPCPLCRNVLKEKK  503 (674)
T ss_pred             cccccccc----cccceeec-ccchHHHHHHHhccccccCCCCcHHHHHHHHHH
Confidence            68999999    34455566 9999999999988753  336999998877654

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

Probab=93.02  E-value=0.028  Score=55.80  Aligned_cols=43  Identities=33%  Similarity=0.720  Sum_probs=36.7

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRH  155 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~  155 (203)
                      ..|.||++.+...-.+..   |+|.++..|+..|+..+..||+|+.
T Consensus      1154 ~~c~ic~dil~~~~~I~~---cgh~~c~~c~~~~l~~~s~~~~~ks 1196 (1394)
T KOG0298|consen 1154 FVCEICLDILRNQGGIAG---CGHEPCCRCDELWLYASSRCPICKS 1196 (1394)
T ss_pred             cchHHHHHHHHhcCCeee---echhHhhhHHHHHHHHhccCcchhh
Confidence            479999999886533332   9999999999999999999999984

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=92.93  E-value=0.084  Score=45.62  Aligned_cols=53  Identities=19%  Similarity=0.476  Sum_probs=36.7

Q ss_pred             CCCCcCccccCcccCCCce-eecCCCCccccHhhHHHHHh-cCCCCcccccccccc
Q 042698          107 GLDNECVICLSDFAPGERV-RILPKCNHGFHVRCIDKWLR-SNSSCPKCRHCLIES  160 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v-~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~l~~~  160 (203)
                      ++++.|+.|++++...|+- .-++ ||-..|.-|...--+ -+..||-||+...+.
T Consensus        12 deed~cplcie~mditdknf~pc~-cgy~ic~fc~~~irq~lngrcpacrr~y~de   66 (480)
T COG5175          12 DEEDYCPLCIEPMDITDKNFFPCP-CGYQICQFCYNNIRQNLNGRCPACRRKYDDE   66 (480)
T ss_pred             cccccCcccccccccccCCcccCC-cccHHHHHHHHHHHhhccCCChHhhhhcccc
Confidence            4556799999999877654 3455 887777777655322 245699999876543

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

Probab=92.88  E-value=0.08  Score=44.96  Aligned_cols=47  Identities=34%  Similarity=0.761  Sum_probs=37.5

Q ss_pred             CcCccccCcccCCC---ceeecCCCCccccHhhHHHHHhcCC-CCccccccc
Q 042698          110 NECVICLSDFAPGE---RVRILPKCNHGFHVRCIDKWLRSNS-SCPKCRHCL  157 (203)
Q Consensus       110 ~~CaICl~~~~~~~---~v~~l~~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~l  157 (203)
                      .+|-||-++|...+   .-+.+. |||.|+..|+..-+.... .||.||...
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~-c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLK-CGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccc-cCceehHhHHHHHhcCceeeccCCCCcc
Confidence            57999999998764   235566 999999999998765544 599999874

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

Probab=92.45  E-value=0.068  Score=45.14  Aligned_cols=45  Identities=27%  Similarity=0.651  Sum_probs=37.3

Q ss_pred             CcCccccCcccCCC-ceeecCCCCccccHhhHHHHHhcCCCCccccc
Q 042698          110 NECVICLSDFAPGE-RVRILPKCNHGFHVRCIDKWLRSNSSCPKCRH  155 (203)
Q Consensus       110 ~~CaICl~~~~~~~-~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~  155 (203)
                      ..|+||.+.+-... .+..++ |||.-|..|+......+-+||+|..
T Consensus       159 ~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  159 FNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             CCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccc
Confidence            34999999876654 445676 9999999999999887888999988

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

Probab=92.31  E-value=0.16  Score=48.53  Aligned_cols=63  Identities=21%  Similarity=0.404  Sum_probs=43.7

Q ss_pred             CCCCCcCccccCcccCCCceeecC-CCC---ccccHhhHHHHHh--cCCCCcccccccccccccccCCCC
Q 042698          106 PGLDNECVICLSDFAPGERVRILP-KCN---HGFHVRCIDKWLR--SNSSCPKCRHCLIESCKKIEGSTQ  169 (203)
Q Consensus       106 ~~~~~~CaICl~~~~~~~~v~~l~-~C~---H~FH~~Ci~~Wl~--~~~~CP~CR~~l~~~~~~~~~~~~  169 (203)
                      .+++..|-||..+-.+++.+- .| .|.   ...|.+|+.+|+.  ....|-+|+.++.-+.-..++-+|
T Consensus         9 N~d~~~CRICr~e~~~d~pLf-hPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~Fk~IY~e~mP~   77 (1175)
T COG5183           9 NEDKRSCRICRTEDIRDDPLF-HPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFKDIYKEDMPQ   77 (1175)
T ss_pred             CccchhceeecCCCCCCCcCc-ccccccchhHHHHHHHHHHHHhcCCCcceeeecceeeeeeecccCCCc
Confidence            345578999999987777653 23 143   5679999999996  345699999887755444344333

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

Probab=92.30  E-value=0.037  Score=51.39  Aligned_cols=43  Identities=28%  Similarity=0.553  Sum_probs=32.8

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRH  155 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~  155 (203)
                      ..|.||+..|.......+...|||..+..|+..  ..+++|| |+.
T Consensus        12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~--lyn~scp-~~~   54 (861)
T KOG3161|consen   12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQL--LYNASCP-TKR   54 (861)
T ss_pred             hhchHHHHHHHHHhcCcccccccchHHHHHHHh--HhhccCC-CCc
Confidence            369999999887654444445999999999987  4567788 654

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

Probab=91.50  E-value=0.16  Score=44.58  Aligned_cols=28  Identities=32%  Similarity=0.961  Sum_probs=20.2

Q ss_pred             CCccccHhhHHHHHhc-------------CCCCcccccccc
Q 042698          131 CNHGFHVRCIDKWLRS-------------NSSCPKCRHCLI  158 (203)
Q Consensus       131 C~H~FH~~Ci~~Wl~~-------------~~~CP~CR~~l~  158 (203)
                      |.-..|.+|+.+|+..             +..||+||+.+-
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FC  351 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFC  351 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccce
Confidence            4455678999999842             235999999754

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

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=91.00  E-value=0.11  Score=32.97  Aligned_cols=44  Identities=25%  Similarity=0.444  Sum_probs=30.9

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  159 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  159 (203)
                      ..|..|...-..   -.+++ |+|+....|++-+  +-.-||.|-..+..
T Consensus         8 ~~~~~~~~~~~~---~~~~p-CgH~I~~~~f~~~--rYngCPfC~~~~~~   51 (55)
T PF14447_consen    8 QPCVFCGFVGTK---GTVLP-CGHLICDNCFPGE--RYNGCPFCGTPFEF   51 (55)
T ss_pred             eeEEEccccccc---ccccc-ccceeeccccChh--hccCCCCCCCcccC
Confidence            346666554333   25677 9999999998875  55569999776653

>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane

Probab=90.22  E-value=0.6  Score=34.72  Aligned_cols=8  Identities=13%  Similarity=0.098  Sum_probs=3.3

Q ss_pred             CCCCChhH
Q 042698           30 ESSLNSNA   37 (203)
Q Consensus        30 ~~~~~~~~   37 (203)
                      .+.|....
T Consensus        58 ~h~fs~~~   65 (122)
T PF01102_consen   58 VHRFSEPA   65 (122)
T ss_dssp             SSSSS-TC
T ss_pred             ccCccccc
Confidence            34555443

Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.

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

Probab=90.12  E-value=0.12  Score=44.06  Aligned_cols=44  Identities=30%  Similarity=0.628  Sum_probs=28.9

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  158 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  158 (203)
                      ..|--|=-.+.  .-=|..+ |+|+||.+|-..  ...+.||.|-..+.
T Consensus        91 HfCd~Cd~PI~--IYGRmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~Vq  134 (389)
T KOG2932|consen   91 HFCDRCDFPIA--IYGRMIP-CKHVFCLECARS--DSDKICPLCDDRVQ  134 (389)
T ss_pred             EeecccCCcce--eeecccc-cchhhhhhhhhc--CccccCcCcccHHH
Confidence            34766743322  2236788 999999999765  34567999965443

>PF15050 SCIMP: SCIMP protein

Probab=89.96  E-value=0.84  Score=33.67  Aligned_cols=29  Identities=14%  Similarity=0.265  Sum_probs=13.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 042698           36 NAVIVLSVLVCGIICSLGLHFLIRCILVS   64 (203)
Q Consensus        36 ~~iiii~il~~~~i~~l~~~~~~~~~~rr   64 (203)
                      ++++.++|+++.+.+.+++++++|+.+|+
T Consensus         9 WiiLAVaII~vS~~lglIlyCvcR~~lRq   37 (133)
T PF15050_consen    9 WIILAVAIILVSVVLGLILYCVCRWQLRQ   37 (133)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            34444444444444444444444554444

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=89.39  E-value=0.31  Score=39.34  Aligned_cols=40  Identities=45%  Similarity=0.880  Sum_probs=29.9

Q ss_pred             CCcCccccCc-----ccCCCceeecCCCCccccHhhHHHHHhcCCCCcccc
Q 042698          109 DNECVICLSD-----FAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCR  154 (203)
Q Consensus       109 ~~~CaICl~~-----~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR  154 (203)
                      +..|.+|-++     |+. +.+...+.|+-+||..|+..     ..||-|-
T Consensus       152 GfiCe~C~~~~~IfPF~~-~~~~~C~~C~~v~H~~C~~~-----~~CpkC~  196 (202)
T PF13901_consen  152 GFICEICNSDDIIFPFQI-DTTVRCPKCKSVFHKSCFRK-----KSCPKCA  196 (202)
T ss_pred             CCCCccCCCCCCCCCCCC-CCeeeCCcCccccchhhcCC-----CCCCCcH
Confidence            4678899753     333 35667778999999999872     6699993

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

Probab=88.62  E-value=0.2  Score=46.35  Aligned_cols=50  Identities=32%  Similarity=0.788  Sum_probs=40.5

Q ss_pred             CCCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccccccccccc
Q 042698          106 PGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKK  163 (203)
Q Consensus       106 ~~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~~  163 (203)
                      .+..+.|.+|+.++    ..+..+ |.   |..|+..|+-.+..||+|+..+......
T Consensus       476 ~~~~~~~~~~~~~~----~~~~~~-~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~~  525 (543)
T KOG0802|consen  476 REPNDVCAICYQEM----SARITP-CS---HALCLRKWLYVQEVCPLCHTYMKEDDFL  525 (543)
T ss_pred             hcccCcchHHHHHH----Hhcccc-cc---chhHHHhhhhhccccCCCchhhhccccc
Confidence            34457899999998    346666 88   8999999999999999999888766443

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

Probab=88.56  E-value=0.17  Score=47.01  Aligned_cols=41  Identities=27%  Similarity=0.784  Sum_probs=27.3

Q ss_pred             CCcCccccCc-----ccCCCceeecCCCCccccHhhHHHHHhcCCCCccc
Q 042698          109 DNECVICLSD-----FAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKC  153 (203)
Q Consensus       109 ~~~CaICl~~-----~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~C  153 (203)
                      ...|.+|-..     |+ .+.++.+..|+++||+.|+..   ....||.|
T Consensus       511 gfiCe~Cq~~~iiyPF~-~~~~~rC~~C~avfH~~C~~r---~s~~CPrC  556 (580)
T KOG1829|consen  511 GFICELCQHNDIIYPFE-TRNTRRCSTCLAVFHKKCLRR---KSPCCPRC  556 (580)
T ss_pred             eeeeeeccCCCcccccc-cccceeHHHHHHHHHHHHHhc---cCCCCCch
Confidence            3567777221     33 344555556999999999765   44559999

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

Probab=88.53  E-value=0.35  Score=41.47  Aligned_cols=44  Identities=20%  Similarity=0.522  Sum_probs=32.1

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  159 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  159 (203)
                      .+|+||.+.+..+  +.+.+ =||.-+..|-.   +....||.||..+..
T Consensus        49 leCPvC~~~l~~P--i~QC~-nGHlaCssC~~---~~~~~CP~Cr~~~g~   92 (299)
T KOG3002|consen   49 LDCPVCFNPLSPP--IFQCD-NGHLACSSCRT---KVSNKCPTCRLPIGN   92 (299)
T ss_pred             ccCchhhccCccc--ceecC-CCcEehhhhhh---hhcccCCcccccccc
Confidence            5799999999886  33322 26877777765   456779999988873

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.03  E-value=0.25  Score=41.18  Aligned_cols=51  Identities=27%  Similarity=0.710  Sum_probs=34.5

Q ss_pred             CCCCcCccccCcccCCC---ceeecCCC---CccccHhhHHHHHhcCC--------CCcccccccc
Q 042698          107 GLDNECVICLSDFAPGE---RVRILPKC---NHGFHVRCIDKWLRSNS--------SCPKCRHCLI  158 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~---~v~~l~~C---~H~FH~~Ci~~Wl~~~~--------~CP~CR~~l~  158 (203)
                      +.+..|=||+..=+++.   .|.-+. |   .|.-|..|+..|+..+.        +||-|+....
T Consensus        18 e~eR~CWiCF~TdeDn~~a~WV~PCr-CRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYi   82 (293)
T KOG3053|consen   18 ELERCCWICFATDEDNRLAAWVHPCR-CRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYI   82 (293)
T ss_pred             ccceeEEEEeccCcccchhhhccccc-ccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchhe
Confidence            34567999998755543   222232 4   39999999999994221        4999987544

>smart00249 PHD PHD zinc finger

Probab=87.93  E-value=0.44  Score=27.99  Aligned_cols=31  Identities=19%  Similarity=0.499  Sum_probs=22.7

Q ss_pred             cCccccCcccCCCceeecCCCCccccHhhHHH
Q 042698          111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDK  142 (203)
Q Consensus       111 ~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~  142 (203)
                      .|.+|.... .++.+.....|+..||..|+..
T Consensus         1 ~C~~C~~~~-~~~~~i~C~~C~~~~H~~C~~~   31 (47)
T smart00249        1 YCSVCGKPD-DGGELLQCDGCDRWYHQTCLGP   31 (47)
T ss_pred             CcccCCCcC-CCCCEEECCCCCchhhhhhCCC
Confidence            378888776 4445555556999999999854

The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the

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

Probab=87.88  E-value=0.44  Score=45.28  Aligned_cols=41  Identities=24%  Similarity=0.484  Sum_probs=30.8

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPK  152 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~  152 (203)
                      -.|.+|-..+..  .....+.|+|.-|.+|+..|+.....||.
T Consensus       780 ~~CtVC~~vi~G--~~~~c~~C~H~gH~sh~~sw~~~~s~ca~  820 (839)
T KOG0269|consen  780 AKCTVCDLVIRG--VDVWCQVCGHGGHDSHLKSWFFKASPCAK  820 (839)
T ss_pred             cCceeecceeee--eEeecccccccccHHHHHHHHhcCCCCcc
Confidence            368888665543  23345569999999999999988877765

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

Probab=87.88  E-value=0.37  Score=40.93  Aligned_cols=52  Identities=27%  Similarity=0.683  Sum_probs=36.1

Q ss_pred             CCcCccccCcccCCCc-eeecC-CCC---ccccHhhHHHHHh--cCCCCcccccccccc
Q 042698          109 DNECVICLSDFAPGER-VRILP-KCN---HGFHVRCIDKWLR--SNSSCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~-v~~l~-~C~---H~FH~~Ci~~Wl~--~~~~CP~CR~~l~~~  160 (203)
                      +..|-||.++...... ....| .|+   +..|..|++.|+.  .+..|.+|.......
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            4689999998765431 23344 143   6779999999997  445699998755544

>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]

Probab=87.71  E-value=0.25  Score=40.80  Aligned_cols=46  Identities=30%  Similarity=0.850  Sum_probs=34.4

Q ss_pred             CCcCccccCc-ccCCC-ceeecCCCCccccHhhHHHHHhcC-CCCc--ccc
Q 042698          109 DNECVICLSD-FAPGE-RVRILPKCNHGFHVRCIDKWLRSN-SSCP--KCR  154 (203)
Q Consensus       109 ~~~CaICl~~-~~~~~-~v~~l~~C~H~FH~~Ci~~Wl~~~-~~CP--~CR  154 (203)
                      +..|+||-.+ |-.++ ++-+-|.|-|..|..|+++-+... ..||  -|-
T Consensus        10 d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~   60 (314)
T COG5220          10 DRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCG   60 (314)
T ss_pred             cccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHH
Confidence            4689999877 34444 444556799999999999998654 5799  773

>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=87.26  E-value=0.56  Score=39.74  Aligned_cols=47  Identities=23%  Similarity=0.664  Sum_probs=33.2

Q ss_pred             cCccccCc-ccCCCceeecCCCCccccHhhHHHHHhc-CCCCccccccc
Q 042698          111 ECVICLSD-FAPGERVRILPKCNHGFHVRCIDKWLRS-NSSCPKCRHCL  157 (203)
Q Consensus       111 ~CaICl~~-~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l  157 (203)
                      .|++|-.. |..++.......|+|-.+..|++.-+.. ...||-|-.-+
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iL   50 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVIL   50 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchh
Confidence            48888765 4555533333349999999999998754 55799995433

>PF01708 Gemini_mov: Geminivirus putative movement protein ; InterPro: IPR002621 This family consists of putative movement proteins from Maize streak virus and Wheat dwarf virus []

Probab=86.27  E-value=1.3  Score=30.94  Aligned_cols=41  Identities=20%  Similarity=0.183  Sum_probs=26.3

Q ss_pred             CCCCCCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHH
Q 042698           19 QPVTAAHPYSSESSLNSNAVIVLSVLVCGIICSLGLHFLIR   59 (203)
Q Consensus        19 ~p~~~~~~~~s~~~~~~~~iiii~il~~~~i~~l~~~~~~~   59 (203)
                      |.++...+.+|+..++....+++++++.+.++.|+..++.|
T Consensus        20 P~~p~~~p~ss~~~ws~vv~v~i~~lvaVg~~YL~y~~fLk   60 (91)
T PF01708_consen   20 PRVPTAAPSSSGLPWSRVVEVAIFTLVAVGCLYLAYTWFLK   60 (91)
T ss_pred             CCCCCCCCCCCCCcceeEeeeeehHHHHHHHHHHHHHHHHH
Confidence            34445667778888888777777666666655555554443

; GO: 0046740 spread of virus in host, cell to cell, 0016021 integral to membrane

>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=86.17  E-value=0.47  Score=29.09  Aligned_cols=44  Identities=23%  Similarity=0.539  Sum_probs=30.4

Q ss_pred             cCccccCcccCCCceeecCCCCccccHhhHHHHHh------cCCCCccccc
Q 042698          111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR------SNSSCPKCRH  155 (203)
Q Consensus       111 ~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~------~~~~CP~CR~  155 (203)
                      .|.||.. ...+..+.....|+..||..|+..=..      ..-.||.|+.
T Consensus         1 ~C~vC~~-~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~   50 (51)
T PF00628_consen    1 YCPVCGQ-SDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP   50 (51)
T ss_dssp             EBTTTTS-SCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred             eCcCCCC-cCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence            3889988 344455666667999999999976432      1235888853

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....

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

Probab=85.93  E-value=0.3  Score=43.38  Aligned_cols=38  Identities=24%  Similarity=0.658  Sum_probs=28.4

Q ss_pred             CCcCccccCcccCC-CceeecCCCCccccHhhHHHHHhcC
Q 042698          109 DNECVICLSDFAPG-ERVRILPKCNHGFHVRCIDKWLRSN  147 (203)
Q Consensus       109 ~~~CaICl~~~~~~-~~v~~l~~C~H~FH~~Ci~~Wl~~~  147 (203)
                      ..+|.||..+.... ++..+.. |+|.|+.+|+...+..+
T Consensus       146 ~~~C~iC~~e~~~~~~~f~~~~-C~H~fC~~C~k~~iev~  184 (384)
T KOG1812|consen  146 KEECGICFVEDPEAEDMFSVLK-CGHRFCKDCVKQHIEVK  184 (384)
T ss_pred             cccCccCccccccHhhhHHHhc-ccchhhhHHhHHHhhhh
Confidence            46899999555544 4445454 99999999999988643

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

Probab=85.62  E-value=0.21  Score=47.06  Aligned_cols=47  Identities=30%  Similarity=0.667  Sum_probs=36.6

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhc---CCCCcccccccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS---NSSCPKCRHCLIES  160 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~---~~~CP~CR~~l~~~  160 (203)
                      .+|+||+..+..+   ..+. |.|.|...|+..-+..   ...||+|+..+.-.
T Consensus        22 lEc~ic~~~~~~p---~~~k-c~~~~l~~~~n~~f~~~~~~~~~~lc~~~~eK~   71 (684)
T KOG4362|consen   22 LECPICLEHVKEP---SLLK-CDHIFLKFCLNKLFESKKGPKQCALCKSDIEKR   71 (684)
T ss_pred             ccCCceeEEeecc---chhh-hhHHHHhhhhhceeeccCccccchhhhhhhhhh
Confidence            5899999999886   4555 9999999998765543   34699998776644

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=85.59  E-value=0.47  Score=40.32  Aligned_cols=29  Identities=21%  Similarity=0.629  Sum_probs=22.3

Q ss_pred             CCccccHhhHHHHHh-------------cCCCCccccccccc
Q 042698          131 CNHGFHVRCIDKWLR-------------SNSSCPKCRHCLIE  159 (203)
Q Consensus       131 C~H~FH~~Ci~~Wl~-------------~~~~CP~CR~~l~~  159 (203)
                      |.-..+.+|+.+|+.             .+.+||+||+.+--
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci  366 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCI  366 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEE
Confidence            667788899999984             23469999987653

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

Probab=85.01  E-value=0.79  Score=40.46  Aligned_cols=44  Identities=18%  Similarity=0.403  Sum_probs=35.2

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC---CCccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS---SCPKC  153 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~---~CP~C  153 (203)
                      -..|+|=.+.-.++..-..+. |||+..++-+..--++..   .||.|
T Consensus       334 vF~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYC  380 (394)
T KOG2817|consen  334 VFICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYC  380 (394)
T ss_pred             eeecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCC
Confidence            357999887777766677787 999999999999665544   59999

>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines

Probab=84.90  E-value=0.53  Score=25.22  Aligned_cols=23  Identities=22%  Similarity=0.658  Sum_probs=14.9

Q ss_pred             cCccccCcccCCCceeecCCCCccc
Q 042698          111 ECVICLSDFAPGERVRILPKCNHGF  135 (203)
Q Consensus       111 ~CaICl~~~~~~~~v~~l~~C~H~F  135 (203)
                      .|+-|..++...  .+..|.|||.|
T Consensus         2 ~CP~C~~~V~~~--~~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCPECGAEVPES--AKFCPHCGYDF   24 (26)
T ss_pred             cCCCCcCCchhh--cCcCCCCCCCC
Confidence            477777766443  45566688877

Several members are annotated as putative helicases.

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=84.14  E-value=0.4  Score=45.73  Aligned_cols=43  Identities=23%  Similarity=0.566  Sum_probs=32.3

Q ss_pred             CCcCccccCcccCC----CceeecCCCCccccHhhHHHHHhcCCCCccc
Q 042698          109 DNECVICLSDFAPG----ERVRILPKCNHGFHVRCIDKWLRSNSSCPKC  153 (203)
Q Consensus       109 ~~~CaICl~~~~~~----~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~C  153 (203)
                      ...|.-|.+..-..    +.+.++. |+|.||+.|+..-..+++ |-.|
T Consensus       784 e~rc~~c~~~~l~~~~~~~~~~v~~-c~h~yhk~c~~~~~~~~~-~~~~  830 (846)
T KOG2066|consen  784 EERCSSCFEPNLPSGAAFDSVVVFH-CGHMYHKECLMMESLRNA-CNIE  830 (846)
T ss_pred             hhhhhhhcccccccCcccceeeEEE-ccchhhhcccccHHHhcc-cChh
Confidence            34799999886532    4567777 999999999998876655 5444

>PF08374 Protocadherin: Protocadherin; InterPro: IPR013585 The structure of protocadherins is similar to that of classic cadherins (IPR002126 from INTERPRO), but they also have some unique features associated with the cytoplasmic domains

Probab=84.02  E-value=1.7  Score=35.30  Aligned_cols=49  Identities=14%  Similarity=0.177  Sum_probs=23.1

Q ss_pred             ccCCCCCCCCCCCCCCCCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042698           12 IQNPLNEQPVTAAHPYSSESSLNSNAVIVLSVLVCGIICSLGLHFLIRCIL   62 (203)
Q Consensus        12 ~~~~~~~~p~~~~~~~~s~~~~~~~~iiii~il~~~~i~~l~~~~~~~~~~   62 (203)
                      |..|..+..++.+++..+....+..+.++-+++.++  +++++..++|+++
T Consensus        16 ~~tPl~~~Ia~d~~~~~~~d~~~I~iaiVAG~~tVI--LVI~i~v~vR~CR   64 (221)
T PF08374_consen   16 LETPLDRNIAGDPASSRSKDYVKIMIAIVAGIMTVI--LVIFIVVLVRYCR   64 (221)
T ss_pred             ccCCCcCcccCCCCccccccceeeeeeeecchhhhH--HHHHHHHHHHHHh
Confidence            346677776665555555444444433443333333  3333333445333

They are expressed in a variety of organisms and are found in high concentrations in the brain where they seem to be localised mainly at cell-cell contact sites. Their expression seems to be developmentally regulated [].

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

Probab=83.29  E-value=0.94  Score=34.09  Aligned_cols=51  Identities=24%  Similarity=0.482  Sum_probs=34.8

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHH-HHH--hcCCCCcccccccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCID-KWL--RSNSSCPKCRHCLIES  160 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~-~Wl--~~~~~CP~CR~~l~~~  160 (203)
                      .+|-||.|.-.+..-+.--..||-..+.-|-. .|-  ..+..||+|+.++-..
T Consensus        81 YeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss  134 (140)
T PF05290_consen   81 YECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSS  134 (140)
T ss_pred             eeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCccccccccc
Confidence            58999998866553333222589888877654 453  2467899999987654

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

Probab=82.78  E-value=0.96  Score=43.36  Aligned_cols=57  Identities=9%  Similarity=0.219  Sum_probs=40.5

Q ss_pred             CCCCcCccccCcccCCC---ceeecCCCCccccHhhHHHHHhc------CCCCccccccccccccc
Q 042698          107 GLDNECVICLSDFAPGE---RVRILPKCNHGFHVRCIDKWLRS------NSSCPKCRHCLIESCKK  163 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~---~v~~l~~C~H~FH~~Ci~~Wl~~------~~~CP~CR~~l~~~~~~  163 (203)
                      ....+|.+|.-++..++   .+-.+.+|+|-|+-.||..|...      +..|+.|...+....+.
T Consensus        94 a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWsR~  159 (1134)
T KOG0825|consen   94 AESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWSRC  159 (1134)
T ss_pred             ccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhhhhhhh
Confidence            34567888888887732   22222359999999999999842      33589999888866544

>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]

Probab=81.39  E-value=0.78  Score=37.21  Aligned_cols=42  Identities=29%  Similarity=0.736  Sum_probs=33.8

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCR  154 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR  154 (203)
                      ..|-+|..-.-.+   +.+..|+-.||..|+..++++...||.|-
T Consensus       182 k~Cn~Ch~LvIqg---~rCg~c~i~~h~~c~qty~q~~~~cphc~  223 (235)
T KOG4718|consen  182 KNCNLCHCLVIQG---IRCGSCNIQYHRGCIQTYLQRRDICPHCG  223 (235)
T ss_pred             HHHhHhHHHhhee---eccCcccchhhhHHHHHHhcccCcCCchh
Confidence            4799998765443   44445999999999999999988899994

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	203
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		9e-12
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		1e-09
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		2e-08
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		6e-07
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		2e-06
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		9e-05

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 24/44 (54%), Positives = 31/44 (70%)
Query: 111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCR 154
           EC +CL++   GE  R LP+C HGFH  C+D WL S+S+CP CR
Sbjct: 7   ECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50

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

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 23/43 (53%), Positives = 33/43 (76%), Gaps = 1/43 (2%)
Query: 112 CVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCR 154
           CV+C+ DF   + +R+LP CNH FH +C+DKWL++N +CP CR
Sbjct: 26  CVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICR 67

>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 = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/66 (45%), Positives = 36/66 (54%), Gaps = 5/66 (7%)
Query: 111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQP 170
           EC +C  D+A GE VR LP CNH FH  CI  WL  + SCP CR  L         +T P
Sbjct: 17  ECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQ----NTATNP 71
Query: 171 SSLSGI 176
             L+G+
Sbjct: 72  PGLTGV 77

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 24/44 (54%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCR 154
           +C ICLS    GE VR LP C H FH  C+D+WL +N  CP CR
Sbjct: 16  KCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICR 58

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 100 SGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKC 153
           SG++K   L   C +CL DF P + + I P C H FH +C+ KWL     CP C
Sbjct: 6   SGKVKELNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLC 58

>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 = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 81  LAKTGIKKKALKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCI 140
           +A     K+++ A   +  + +    G +  C IC S++  G+    LP C+H FH  C+
Sbjct: 12  VANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCV 70
Query: 141 DKWLRSNSSCPKCR 154
             WL+ + +CP CR
Sbjct: 71  SIWLQKSGTCPVCR 84

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	203
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	3e-27
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	3e-27
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	9e-26
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	4e-23
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	9e-23
2ect_A	78	Ring finger protein 126; metal binding protein, st	2e-22
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	1e-17
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	1e-17
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	2e-15
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	2e-13
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	2e-12
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	4e-11
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-10
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	8e-10
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	1e-09
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	1e-09
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	2e-09
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	2e-09
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	3e-08
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	2e-07
3nw0_A	238	Non-structural maintenance of chromosomes element	2e-07
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	2e-07
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	9e-07
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	2e-06
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	2e-06
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	2e-06
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	5e-06
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	8e-04
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	1e-05
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	4e-05
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	1e-04
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	3e-04
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	9e-04

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

 Score = 97.3 bits (243), Expect = 3e-27
 Identities = 24/50 (48%), Positives = 33/50 (66%)

Query: 109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI 158
             EC +CL++   GE  R LP+C HGFH  C+D WL S+S+CP CR  ++
Sbjct: 5   GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

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

 Score = 98.2 bits (245), Expect = 3e-27
 Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 1/82 (1%)

Query: 76  NSSTPLAKTGIKKKALKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGF 135
           + S  +A     K+++ A   +  + +    G +  C IC S++  G+    LP C+H F
Sbjct: 7   HHSHMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYF 65

Query: 136 HVRCIDKWLRSNSSCPKCRHCL 157
           H  C+  WL+ + +CP CR   
Sbjct: 66  HKPCVSIWLQKSGTCPVCRCMF 87

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

 Score = 93.9 bits (234), Expect = 9e-26
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 88  KKALKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN 147
             +       +++           CV+C+ DF   + +R+LP CNH FH +C+DKWL++N
Sbjct: 3   SGSSGQLPSYRFN-PNNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKAN 60

Query: 148 SSCPKCRHCLIES 160
            +CP CR     S
Sbjct: 61  RTCPICRADSGPS 73

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

 Score = 87.1 bits (216), Expect = 4e-23
 Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 5/73 (6%)

Query: 100 SGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE 159
           SG++K   L   C +CL DF P + + I P C H FH +C+ KWL     CP C   +++
Sbjct: 6   SGKVKELNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQ 64

Query: 160 SCKKIEGSTQPSS 172
                   + PSS
Sbjct: 65  L----AQLSGPSS 73

>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 = 86.3 bits (214), Expect = 9e-23
 Identities = 27/60 (45%), Positives = 33/60 (55%), Gaps = 2/60 (3%)

Query: 97  VKYSGELKL-PGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRH 155
           +K  GE       + +C ICLS    GE VR LP C H FH  C+D+WL +N  CP CR 
Sbjct: 1   MKQDGEEGTEEDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRV 59

>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 = 85.6 bits (212), Expect = 2e-22
 Identities = 30/67 (44%), Positives = 35/67 (52%), Gaps = 5/67 (7%)

Query: 109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGST 168
             EC +C  D+A GE VR LP CNH FH  CI  WL  + SCP CR  L         +T
Sbjct: 15  GLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQ----NTAT 69

Query: 169 QPSSLSG 175
            P  L+G
Sbjct: 70  NPPGLTG 76

>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 = 72.7 bits (179), Expect = 1e-17
 Identities = 14/46 (30%), Positives = 19/46 (41%)

Query: 109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCR 154
            + C ICL D      V  +  C H  H  C ++ L+    CP C 
Sbjct: 5   SSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCS 50

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

 Score = 73.4 bits (180), Expect = 1e-17
 Identities = 14/47 (29%), Positives = 27/47 (57%)

Query: 108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCR 154
           + + C+ C ++    + V +  +CNH FH  C+  W++ N+ CP C+
Sbjct: 25  VMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71

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

 Score = 67.0 bits (164), Expect = 2e-15
 Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 5/61 (8%)

Query: 100 SGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE 159
           SG +K    + EC IC+   A      ILP C H F  +CIDKW   + +CP CR  +  
Sbjct: 6   SGRVKQLTDEEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTG 60

Query: 160 S 160
           +
Sbjct: 61  A 61

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

 Score = 61.7 bits (150), Expect = 2e-13
 Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 3/51 (5%)

Query: 105 LPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRH 155
           +  +   C ICL D         LP C H F   CI +W+R N +CP C+ 
Sbjct: 1   MATVAERCPICLEDP--SNYSMALP-CLHAFCYVCITRWIRQNPTCPLCKV 48

>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 = 59.8 bits (144), Expect = 2e-12
 Identities = 20/91 (21%), Positives = 30/91 (32%), Gaps = 17/91 (18%)

Query: 78  STPLAKTGIKKKALKAFTIVKYSGELKLPGLDNECVIC--------------LSDFAPGE 123
           S   +  G K+  +K +  V          + + C IC               +     E
Sbjct: 9   SGTNSGAGKKRFEVKKWNAVALW---AWDIVVDNCAICRNHIMDLCIECQANQASATSEE 65

Query: 124 RVRILPKCNHGFHVRCIDKWLRSNSSCPKCR 154
                  CNH FH  CI +WL++   CP   
Sbjct: 66  CTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 96

>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 = 57.2 bits (137), Expect = 4e-11
 Identities = 19/93 (20%), Positives = 29/93 (31%), Gaps = 17/93 (18%)

Query: 76  NSSTPLAKTGIKKKALKAFTIVKYSGELKLPGLDNECVIC--------------LSDFAP 121
                 +  G K+  +K +  V          + + C IC               +    
Sbjct: 18  GGRGTNSGAGKKRFEVKKWNAVALW---AWDIVVDNCAICRNHIMDLCIECQANQASATS 74

Query: 122 GERVRILPKCNHGFHVRCIDKWLRSNSSCPKCR 154
            E       CNH FH  CI +WL++   CP   
Sbjct: 75  EECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

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

 Score = 53.8 bits (129), Expect = 2e-10
 Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 3/59 (5%)

Query: 100 SGELKLPGLDNECVICLSDFA---PGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRH 155
           SG    P     C IC+  ++      R+ +  +C H F  +C+   L++ ++CP CR 
Sbjct: 6   SGTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 64

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

 Score = 52.1 bits (125), Expect = 8e-10
 Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 3/48 (6%)

Query: 111 ECVICLSDF---APGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRH 155
            C IC+  +       R+ +  +C H F  +C+   L++ ++CP CR 
Sbjct: 5   SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 52

>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 = 52.9 bits (126), Expect = 1e-09
 Identities = 21/84 (25%), Positives = 33/84 (39%), Gaps = 20/84 (23%)

Query: 92  KAFTIVKYSGELKLPGLDNECVICLSDFAPG--------------ERVRILPKCNHGFHV 137
               I KY+ ELK+   + +C+IC+   A                  V  L KC+H FH+
Sbjct: 9   PEQVIRKYTEELKVA-PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHL 67

Query: 138 RCIDKWLRSNS-----SCPKCRHC 156
            C+     + +      CP C+  
Sbjct: 68  LCLLAMYCNGNKDGSLQCPSCKTI 91

>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 = 51.4 bits (123), Expect = 1e-09
 Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 3/48 (6%)

Query: 111 ECVICLSDFAPGERVRILP---KCNHGFHVRCIDKWLRSNSSCPKCRH 155
            C IC+  ++   +   L    +C H F  +C+   L++ ++CP CR 
Sbjct: 12  SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 59

>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 = 52.2 bits (125), Expect = 2e-09
 Identities = 15/51 (29%), Positives = 20/51 (39%), Gaps = 4/51 (7%)

Query: 111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWL-RSNSSCPKCRHCLIES 160
            C IC+         R+ P C+      CI +WL    + CP CR  L   
Sbjct: 24  RCFICMEKL---RDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLR 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 = 51.5 bits (123), Expect = 2e-09
 Identities = 13/47 (27%), Positives = 18/47 (38%), Gaps = 5/47 (10%)

Query: 110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS--NSSCPKCR 154
             C IC S    G+       C    H+ C+ K+ +S     CP C 
Sbjct: 16  KICNICHSLLIQGQS---CETCGIRMHLPCVAKYFQSNAEPRCPHCN 59

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

 Score = 51.8 bits (123), Expect = 3e-08
 Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 15/62 (24%)

Query: 109 DNECVICLSDFAPGERVRIL----PKCNHGFHVRCIDKWLRSNSS-----------CPKC 153
           +  C IC +    G  V ++     KC    H  C+++W ++              CP C
Sbjct: 308 ELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFC 367

Query: 154 RH 155
           + 
Sbjct: 368 KA 369

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

 Score = 46.0 bits (109), Expect = 2e-07
 Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 4/47 (8%)

Query: 108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCR 154
           +   C IC   F    +  ++ KC H F   C  +  R+   C  C 
Sbjct: 14  IPFRCFICRQAF----QNPVVTKCRHYFCESCALEHFRATPRCYICD 56

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

 Score = 48.6 bits (115), Expect = 2e-07
 Identities = 14/52 (26%), Positives = 19/52 (36%), Gaps = 5/52 (9%)

Query: 106 PGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS--NSSCPKCRH 155
           P     C IC S    G+       C    H+ C+ K+ +S     CP C  
Sbjct: 177 PDAVKICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCND 225

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

 Score = 45.9 bits (109), Expect = 2e-07
 Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 3/50 (6%)

Query: 111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES 160
            C IC            + +C H F   CI +    ++ CPKC   + ++
Sbjct: 17  LCSICKGYL---IDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQT 63

>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 = 44.8 bits (106), Expect = 9e-07
 Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 5/60 (8%)

Query: 103 LKLPGLDNE--CVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES 160
           +K+  L+    CV+C   F        + +C H F   CI ++L ++  CP C   + ++
Sbjct: 7   IKITELNPHLMCVLCGGYF---IDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT 63

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

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 14/49 (28%), Positives = 16/49 (32%), Gaps = 4/49 (8%)

Query: 109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCL 157
             EC ICL           LP C H F   C+         C  CR  +
Sbjct: 15  VPECAICLQTC---VHPVSLP-CKHVFCYLCVKGASWLGKRCALCRQEI 59

>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 = 46.7 bits (110), Expect = 2e-06
 Identities = 19/68 (27%), Positives = 27/68 (39%), Gaps = 6/68 (8%)

Query: 98  KYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS-SCPKCRHC 156
           +Y    ++      C IC  +      V+I P C H     C+  W  S    CP CR C
Sbjct: 321 QYELYCEMGSTFQLCKICAENDK---DVKIEP-CGHLMCTSCLTSWQESEGQGCPFCR-C 375

Query: 157 LIESCKKI 164
            I+  + I
Sbjct: 376 EIKGTEPI 383

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

 Score = 44.6 bits (105), Expect = 2e-06
 Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCL 157
           + +C+IC   F       +   C H F   CI++W++    CP CR  +
Sbjct: 64  ELQCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDI 108

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

 Score = 43.2 bits (101), Expect = 5e-06
 Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 3/54 (5%)

Query: 111 ECVICLSDFAPGERVRILP---KCNHGFHVRCIDKWLRSNSSCPKCRHCLIESC 161
            C IC+  ++   +   L    +C H F  +C+   L++ ++CP CR  +    
Sbjct: 9   SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR 62

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

 Score = 37.1 bits (85), Expect = 8e-04
 Identities = 13/53 (24%), Positives = 25/53 (47%), Gaps = 3/53 (5%)

Query: 111 ECVICLSDF---APGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES 160
            C IC+  +       R+ +  +C H F  +C+   L++ ++CP CR  +   
Sbjct: 74  SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHK 126

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

 Score = 41.3 bits (97), Expect = 1e-05
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 5/50 (10%)

Query: 112 CVICLSDF-APGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES 160
           C IC   F        I+P+C+H +   CI K+L   + CP C   + E 
Sbjct: 25  CGICFEYFNIA----MIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEP 70

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

 Score = 39.7 bits (92), Expect = 4e-05
 Identities = 10/48 (20%), Positives = 15/48 (31%), Gaps = 1/48 (2%)

Query: 109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS-NSSCPKCRH 155
             EC +C+      +       C +     C  +     N  CP CR 
Sbjct: 11  PVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRK 58

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

 Score = 38.5 bits (90), Expect = 1e-04
 Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 3/48 (6%)

Query: 111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS---SCPKCRH 155
           EC IC+  F   +    L  C H    +C++K L S+     CP C  
Sbjct: 17  ECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSK 64

>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 = 38.4 bits (89), Expect = 3e-04
 Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 5/51 (9%)

Query: 111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS-SCPKCRHCLIES 160
           +C+ C        R      C H     C+D+  R+   SCP CR+ L  S
Sbjct: 54  QCICCQELV---FRPITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGRS 100

>1wim_A KIAA0161 protein; ring finger domain, UBCM4-interacting protein 4, UIP4, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.1 Length = 94

 Score = 36.4 bits (84), Expect = 9e-04
 Identities = 11/55 (20%), Positives = 23/55 (41%), Gaps = 3/55 (5%)

Query: 111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS--NSSCPKCRHCLIESCKK 163
            C +CL ++ P E++  + +C   F   C+ +++             C   +C K
Sbjct: 7   GCKLCLGEY-PVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPK 60

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	203
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.78
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.68
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.64
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.63
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.62
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.61
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.59
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.53
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.53
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.5
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.49
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.49
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.48
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.47
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.47
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.45
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.42
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.42
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.39
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.38
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.36
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.35
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.35
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.34
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.33
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.3
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.27
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.26
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.26
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.26
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.26
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.24
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.24
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.24
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.22
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.22
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.22
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.21
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.18
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.16
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.15
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.12
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.09
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.08
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.07
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.06
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.05
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.02
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.01
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.0
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	98.96
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	98.96
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.96
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	98.94
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	98.91
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.9
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.88
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.82
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.79
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.78
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.72
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.71
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.69
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.69
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.64
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.51
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.5
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.43
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.39
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.34
3nw0_A	238	Non-structural maintenance of chromosomes element	98.26
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.11
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	96.82
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	95.86
1we9_A	64	PHD finger family protein; structural genomics, PH	95.67
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	95.44
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	94.87
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	94.7
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	94.4
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	94.08
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	93.6
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	93.46
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	93.05
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	93.05
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	93.05
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	92.8
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	92.34
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	92.29
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	91.93
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	91.79
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	91.68
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	91.46
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	91.26
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	90.81
1wem_A	76	Death associated transcription factor 1; structura	90.4
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	90.04
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	89.99
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	89.61
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	89.25
1wee_A	72	PHD finger family protein; structural genomics, PH	89.08
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	89.08
2yt5_A	66	Metal-response element-binding transcription facto	88.46
1weu_A	91	Inhibitor of growth family, member 4; structural g	88.39
2knc_A	54	Integrin alpha-IIB; transmembrane signaling, prote	88.31
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	88.06
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	87.27
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	86.99
2l8s_A	54	Integrin alpha-1; transmembrane region, detergent	86.63
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	86.31
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	85.46
1wew_A	78	DNA-binding family protein; structural genomics, P	84.99
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	84.95
3c6w_A	59	P28ING5, inhibitor of growth protein 5; chromatin,	84.82
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	84.57
2klu_A	70	T-cell surface glycoprotein CD4; cell membrane, di	84.51
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	82.69
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	81.99
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	81.84
3o7a_A	52	PHD finger protein 13 variant; PHF13, zinc finger,	80.55

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

Probab=99.78  E-value=5e-19  Score=124.49  Aligned_cols=82  Identities=28%  Similarity=0.621  Sum_probs=72.2

Q ss_pred             CCChhhhcCCCHHHHhhcCeEEccCCCCCCCCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccc
Q 042698           77 SSTPLAKTGIKKKALKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHC  156 (203)
Q Consensus        77 ~~~~~~~~~~~~~~~~~lp~~~~~~~~~~~~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~  156 (203)
                      ........+.+++.++.+|.+.+.......+.+.+|+||+++|..++.++.++ |+|.||..||..|++.+.+||+||..
T Consensus         8 ~~~~~~~~~~s~~~i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~Cr~~   86 (91)
T 2l0b_A            8 HSHMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCM   86 (91)
T ss_dssp             SCCSSCCCCCCHHHHHTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTTTCCB
T ss_pred             CCCCcCCCCCCHHHHHhCCCeeecccccccCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcCcCcc
Confidence            34455678899999999999999876655566788999999999999899999 99999999999999999999999998


Q ss_pred             ccc
Q 042698          157 LIE  159 (203)
Q Consensus       157 l~~  159 (203)
                      +..
T Consensus        87 ~~~   89 (91)
T 2l0b_A           87 FPP   89 (91)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            764

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

Probab=99.68  E-value=2.1e-17  Score=111.75  Aligned_cols=68  Identities=35%  Similarity=0.842  Sum_probs=57.2

Q ss_pred             HhhcCeEEccCCCCCCCCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698           91 LKAFTIVKYSGELKLPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus        91 ~~~lp~~~~~~~~~~~~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      ++.+|...+..... ...+.+|+||+++|..++.++.++ |+|.||..||..|++.+.+||+||+.+.+.
T Consensus         6 i~~lp~~~~~~~~~-~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A            6 SGQLPSYRFNPNNH-QSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             CSSCCCEEBCSSSC-SSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             HhhCCcEEecCccc-cCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            45677777765432 235578999999999999999999 999999999999999999999999988764

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

Probab=99.64  E-value=1.1e-16  Score=101.63  Aligned_cols=51  Identities=47%  Similarity=1.171  Sum_probs=46.0

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  158 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  158 (203)
                      ++.+|+||+++|..++.+..++.|+|.||..||..|++.+.+||+||..+.
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            456899999999998888888669999999999999999999999998764

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

Probab=99.63  E-value=3.5e-16  Score=105.33  Aligned_cols=54  Identities=37%  Similarity=0.971  Sum_probs=48.7

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESC  161 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  161 (203)
                      ..+.+|+||+++|..++.+..++ |+|.||..||..|++.+.+||+||..+....
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLA   66 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSSCC
T ss_pred             CCCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCccccccc
Confidence            45678999999999988888898 9999999999999999899999999987653

>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=99.62  E-value=5.6e-16  Score=102.94  Aligned_cols=54  Identities=44%  Similarity=0.938  Sum_probs=48.3

Q ss_pred             CCCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          106 PGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       106 ~~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      ...+.+|+||++.|..++.++.++ |+|.||..||..|++.+.+||+||..+...
T Consensus        11 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           11 EDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             TTCCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             CCCCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            345678999999999888888998 999999999999999999999999988764

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

Probab=99.61  E-value=7.8e-16  Score=104.64  Aligned_cols=53  Identities=51%  Similarity=1.030  Sum_probs=48.3

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      ..+.+|+||++.|..++.++.++ |+|.||..||..|++.+.+||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (78)
T 2ect_A           13 GSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQ   65 (78)
T ss_dssp             SSSCCCTTTTSCCCTTSCEEECT-TSCEEETTTTHHHHTTTCSCTTTCCCCCCS
T ss_pred             CCCCCCeeCCccccCCCCEEEeC-CCCeecHHHHHHHHHcCCcCcCcCCccCCc
Confidence            45678999999999988888898 999999999999999999999999998765

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

Probab=99.59  E-value=6.9e-16  Score=106.06  Aligned_cols=53  Identities=28%  Similarity=0.739  Sum_probs=43.2

Q ss_pred             CCCcCccccCcccC-----------CCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          108 LDNECVICLSDFAP-----------GERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       108 ~~~~CaICl~~~~~-----------~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      ++++|+||+++|..           ++.++.++.|+|.||.+||..|++.+.+||+||+.+...
T Consensus        14 ~~~~C~IC~~~~~~~C~iC~~~~~~~~~~~~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~   77 (81)
T 2ecl_A           14 ECDTCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQ   77 (81)
T ss_dssp             CCSCBTTTTBCTTSCCTTHHHHTCTTTCCEEEETTSCEEEHHHHHHHTTTCCBCTTTCCBCCEE
T ss_pred             CCCCCcccChhhhccCcccccccCCCceEEEeCCCCCccChHHHHHHHHhCCCCCCcCCCcchh
Confidence            35679999888854           344555555999999999999999999999999987654

>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=99.53  E-value=5.6e-15  Score=93.56  Aligned_cols=50  Identities=30%  Similarity=0.686  Sum_probs=43.0

Q ss_pred             CCCcCccccCcccCCC-ceeecCCCCccccHhhHHHHHhcCCCCcccccccc
Q 042698          108 LDNECVICLSDFAPGE-RVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  158 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~-~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  158 (203)
                      .+.+|+||++++..++ .+..++ |+|.||..||..|++.+.+||+||..+.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            4 GSSGCPICLEDIHTSRVVAHVLP-CGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             CCCSCTTTCCCCCTTTSCEEECT-TSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCcCcccChhhcCCCcCeEecC-CCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            3568999999996644 567777 9999999999999999899999998764

>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=99.53  E-value=6e-15  Score=107.28  Aligned_cols=52  Identities=27%  Similarity=0.729  Sum_probs=42.3

Q ss_pred             CCcCccccCcccCCC---------------ceeecCCCCccccHhhHHHHH-----hcCCCCccccccccccc
Q 042698          109 DNECVICLSDFAPGE---------------RVRILPKCNHGFHVRCIDKWL-----RSNSSCPKCRHCLIESC  161 (203)
Q Consensus       109 ~~~CaICl~~~~~~~---------------~v~~l~~C~H~FH~~Ci~~Wl-----~~~~~CP~CR~~l~~~~  161 (203)
                      +.+|+||+++|..+.               .++.++ |+|+||..||..|+     +.+.+||+||..+....
T Consensus        25 ~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~~   96 (114)
T 1v87_A           25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKT   96 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCS
T ss_pred             CCcCccCChhhcCcccccccccccccCcccceecCC-CCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCCC
Confidence            468999999997643               344677 99999999999999     45668999999887653

>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=99.50  E-value=1.4e-14  Score=104.47  Aligned_cols=50  Identities=30%  Similarity=0.663  Sum_probs=42.6

Q ss_pred             CCCcCccccCcccCCC---------------ceeecCCCCccccHhhHHHHHhcCCCCcccccccc
Q 042698          108 LDNECVICLSDFAPGE---------------RVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  158 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~---------------~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  158 (203)
                      .++.|+||+++|...-               .++.++ |+|.||..||..||+.+.+||+||+.+.
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWE  100 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecc-cCcEECHHHHHHHHHcCCcCcCCCCcce
Confidence            3578999999998541               356677 9999999999999999999999999854

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

Probab=99.49  E-value=9.3e-15  Score=97.26  Aligned_cols=53  Identities=23%  Similarity=0.597  Sum_probs=45.0

Q ss_pred             CCCCcCccccCcccCC----CceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          107 GLDNECVICLSDFAPG----ERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~----~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      .++.+|+||++.+.+.    +.+..++ |||.||..||..|++.+.+||+||..+...
T Consensus         8 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (71)
T 3ng2_A            8 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   64 (71)
T ss_dssp             TTCCBCTTTCCBHHHHHTTTCCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCCC
T ss_pred             CCCCCCcccChhhhccccccCCeEeCC-CCChHhHHHHHHHHHcCCCCCCCCCccChh
Confidence            3457899999998763    4556777 999999999999999999999999988754

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

Probab=99.49  E-value=1.4e-14  Score=95.75  Aligned_cols=52  Identities=23%  Similarity=0.608  Sum_probs=43.9

Q ss_pred             CCCCcCccccCcccCC----CceeecCCCCccccHhhHHHHHhcCCCCccccccccc
Q 042698          107 GLDNECVICLSDFAPG----ERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  159 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~----~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  159 (203)
                      ....+|+||++.|...    ..+..++ |+|.||..||..|++.+..||+||..+..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           13 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             TCCCCCTTTCCCHHHHTTTTCCEEECS-SSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCcccCccccccccccCCeEeCC-CCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            4457899999999764    3446777 99999999999999999999999998753

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

Probab=99.48  E-value=4.6e-14  Score=93.20  Aligned_cols=50  Identities=36%  Similarity=0.834  Sum_probs=43.3

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      .+.+|+||++.+.++  ...++ |||.||..|+..|++.+.+||+||..+...
T Consensus         4 ~~~~C~IC~~~~~~~--~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   53 (68)
T 1chc_A            4 VAERCPICLEDPSNY--SMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVESV   53 (68)
T ss_dssp             CCCCCSSCCSCCCSC--EEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCCE
T ss_pred             CCCCCeeCCccccCC--cEecC-CCCeeHHHHHHHHHhCcCcCcCCChhhHhh
Confidence            456899999998653  56787 999999999999999999999999988754

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

Probab=99.47  E-value=1.4e-14  Score=94.32  Aligned_cols=51  Identities=24%  Similarity=0.627  Sum_probs=43.9

Q ss_pred             CCcCccccCcccCC----CceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          109 DNECVICLSDFAPG----ERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~~~~~~----~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      +.+|+||++.+...    +.+..++ |||.||..||..|++.+.+||+||..+...
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   57 (64)
T 2xeu_A            3 MVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   57 (64)
T ss_dssp             CCBCTTTCCBHHHHHHTTCCEEEET-TSCEEEHHHHHHHHHHCSBCTTTCCBCTTT
T ss_pred             CCCCCccChhhhCccccCCCEEeCC-CCCchhHHHHHHHHHcCCCCCCCCccCCcc
Confidence            46899999999753    4556777 999999999999999999999999988754

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

Probab=99.47  E-value=4.3e-14  Score=96.92  Aligned_cols=53  Identities=28%  Similarity=0.727  Sum_probs=44.2

Q ss_pred             CCCCCcCccccCcccCCCceeecCCCC-----ccccHhhHHHHHhcC--CCCcccccccccc
Q 042698          106 PGLDNECVICLSDFAPGERVRILPKCN-----HGFHVRCIDKWLRSN--SSCPKCRHCLIES  160 (203)
Q Consensus       106 ~~~~~~CaICl~~~~~~~~v~~l~~C~-----H~FH~~Ci~~Wl~~~--~~CP~CR~~l~~~  160 (203)
                      ...+..|.||++++.+++.+ ++| |+     |.||..||+.|+..+  .+||+||..+...
T Consensus        12 ~~~~~~C~IC~~~~~~~~~l-~~p-C~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~   71 (80)
T 2d8s_A           12 PSSQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIME   71 (80)
T ss_dssp             CTTSCCCSSSCCCCCSSSCE-ECS-SSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCC
T ss_pred             CCCCCCCeEcCccccCCCee-Eec-cccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecC
Confidence            34567899999999877776 578 86     999999999999765  4899999988754

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

Probab=99.45  E-value=3.8e-14  Score=94.22  Aligned_cols=50  Identities=40%  Similarity=0.902  Sum_probs=43.6

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESC  161 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  161 (203)
                      ..+.+|+||++.+..    ..++ |+|.||..||..|++.+..||+||..+....
T Consensus        13 ~~~~~C~IC~~~~~~----~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (70)
T 2ecn_A           13 TDEEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGAN   62 (70)
T ss_dssp             CCCCCCSSSCCSCCS----EEET-TTEEECHHHHHHSSCCCSSCHHHHHCTTCCC
T ss_pred             CCCCCCeeCCcCccC----cccC-CCCcccHHHHHHHHHCcCcCCCcCCcccCCC
Confidence            445789999999876    5677 9999999999999999899999999887553

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

Probab=99.42  E-value=1.7e-13  Score=91.73  Aligned_cols=51  Identities=25%  Similarity=0.517  Sum_probs=43.2

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      .....|+||++.+.+.  +..++ |+|.||..||..|++.+..||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (72)
T 2djb_A           13 TPYILCSICKGYLIDA--TTITE-CLHTFCKSCIVRHFYYSNRCPKCNIVVHQT   63 (72)
T ss_dssp             CGGGSCTTTSSCCSSC--EECSS-SCCEECHHHHHHHHHHCSSCTTTCCCCCSS
T ss_pred             CCCCCCCCCChHHHCc--CEECC-CCCHHHHHHHHHHHHcCCcCCCcCcccCcc
Confidence            4567899999999774  44447 999999999999999889999999988754

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

Probab=99.42  E-value=9e-14  Score=92.80  Aligned_cols=50  Identities=30%  Similarity=0.537  Sum_probs=43.1

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      ..+.+|+||++.+.+.   ..++ |+|.||..||..|++.+..||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~~---~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   62 (71)
T 2d8t_A           13 LTVPECAICLQTCVHP---VSLP-CKHVFCYLCVKGASWLGKRCALCRQEIPED   62 (71)
T ss_dssp             SSCCBCSSSSSBCSSE---EEET-TTEEEEHHHHHHCTTCSSBCSSSCCBCCHH
T ss_pred             CCCCCCccCCcccCCC---EEcc-CCCHHHHHHHHHHHHCCCcCcCcCchhCHh
Confidence            3456899999998664   5667 999999999999999999999999998754

>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=99.39  E-value=3.2e-14  Score=104.23  Aligned_cols=50  Identities=32%  Similarity=0.707  Sum_probs=0.9

Q ss_pred             CCCcCccccCcccCC-------------C--ceeecCCCCccccHhhHHHHHhcCCCCcccccccc
Q 042698          108 LDNECVICLSDFAPG-------------E--RVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  158 (203)
Q Consensus       108 ~~~~CaICl~~~~~~-------------~--~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  158 (203)
                      .++.|+||+++|...             +  .+..++ |+|.||..||..|++.+.+||+||+.+.
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~-C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~  111 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWE  111 (117)
T ss_dssp             CC----------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCC-cCceEcHHHHHHHHHcCCcCCCCCCeee
Confidence            356899999999752             2  223345 9999999999999999999999999854

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

Probab=99.38  E-value=4.9e-13  Score=92.38  Aligned_cols=53  Identities=28%  Similarity=0.614  Sum_probs=44.5

Q ss_pred             CCCCcCccccCcccCCCc-eeecCCCCccccHhhHHHHHhcC---CCCcccccccccc
Q 042698          107 GLDNECVICLSDFAPGER-VRILPKCNHGFHVRCIDKWLRSN---SSCPKCRHCLIES  160 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~-v~~l~~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~l~~~  160 (203)
                      ....+|+||++.|...+. ...++ |||.||..||..|++.+   ..||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           13 REVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSSCEEECS-SSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             cCCCCCccCCccccccCCCeEECC-CCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            455789999999988664 56777 99999999999999875   6899999987543

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

Probab=99.36  E-value=6.8e-13  Score=89.29  Aligned_cols=52  Identities=21%  Similarity=0.535  Sum_probs=42.0

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC--CCCccccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN--SSCPKCRHCLIESC  161 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~--~~CP~CR~~l~~~~  161 (203)
                      ..+..|+||++.|.++   ..++.|||.||..||..|++.+  ..||+||..+....
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2yur_A           13 PDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD   66 (74)
T ss_dssp             CGGGSCSSSCCCCTTC---EECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTT
T ss_pred             CCCCCCcCCChHHhCC---eEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCcc
Confidence            4457899999999865   3455599999999999999865  58999999765443

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

Probab=99.35  E-value=9.7e-13  Score=88.64  Aligned_cols=51  Identities=27%  Similarity=0.667  Sum_probs=42.0

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC--CCCcccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN--SSCPKCRHCLIES  160 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~--~~CP~CR~~l~~~  160 (203)
                      +...+|+||.+.+..++...   .|+|.||..||..||+.+  .+||+||..+...
T Consensus        13 ~~i~~C~IC~~~i~~g~~C~---~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~   65 (74)
T 2ct0_A           13 DAVKICNICHSLLIQGQSCE---TCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE   65 (74)
T ss_dssp             SSSCBCSSSCCBCSSSEECS---SSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSC
T ss_pred             CCCCcCcchhhHcccCCccC---CCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCC
Confidence            44578999999998764333   499999999999999887  7899999887643

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

Probab=99.35  E-value=6.8e-13  Score=90.66  Aligned_cols=48  Identities=23%  Similarity=0.485  Sum_probs=41.5

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  158 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  158 (203)
                      .....|+||++.|...   .+++ |+|.||..||..|++....||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQNP---VVTK-CRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCCSE---EECT-TSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhcCe---eEcc-CCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            3456899999999763   4577 9999999999999998889999999875

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

Probab=99.34  E-value=8.5e-13  Score=86.70  Aligned_cols=50  Identities=20%  Similarity=0.539  Sum_probs=41.3

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHh-cCCCCcccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR-SNSSCPKCRHCLIES  160 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~l~~~  160 (203)
                      .....|+||++.+.++   ..++ |||.||..||..|+. .+..||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCSP---KQTE-CGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             CCCEECTTTCCEESSC---CCCS-SSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             CcCCCCCCCChHhcCe---eECC-CCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            4457899999999875   2366 999999999999994 566899999987654

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

Probab=99.33  E-value=1.1e-12  Score=87.54  Aligned_cols=50  Identities=24%  Similarity=0.573  Sum_probs=41.2

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHh---cCCCCcccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR---SNSSCPKCRHCLIES  160 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~---~~~~CP~CR~~l~~~  160 (203)
                      ..+..|+||++.+.+.   ..++ |||.||..||..|++   .+..||+||..+...
T Consensus        18 ~~~~~C~IC~~~~~~~---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   70 (73)
T 2ysl_A           18 QEEVICPICLDILQKP---VTID-CGHNFCLKCITQIGETSCGFFKCPLCKTSVRKN   70 (73)
T ss_dssp             CCCCBCTTTCSBCSSE---EECT-TCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCC
T ss_pred             ccCCEeccCCcccCCe---EEcC-CCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcc
Confidence            4457899999998753   4567 999999999999996   455799999988654

>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=9.1e-13  Score=99.08  Aligned_cols=48  Identities=31%  Similarity=0.855  Sum_probs=41.6

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      +..|+||++.|..+   ..++ |||.||..||..|+..+.+||+||..+...
T Consensus        53 ~~~C~iC~~~~~~~---~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  100 (138)
T 4ayc_A           53 ELQCIICSEYFIEA---VTLN-CAHSFCSYCINEWMKRKIECPICRKDIKSK  100 (138)
T ss_dssp             HSBCTTTCSBCSSE---EEET-TSCEEEHHHHHHHTTTCSBCTTTCCBCCCE
T ss_pred             cCCCcccCcccCCc---eECC-CCCCccHHHHHHHHHcCCcCCCCCCcCCCC
Confidence            35799999999764   5677 999999999999999999999999988543

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

Probab=99.27  E-value=1.4e-12  Score=96.43  Aligned_cols=53  Identities=23%  Similarity=0.581  Sum_probs=45.3

Q ss_pred             CCCcCccccCcccCC----CceeecCCCCccccHhhHHHHHhcCCCCccccccccccc
Q 042698          108 LDNECVICLSDFAPG----ERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESC  161 (203)
Q Consensus       108 ~~~~CaICl~~~~~~----~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  161 (203)
                      +..+|+||++.|.++    +.+..++ |||.||..||..|++.+.+||+||..+....
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~   62 (133)
T 4ap4_A            6 GTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKR   62 (133)
T ss_dssp             CSCBCTTTCCBHHHHHHTTCCEEEET-TCCEEEHHHHHHHHTTCSBCTTTCCBCTTTC
T ss_pred             CCCCCcccChhhhCccccccCeEecC-CCChhhHHHHHHHHHhCCCCCCCCCcCcccc
Confidence            456899999999764    4557777 9999999999999999999999999887554

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

Probab=99.26  E-value=6.7e-12  Score=81.54  Aligned_cols=43  Identities=28%  Similarity=0.634  Sum_probs=36.2

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHh---cCCCCccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR---SNSSCPKC  153 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~---~~~~CP~C  153 (203)
                      ..+..|+||++.+.+.   ..++ |||.||..||..|++   .+..||+|
T Consensus        18 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           18 QEEVICPICLDILQKP---VTID-CGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCBCTTTCSBCSSC---EECT-TSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             ccCCCCCcCCchhCCe---EEeC-CCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            4567899999999864   4567 999999999999997   45579998

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

Probab=99.26  E-value=6.1e-12  Score=86.03  Aligned_cols=50  Identities=30%  Similarity=0.517  Sum_probs=42.0

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc------CCCCcccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS------NSSCPKCRHCLIES  160 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~------~~~CP~CR~~l~~~  160 (203)
                      ..+.+|+||++.+...   ..++ |+|.||..||..|+..      ...||+||..+...
T Consensus        17 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~   72 (85)
T 2ecw_A           17 KEEVTCPICLELLKEP---VSAD-CNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFG   72 (85)
T ss_dssp             CTTTSCTTTCSCCSSC---EECT-TSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTT
T ss_pred             ccCCCCcCCChhhCcc---eeCC-CCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHH
Confidence            3457899999999775   4677 9999999999999987      56799999987643

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

Probab=99.26  E-value=4.5e-12  Score=85.79  Aligned_cols=49  Identities=24%  Similarity=0.487  Sum_probs=41.5

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc-CCCCccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIE  159 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~  159 (203)
                      ..+..|+||++.|.++   ..++ |||.||..||..|+.. +.+||+||..+..
T Consensus         6 ~~~~~C~IC~~~~~~P---v~~~-CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~   55 (78)
T 1t1h_A            6 PEYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             cccCCCCCccccccCC---EEcC-CCCeecHHHHHHHHHHCcCCCCCCcCCCCh
Confidence            3457899999999764   4567 9999999999999987 7789999998764

>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=99.26  E-value=2.6e-12  Score=91.37  Aligned_cols=48  Identities=27%  Similarity=0.648  Sum_probs=40.5

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC-CCCccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN-SSCPKCRHCLIE  159 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~l~~  159 (203)
                      +..|+||++.|...  +..++ |||.||..||..|++.+ ..||+||..+..
T Consensus        22 ~~~C~IC~~~~~~p--~~~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   70 (100)
T 3lrq_A           22 VFRCFICMEKLRDA--RLCPH-CSKLCCFSCIRRWLTEQRAQCPHCRAPLQL   70 (100)
T ss_dssp             HTBCTTTCSBCSSE--EECTT-TCCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             CCCCccCCccccCc--cccCC-CCChhhHHHHHHHHHHCcCCCCCCCCcCCH
Confidence            46799999999763  33377 99999999999999887 689999998864

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

Probab=99.24  E-value=6.4e-12  Score=85.89  Aligned_cols=49  Identities=31%  Similarity=0.609  Sum_probs=41.6

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc------CCCCccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS------NSSCPKCRHCLIE  159 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~------~~~CP~CR~~l~~  159 (203)
                      ....+|+||++.+...   ..++ |+|.||..||..|+..      ...||+||..+..
T Consensus        17 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecv_A           17 KEEVTCPICLELLTQP---LSLD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISYQP   71 (85)
T ss_dssp             CCCCCCTTTCSCCSSC---BCCS-SSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCS
T ss_pred             cCCCCCCCCCcccCCc---eeCC-CCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCH
Confidence            3457899999999764   4567 9999999999999977      6789999998875

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

Probab=99.24  E-value=1.8e-12  Score=87.79  Aligned_cols=50  Identities=28%  Similarity=0.495  Sum_probs=41.7

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc-------CCCCcccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS-------NSSCPKCRHCLIES  160 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~-------~~~CP~CR~~l~~~  160 (203)
                      ..+.+|+||++.|.+.   ..++ |||.||..||..|++.       ...||+||..+...
T Consensus        10 ~~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~   66 (79)
T 2egp_A           10 QEEVTCPICLELLTEP---LSLD-CGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFE   66 (79)
T ss_dssp             CCCCEETTTTEECSSC---CCCS-SSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSS
T ss_pred             ccCCCCcCCCcccCCe---eECC-CCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHh
Confidence            4467899999999775   4467 9999999999999976       56799999988753

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

Probab=99.24  E-value=7.4e-12  Score=79.73  Aligned_cols=43  Identities=30%  Similarity=0.899  Sum_probs=35.8

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHh---cCCCCccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR---SNSSCPKC  153 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~---~~~~CP~C  153 (203)
                      ..+..|+||++.+.+.   ..++ |+|.||..||..|+.   .+..||+|
T Consensus        13 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLKEP---VIIE-CGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCSSC---CCCS-SCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccCCCCccCCcccCcc---EeCC-CCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            4457899999999875   4467 999999999999954   56679998

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

Probab=99.22  E-value=6e-12  Score=89.11  Aligned_cols=48  Identities=31%  Similarity=0.683  Sum_probs=40.9

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  159 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  159 (203)
                      ...|+||++.|.++  +..++ |||.||..||..|+..+..||+||..+..
T Consensus        22 ~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           22 LLRCGICFEYFNIA--MIIPQ-CSHNYCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             HTBCTTTCSBCSSE--EECTT-TCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCCcccCChhhCCc--CEECC-CCCHhhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            35799999999763  33346 99999999999999988999999998775

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

Probab=99.22  E-value=6.1e-12  Score=82.30  Aligned_cols=51  Identities=24%  Similarity=0.545  Sum_probs=40.5

Q ss_pred             CCcCccccC-cccCCCce-eecCCCCccccHhhHHHHHhc-CCCCcccccccccc
Q 042698          109 DNECVICLS-DFAPGERV-RILPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~-~~~~~~~v-~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~  160 (203)
                      +..|+||++ .+.++... ..++ |||.||..||..|+.. +..||+||..+...
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   56 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCcCCcCCCCccCCCccCeecCC-CCCHhHHHHHHHHHHcCCCcCCCCCCccccc
Confidence            467999999 77766543 3466 9999999999999754 45799999988654

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

Probab=99.22  E-value=5.2e-12  Score=93.32  Aligned_cols=53  Identities=23%  Similarity=0.597  Sum_probs=44.6

Q ss_pred             CCCCcCccccCcccCC----CceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          107 GLDNECVICLSDFAPG----ERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~----~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      +....|+||++.+...    .....++ |||.||..||+.|++.+.+||+||..+...
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  126 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK  126 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEET-TSBEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCCCccccccccCcceEeCC-CCChhhHHHHHHHHHcCCCCCCCCCcCChh
Confidence            3457899999998753    3446677 999999999999999999999999998765

>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=99.21  E-value=6.6e-12  Score=90.34  Aligned_cols=50  Identities=28%  Similarity=0.646  Sum_probs=42.3

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      .+..|+||++.|.+.  +..++ |||.||..||..|+..+..||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           14 PHLMCVLCGGYFIDA--TTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GGTBCTTTSSBCSSE--EEETT-TCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             CcCCCccCChHHhCc--CEeCC-CCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            346899999999763  44447 999999999999999989999999988753

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

Probab=99.18  E-value=2e-11  Score=85.12  Aligned_cols=49  Identities=22%  Similarity=0.585  Sum_probs=40.2

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC--CCCcccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN--SSCPKCRHCLI  158 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~--~~CP~CR~~l~  158 (203)
                      ..+..|+||++.|.++   ..++.|||.||..||..|+..+  ..||+||..+.
T Consensus        11 ~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           11 PDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CTTTEETTTTEECSSC---EECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CcCCCCCCCChhhcCc---eECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            4567899999999865   4555599999999999999643  58999999874

>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=99.16  E-value=1.8e-11  Score=94.50  Aligned_cols=48  Identities=38%  Similarity=0.728  Sum_probs=40.6

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc-CCCCccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIE  159 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~  159 (203)
                      ...|+||++.|.+.  +..++ |||.||..||..|+.. +..||+||..+..
T Consensus        54 ~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           54 ELMCPICLDMLKNT--MTTKE-CLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHBCTTTSSBCSSE--EEETT-TCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCcccChHhhCc--CEeCC-CCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            45899999999863  44457 9999999999999987 7789999998853

>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=99.15  E-value=1.7e-11  Score=90.31  Aligned_cols=47  Identities=28%  Similarity=0.570  Sum_probs=40.0

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC-CCccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS-SCPKCRHCLIE  159 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~l~~  159 (203)
                      +..|+||++.|..+   ..++ |||.||..||..|+..+. .||+||..+..
T Consensus        52 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           52 TFQCICCQELVFRP---ITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HTBCTTTSSBCSSE---EECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             CCCCCcCChHHcCc---EEee-CCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            45799999999864   4567 999999999999998554 89999998865

>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=99.12  E-value=3.2e-11  Score=86.91  Aligned_cols=48  Identities=29%  Similarity=0.566  Sum_probs=39.8

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC---CCcccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS---SCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~---~CP~CR~~l~~~  160 (203)
                      ...|+||++.+...   ..++ |||.||..||..|+..+.   .||+||..+...
T Consensus        21 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (112)
T 1jm7_A           21 ILECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (112)
T ss_dssp             HTSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             CCCCcccChhhcCe---EECC-CCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHh
Confidence            35799999999765   3467 999999999999998654   799999987653

>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=99.09  E-value=4.8e-11  Score=87.20  Aligned_cols=50  Identities=34%  Similarity=0.642  Sum_probs=42.0

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC-CCcccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS-SCPKCRHCLIES  160 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~l~~~  160 (203)
                      ..+..|+||++.+..+   ..++ |||.||..||..|++.+. .||+||..+...
T Consensus        16 ~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           16 ESKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCcCChhhcCe---EECC-cCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            4457899999999765   4567 999999999999997765 899999988753

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

Probab=99.08  E-value=2.3e-10  Score=77.76  Aligned_cols=54  Identities=20%  Similarity=0.358  Sum_probs=41.6

Q ss_pred             CCCCcCccccCcccCCCce-eecCCCCccccHhhHHHHHhc-CCCCccccccccccc
Q 042698          107 GLDNECVICLSDFAPGERV-RILPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIESC  161 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v-~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~~  161 (203)
                      +++.+|+||++.+...+.. .-++ |||.||..|+..|+.. ...||+||..+....
T Consensus         9 ~~~~~CpICle~~~~~d~~~~p~~-CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~   64 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPEDP   64 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTTTCCSST-TSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCS
T ss_pred             ccCCcCCccCccCccccccccccC-CCCCcCHHHHHHHHhcCCCCCCCCCCccCCCc
Confidence            4557899999998754432 2345 9999999999998753 567999999887653

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

Probab=99.07  E-value=6.8e-11  Score=90.16  Aligned_cols=48  Identities=27%  Similarity=0.561  Sum_probs=40.8

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC-CCcccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS-SCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~l~~~  160 (203)
                      ...|+||++.|..+   ..++ |||.||..||..|+.... .||+||..+...
T Consensus        78 ~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           78 SFMCVCCQELVYQP---VTTE-CFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HTBCTTTSSBCSSE---EECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             CCEeecCChhhcCC---EEcC-CCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            45799999999764   4477 999999999999998655 799999988765

>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=99.06  E-value=8e-11  Score=85.61  Aligned_cols=48  Identities=31%  Similarity=0.546  Sum_probs=40.8

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc-CCCCcccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~  160 (203)
                      +..|+||++.+.++   ..++ |||.||..||..|+.. +..||+||..+...
T Consensus        23 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (116)
T 1rmd_A           23 SISCQICEHILADP---VETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (116)
T ss_dssp             HTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCcHhcCc---EEcC-CCCcccHHHHHHHHhHCcCcCCCCCCCCCHh
Confidence            35799999999764   4477 9999999999999986 67899999988754

>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=3.4e-11  Score=87.44  Aligned_cols=48  Identities=27%  Similarity=0.643  Sum_probs=40.5

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc-CCCCccccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIE  159 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~  159 (203)
                      .+..|+||++.+...   ..++ |||.||..||..|+.. +..||+||..+..
T Consensus        14 ~~~~C~iC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           14 SECQCGICMEILVEP---VTLP-CNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHBCTTTCSBCSSC---EECT-TSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCccCCcccCce---eEcC-CCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            346799999999864   5567 9999999999999976 5679999998864

>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=99.02  E-value=1.2e-10  Score=76.14  Aligned_cols=49  Identities=27%  Similarity=0.430  Sum_probs=40.0

Q ss_pred             CCCcCccccCcccCCCcee-ecCCCCcc-ccHhhHHHHHhcCCCCccccccccc
Q 042698          108 LDNECVICLSDFAPGERVR-ILPKCNHG-FHVRCIDKWLRSNSSCPKCRHCLIE  159 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~-~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~~  159 (203)
                      ++.+|.||++...+.  +. .+| |||. |+..|+..|.+.+..||+||..+..
T Consensus         7 ~~~~C~IC~~~~~~~--~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~   57 (64)
T 2vje_A            7 AIEPCVICQGRPKNG--CIVHGK-TGHLMACFTCAKKLKKRNKPCPVCRQPIQM   57 (64)
T ss_dssp             GGSCCTTTSSSCSCE--EEEETT-EEEEEECHHHHHHHHHTTCCCTTTCCCCCE
T ss_pred             CcCCCCcCCCCCCCE--EEECCC-CCChhhHHHHHHHHHHcCCcCCCcCcchhc
Confidence            346899999987653  22 238 9999 7899999999988899999998864

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

Probab=99.01  E-value=9e-11  Score=74.64  Aligned_cols=48  Identities=21%  Similarity=0.439  Sum_probs=39.6

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESC  161 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  161 (203)
                      .+...|+||++.|...   +.++ |||.||..||..|   ...||+||..+....
T Consensus         4 ~~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CCCSSCSSSCSSCBCC---SCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             ccCCCceEeCCccCCe---EEcC-CCCcccHHHHccC---CCCCCcCCcEeecCC
Confidence            3456899999999875   5677 9999999999884   567999999887543

>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=99.00  E-value=2.3e-10  Score=99.26  Aligned_cols=50  Identities=28%  Similarity=0.646  Sum_probs=42.6

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHh-cCCCCcccccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR-SNSSCPKCRHCLIESCK  162 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~l~~~~~  162 (203)
                      ..+|+||++.+..   ...++ |||.||..|+..|+. .+.+||+||..+.....
T Consensus       332 ~~~C~ICle~~~~---pv~lp-CGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~~~  382 (389)
T 2y1n_A          332 FQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP  382 (389)
T ss_dssp             SSBCTTTSSSBCC---EEEET-TCCEECHHHHHHHHHHTCSBCTTTCCBCCEEEE
T ss_pred             CCCCCccCcCCCC---eEEeC-CCChhhHHHHHHHHhcCCCCCCCCCCccCCcee
Confidence            4689999999865   46677 999999999999998 67889999998876543

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

Probab=98.96  E-value=6.4e-10  Score=76.72  Aligned_cols=49  Identities=16%  Similarity=0.045  Sum_probs=42.7

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  159 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  159 (203)
                      .....|+||++-|.++   .+++ |||.|...||..|+..+.+||+||..+..
T Consensus        12 p~~~~CpI~~~~m~dP---V~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   60 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTDP---VRLP-SGTVMDRSIILRHLLNSPTDPFNRQMLTE   60 (85)
T ss_dssp             CTTTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             chheECcccCchhcCC---eECC-CCCEECHHHHHHHHhcCCCCCCCcCCCCh
Confidence            3467899999999885   5677 99999999999999988899999988764

>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=98.96  E-value=2.5e-10  Score=74.39  Aligned_cols=51  Identities=20%  Similarity=0.390  Sum_probs=40.4

Q ss_pred             CCCcCccccCcccCCCceeecCCCCcc-ccHhhHHHHHhcCCCCcccccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHG-FHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      .+.+|.||++...+. .+..+| |||. |+..|+..|.+.+..||+||..+...
T Consensus         6 ~~~~C~IC~~~~~~~-~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~~   57 (63)
T 2vje_B            6 LLKPCSLCEKRPRDG-NIIHGR-TGHLVTCFHCARRLKKAGASCPICKKEIQLV   57 (63)
T ss_dssp             GGSBCTTTSSSBSCE-EEEETT-EEEEEECHHHHHHHHHTTCBCTTTCCBCCEE
T ss_pred             cCCCCcccCCcCCCe-EEEecC-CCCHhHHHHHHHHHHHhCCcCCCcCchhhce
Confidence            356899999986553 122248 9998 99999999998888999999988643

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

Probab=98.96  E-value=2.8e-10  Score=96.69  Aligned_cols=55  Identities=27%  Similarity=0.611  Sum_probs=41.9

Q ss_pred             CCCCcCccccCcccCCCcee--e--cCCCCccccHhhHHHHHhcC-----------CCCccccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVR--I--LPKCNHGFHVRCIDKWLRSN-----------SSCPKCRHCLIESC  161 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~--~--l~~C~H~FH~~Ci~~Wl~~~-----------~~CP~CR~~l~~~~  161 (203)
                      +.+.+|+||++.+.++..+.  .  .+.|+|.||..||..|++..           .+||+||..+..+-
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~sf  375 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTSF  375 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGGG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCccH
Confidence            45678999999998744332  1  12499999999999999742           35999999887553

>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=98.94  E-value=2e-10  Score=86.73  Aligned_cols=49  Identities=22%  Similarity=0.416  Sum_probs=41.0

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC-CCccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS-SCPKCRHCLIE  159 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~-~CP~CR~~l~~  159 (203)
                      ..+..|+||++.+.++   ..++ |||.||..||..|++... .||+||..+..
T Consensus        29 ~~~~~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   78 (141)
T 3knv_A           29 EAKYLCSACRNVLRRP---FQAQ-CGHRYCSFCLASILSSGPQNCAACVHEGIY   78 (141)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHGGGSCEECHHHHHTTCC
T ss_pred             CcCcCCCCCChhhcCc---EECC-CCCccCHHHHHHHHhcCCCCCCCCCCcccc
Confidence            4567899999999876   4467 999999999999998665 79999998643

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B

Probab=98.91  E-value=9.1e-10  Score=78.30  Aligned_cols=49  Identities=16%  Similarity=0.039  Sum_probs=42.6

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  159 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  159 (203)
                      .....|+||++-|.++   .+++ |||.|+..||..|+..+.+||+||..+..
T Consensus        27 p~~~~CpI~~~~m~dP---V~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   75 (100)
T 2kre_A           27 PDEFRDPLMDTLMTDP---VRLP-SGTIMDRSIILRHLLNSPTDPFNRQTLTE   75 (100)
T ss_dssp             STTTBCTTTCSBCSSE---EEET-TTEEEEHHHHHHHTTSCSBCSSSCCBCCT
T ss_pred             cHhhCCcCccCcccCC---eECC-CCCEEchHHHHHHHHcCCCCCCCCCCCCh
Confidence            3457899999999886   5677 99999999999999988899999988764

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2

Probab=98.90  E-value=1.4e-09  Score=77.08  Aligned_cols=49  Identities=18%  Similarity=0.057  Sum_probs=42.3

Q ss_pred             CCCCcCccccCcccCCCceeecCCCC-ccccHhhHHHHHhcCCCCccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCN-HGFHVRCIDKWLRSNSSCPKCRHCLIE  159 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~-H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  159 (203)
                      ..+..|+||++-|.++   .+++ || |.|...||..|+..+.+||+||..+..
T Consensus        20 p~~~~CpI~~~~m~dP---V~~~-cG~htf~r~cI~~~l~~~~~cP~~~~~l~~   69 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCDP---VVLP-SSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             CTTTBCTTTCSBCSSE---EECT-TTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             cHhcCCcCccccccCC---eECC-CCCeEECHHHHHHHHHhCCCCCCCCCCCCh
Confidence            3457899999999886   4567 99 999999999999988899999988764

>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=98.88  E-value=3.7e-10  Score=82.32  Aligned_cols=44  Identities=23%  Similarity=0.495  Sum_probs=37.9

Q ss_pred             CCcCccccCcccCCCceeec-CCCCccccHhhHHHHHhcCCCCcccccccc
Q 042698          109 DNECVICLSDFAPGERVRIL-PKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  158 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l-~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  158 (203)
                      ...|+||++.|..+   ..+ + |||.||..||..|+.  ..||+||..+.
T Consensus        22 ~~~C~IC~~~~~~p---v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~   66 (117)
T 1jm7_B           22 LLRCSRCTNILREP---VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAW   66 (117)
T ss_dssp             TTSCSSSCSCCSSC---BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCS
T ss_pred             CCCCCCCChHhhCc---cEeCC-CCCHHHHHHHHHHhc--CCCcCCCCcCc
Confidence            46899999999765   444 6 999999999999987  78999999874

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

Probab=98.82  E-value=8e-10  Score=74.17  Aligned_cols=44  Identities=23%  Similarity=0.631  Sum_probs=37.4

Q ss_pred             CCcCccccCcccCCCceeecCCCCcc-ccHhhHHHHHhcCCCCcccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHG-FHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      +..|+||++.+.+   ...++ |||. |+..|+..|    ..||+||..+...
T Consensus        24 ~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~   68 (74)
T 4ic3_A           24 EKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEAV----DKCPMCYTVITFK   68 (74)
T ss_dssp             HTBCTTTSSSBCC---EEEET-TCCBCCCHHHHTTC----SBCTTTCCBCSEE
T ss_pred             CCCCCCCCCCCCC---EEEcC-CCChhHHHHhhhcC----ccCCCcCcCccCc
Confidence            3579999998766   35678 9999 999999998    7899999988754

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

Probab=98.79  E-value=3.3e-09  Score=68.42  Aligned_cols=48  Identities=23%  Similarity=0.569  Sum_probs=36.5

Q ss_pred             CCCCcCccccCcccCCCceeecCCCC--c---cccHhhHHHHHhc--CCCCcccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCN--H---GFHVRCIDKWLRS--NSSCPKCRHCLI  158 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~--H---~FH~~Ci~~Wl~~--~~~CP~CR~~l~  158 (203)
                      ++...|.||+++..  +.+ ++| |.  |   .||..|+..|+..  +.+||+||..+.
T Consensus         4 ~~~~~CrIC~~~~~--~~l-~~P-C~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            4 EDVPVCWICNEELG--NER-FRA-CGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECS--CCC-CCS-CCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCEeEEeecCCC--Cce-ecC-cCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            34568999999843  334 467 54  4   9999999999964  567999998764

>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=98.78  E-value=3.1e-09  Score=82.19  Aligned_cols=50  Identities=34%  Similarity=0.638  Sum_probs=41.7

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC-CCCcccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN-SSCPKCRHCLIES  160 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~l~~~  160 (203)
                      .....|+||++.+.++   ..++ |||.|+..||..|+... ..||+||..+...
T Consensus        16 ~~~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           16 ESKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCChhhcCc---EECC-CCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            4557899999999875   4577 99999999999999764 4899999988654

>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=98.72  E-value=7.6e-09  Score=85.27  Aligned_cols=49  Identities=16%  Similarity=0.061  Sum_probs=41.2

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC-CCCccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN-SSCPKCRHCLIE  159 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~l~~  159 (203)
                      .....|+||++-|.++   .+++ |||.|+..||..|+..+ .+||+||..+..
T Consensus       206 ~~~~~c~i~~~~~~dP---v~~~-~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~  255 (281)
T 2c2l_A          206 PDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQ  255 (281)
T ss_dssp             CSTTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CcccCCcCcCCHhcCC---eECC-CCCEECHHHHHHHHHHCCCCCcCCCCCCch
Confidence            3567899999999876   5677 99999999999999764 459999998864

>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=98.71  E-value=6.4e-09  Score=72.75  Aligned_cols=50  Identities=26%  Similarity=0.678  Sum_probs=40.6

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc--------CCCCcc--cccc--ccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS--------NSSCPK--CRHC--LIE  159 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~--------~~~CP~--CR~~--l~~  159 (203)
                      ..+|+||++++..++.+...+ |+|.|+.+|+..|+..        ...||.  ||..  +.+
T Consensus         5 ~~~C~IC~~~~~~~~~~~l~~-CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~   66 (94)
T 1wim_A            5 SSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQE   66 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECH
T ss_pred             CcCCcccCcccccccceEcCC-CCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCH
Confidence            468999999998776666667 9999999999999853        136999  9988  554

>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=98.69  E-value=8.3e-09  Score=72.35  Aligned_cols=46  Identities=24%  Similarity=0.529  Sum_probs=37.0

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC------CCCcc--cccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN------SSCPK--CRHC  156 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~------~~CP~--CR~~  156 (203)
                      .+..|+||++.|.++  |.... |||.|+..||..|+..+      .+||+  |+..
T Consensus         6 ~~~~CPI~~~~~~dP--V~~~~-cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            6 SGFTCPITKEEMKKP--VKNKV-CGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             SCCBCTTTCSBCSSE--EEESS-SCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             cEeECcCcCchhcCC--EEcCC-CCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            456899999999874  44324 99999999999999754      47999  9855

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

Probab=98.69  E-value=2.5e-08  Score=65.83  Aligned_cols=48  Identities=29%  Similarity=0.684  Sum_probs=39.0

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCcc-ccHhhHHHHHhcCCCCcccccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHG-FHVRCIDKWLRSNSSCPKCRHCLIESCK  162 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~~~~~  162 (203)
                      .+...|.||++....   +..+| |+|. |+..|+..    ...||+||..+...-+
T Consensus        13 ~~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~----~~~CP~CR~~i~~~~~   61 (68)
T 2ea5_A           13 ENSKDCVVCQNGTVN---WVLLP-CRHTCLCDGCVKY----FQQCPMCRQFVQESFA   61 (68)
T ss_dssp             CCSSCCSSSSSSCCC---CEETT-TTBCCSCTTHHHH----CSSCTTTCCCCCCEEC
T ss_pred             CCCCCCCCcCcCCCC---EEEEC-CCChhhhHHHHhc----CCCCCCCCcchhceEE
Confidence            345789999998655   57788 9999 99999984    4789999999887543

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

Probab=98.64  E-value=1.2e-08  Score=68.38  Aligned_cols=44  Identities=23%  Similarity=0.634  Sum_probs=35.8

Q ss_pred             CCcCccccCcccCCCceeecCCCCcc-ccHhhHHHHHhcCCCCcccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHG-FHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      +.+|+||++.+.+   ...++ |||. |+..|+..    ...||+||..+...
T Consensus        25 ~~~C~IC~~~~~~---~~~~p-CgH~~~C~~C~~~----~~~CP~Cr~~i~~~   69 (75)
T 2ecg_A           25 EKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEA----VDKCPMCYTVITFK   69 (75)
T ss_dssp             HHSCSSSCSSCCC---BCCSS-SCCCCBCHHHHHH----CSBCTTTCCBCCCC
T ss_pred             CCCCCcCCCCCCC---EEEec-CCCHHHHHHHhhC----CCCCccCCceecCc
Confidence            3579999999766   35678 9999 99999964    37899999988654

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

Probab=98.51  E-value=7.6e-08  Score=75.18  Aligned_cols=49  Identities=16%  Similarity=0.052  Sum_probs=41.0

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC-CCCccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN-SSCPKCRHCLIE  159 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~l~~  159 (203)
                      .....|+||++-|.++   .+++ |||.|...||..|+..+ .+||+||..+..
T Consensus       104 p~~f~CPI~~elm~DP---V~~~-~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~  153 (179)
T 2f42_A          104 PDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFDPVTRSPLTQ  153 (179)
T ss_dssp             CGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             cHhhcccCccccCCCC---eECC-CCCEECHHHHHHHHHhCCCCCCCCcCCCCh
Confidence            4567899999999875   4567 99999999999999764 469999988764

>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=98.50  E-value=3.5e-08  Score=67.01  Aligned_cols=45  Identities=24%  Similarity=0.575  Sum_probs=37.5

Q ss_pred             CCcCccccCcccCCCceeecCCCCcc-ccHhhHHHHHhcCCCCccccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHG-FHVRCIDKWLRSNSSCPKCRHCLIESC  161 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  161 (203)
                      +..|.||++.+..   ...+| |||. |+..|+..|    ..||+||..+...-
T Consensus        18 ~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~~   63 (79)
T 2yho_A           18 AMLCMVCCEEEIN---STFCP-CGHTVCCESCAAQL----QSCPVCRSRVEHVQ   63 (79)
T ss_dssp             HTBCTTTSSSBCC---EEEET-TCBCCBCHHHHTTC----SBCTTTCCBCCEEE
T ss_pred             CCEeEEeCcccCc---EEEEC-CCCHHHHHHHHHhc----CcCCCCCchhhCeE
Confidence            3579999998765   46778 9999 999999987    38999999888653

>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=98.43  E-value=1.1e-07  Score=78.24  Aligned_cols=49  Identities=22%  Similarity=0.537  Sum_probs=39.8

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC--CCCcc--ccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN--SSCPK--CRHCLIE  159 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~--~~CP~--CR~~l~~  159 (203)
                      .+..|+||++.|.++  |+... |||.|++.||..|+..+  ..||+  ||..+..
T Consensus       180 ~el~CPIcl~~f~DP--Vts~~-CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~  232 (267)
T 3htk_C          180 IELTCPITCKPYEAP--LISRK-CNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSM  232 (267)
T ss_dssp             CCSBCTTTSSBCSSE--EEESS-SCCEEEHHHHHHHSTTCSCEECSGGGCSCEECG
T ss_pred             eeeECcCccCcccCC--eeeCC-CCCcccHHHHHHHHHhCCCCCCCcccccCcCch
Confidence            345799999999765  65556 99999999999999764  36999  9987653

>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=98.39  E-value=1.5e-07  Score=60.72  Aligned_cols=48  Identities=13%  Similarity=0.070  Sum_probs=40.7

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      ..|+||++.|.++  +...+ |||+|-+.||..|++.+.+||+++..+...
T Consensus         4 ~~CpIs~~~m~dP--V~~~~-sG~~yer~~I~~~l~~~~~cP~t~~~L~~~   51 (61)
T 2bay_A            4 MLCAISGKVPRRP--VLSPK-SRTIFEKSLLEQYVKDTGNDPITNEPLSIE   51 (61)
T ss_dssp             CCCTTTCSCCSSE--EEETT-TTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             EEecCCCCCCCCC--EEeCC-CCcEEcHHHHHHHHHhCCCCcCCcCCCChh
Confidence            5799999999864  44325 999999999999998888899999888654

>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=98.34  E-value=8.8e-08  Score=82.16  Aligned_cols=44  Identities=25%  Similarity=0.705  Sum_probs=37.5

Q ss_pred             CCcCccccCcccCCCceeecCCCCcc-ccHhhHHHHHhcCCCCcccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHG-FHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      +..|+||++.+..   ...+| |||. ||..|+..|    ..||+||..+...
T Consensus       295 ~~~C~IC~~~~~~---~v~lp-CgH~~fC~~C~~~~----~~CP~CR~~i~~~  339 (345)
T 3t6p_A          295 ERTCKVCMDKEVS---VVFIP-CGHLVVCQECAPSL----RKCPICRGIIKGT  339 (345)
T ss_dssp             TCBCTTTSSSBCC---EEEET-TCCEEECTTTGGGC----SBCTTTCCBCCEE
T ss_pred             CCCCCccCCcCCc---eEEcC-CCChhHhHHHHhcC----CcCCCCCCCccCe
Confidence            4689999999866   35678 9999 999999998    7899999988654

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

Probab=98.26  E-value=1e-06  Score=71.85  Aligned_cols=50  Identities=28%  Similarity=0.656  Sum_probs=40.9

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC--CCcccccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS--SCPKCRHCLIES  160 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~--~CP~CR~~l~~~  160 (203)
                      ...+|+||.+-+..+   ..++.|+|.||..|+..|++.+.  .||.|+......
T Consensus       179 ~i~~C~iC~~iv~~g---~~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~  230 (238)
T 3nw0_A          179 AVKICNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE  230 (238)
T ss_dssp             TCCBCTTTCSBCSSC---EECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSC
T ss_pred             CCCcCcchhhHHhCC---cccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCC
Confidence            467899999998876   44555999999999999997654  799999876544

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

Probab=98.11  E-value=1.8e-06  Score=60.56  Aligned_cols=49  Identities=22%  Similarity=0.452  Sum_probs=39.2

Q ss_pred             cCccccCcccCCCceeecCCCCccccHhhHHHHHh-cCCCCcccccccccccc
Q 042698          111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR-SNSSCPKCRHCLIESCK  162 (203)
Q Consensus       111 ~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~l~~~~~  162 (203)
                      -|.+|--++..  ..|..| |+|+|+.+|+..|.+ ..+.||+|+..+..-+.
T Consensus         3 fC~~C~~Pi~i--ygRmIP-CkHvFCydCa~~~~~~~~k~Cp~C~~~V~rVe~   52 (101)
T 3vk6_A            3 FCDKCGLPIKV--YGRMIP-CKHVFCYDCAILHEKKGDKMCPGCSDPVQRIEQ   52 (101)
T ss_dssp             BCTTTCSBCSE--EEEEET-TCCEEEHHHHHHHHHTTCCBCTTTCCBCSEEEE
T ss_pred             ecCccCCCeEE--Eeeecc-ccccHHHHHHHHHHhccCCCCcCcCCeeeeeEE
Confidence            47888666543  468899 999999999999985 46789999998886554

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=96.82  E-value=0.0011  Score=43.01  Aligned_cols=49  Identities=22%  Similarity=0.382  Sum_probs=36.0

Q ss_pred             CCCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC----CCcccccccc
Q 042698          106 PGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS----SCPKCRHCLI  158 (203)
Q Consensus       106 ~~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~l~  158 (203)
                      ...+..|.||.+.    ..+.....|...||..|++..+....    .||.|+....
T Consensus         9 ~~~~~~C~vC~~~----~~ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~~   61 (66)
T 2lri_C            9 LAPGARCGVCGDG----TDVLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDVT   61 (66)
T ss_dssp             CCTTCCCTTTSCC----TTCEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCCC
T ss_pred             CCCCCCcCCCCCC----CeEEECCCCCCceecccCCCccCcCCCCCEECccccCCCc
Confidence            3445679999753    34556667999999999998876543    5999976543

>1we9_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=95.67  E-value=0.003  Score=40.46  Aligned_cols=49  Identities=24%  Similarity=0.525  Sum_probs=36.7

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHh-----cCCCCccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR-----SNSSCPKCRH  155 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~-----~~~~CP~CR~  155 (203)
                      ++...|+||...+.++..++....|...||..|+..-..     ..-.||.|+.
T Consensus         4 ~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~   57 (64)
T 1we9_A            4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcC
Confidence            345679999998876666777777999999999975432     2345999975

>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=95.44  E-value=0.019  Score=38.73  Aligned_cols=36  Identities=19%  Similarity=0.435  Sum_probs=24.9

Q ss_pred             CCCCCcCccccCcccCCCceeecCCCCccccHhhHHHH
Q 042698          106 PGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKW  143 (203)
Q Consensus       106 ~~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~W  143 (203)
                      ...++.|.|| +.+..++... ..-|+-+||..|+.+-
T Consensus        12 ~~~D~~C~VC-~~~t~~~l~p-CRvC~RvfH~~CL~r~   47 (89)
T 1wil_A           12 VVNDEMCDVC-EVWTAESLFP-CRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCSCCCTTT-CCCCSSCCSS-CSSSSSCCCHHHHHHH
T ss_pred             CCCCcccCcc-ccccccceec-cccccccccHhhcccc
Confidence            4567889999 3444443322 2239999999999995

>3lqh_A Histone-lysine N-methyltransferase MLL; PHD finger, bromodomain, leukemia, apoptosis, chromati regulator, DNA-binding, isopeptide bond; 1.72A {Homo sapiens} PDB: 3lqi_A* 3lqj_A* 2kyu_A

Probab=94.87  E-value=0.011  Score=45.90  Aligned_cols=49  Identities=20%  Similarity=0.418  Sum_probs=37.3

Q ss_pred             CcCccccCcccCCCc---eeecCCCCccccHhhHHHH------Hh-----cCCCCcccccccc
Q 042698          110 NECVICLSDFAPGER---VRILPKCNHGFHVRCIDKW------LR-----SNSSCPKCRHCLI  158 (203)
Q Consensus       110 ~~CaICl~~~~~~~~---v~~l~~C~H~FH~~Ci~~W------l~-----~~~~CP~CR~~l~  158 (203)
                      ..|+||...|.+++.   ++.+..|...||..|+..=      +.     ..-.||.|+..-.
T Consensus         3 ~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~~   65 (183)
T 3lqh_A            3 NFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHP   65 (183)
T ss_dssp             CBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSSS
T ss_pred             CcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCCC
Confidence            569999999988763   7777789999999998431      11     1457999987544

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

Probab=94.70  E-value=0.027  Score=38.89  Aligned_cols=34  Identities=18%  Similarity=0.367  Sum_probs=25.6

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHH
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKW  143 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~W  143 (203)
                      +..|.||++.+..+....-+. |+|.|+..|+..+
T Consensus         3 e~~C~~C~~~~~~~av~~C~~-C~~~~C~~Cl~~~   36 (101)
T 2jun_A            3 KVLCQFCDQDPAQDAVKTCVT-CEVSYCDECLKAT   36 (101)
T ss_dssp             CCBCTTCCSSSCCBCCEEETT-TTEEECHHHHHHH
T ss_pred             CCCCcCCCCCCCCCceEECCc-CChHHhHHHCHHH
Confidence            357999998754433344466 9999999999984

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=94.40  E-value=0.026  Score=35.71  Aligned_cols=46  Identities=22%  Similarity=0.647  Sum_probs=33.1

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC----CCCcccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN----SSCPKCRHC  156 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~----~~CP~CR~~  156 (203)
                      ..+..|.+|.+.    ..+.....|...||..|+..-+...    -.||.|+..
T Consensus         9 ~~~~~C~vC~~~----g~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A            9 DHQDYCEVCQQG----GEIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             CCCSSCTTTSCC----SSEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCCccCCCC----CcEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            345689999863    3566666799999999999754322    259999653

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=94.08  E-value=0.015  Score=38.22  Aligned_cols=50  Identities=20%  Similarity=0.337  Sum_probs=35.8

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc----CCCCcccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS----NSSCPKCRHCLI  158 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~l~  158 (203)
                      +...|.||..... ++.++....|...||..|+..-...    .-.||.|+..+.
T Consensus        17 ~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~   70 (75)
T 2k16_A           17 QIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIK   70 (75)
T ss_dssp             EEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHC
T ss_pred             CCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchh
Confidence            3456999987653 4456677779999999999865432    235999977654

>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=93.60  E-value=0.037  Score=42.69  Aligned_cols=47  Identities=23%  Similarity=0.474  Sum_probs=34.2

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC----CCcccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS----SCPKCRHCLI  158 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~l~  158 (203)
                      +++.|.+|.+.    ..+..+..|...||..|+..-+....    .||.|+..-.
T Consensus         3 ~~~~C~~C~~~----g~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   53 (184)
T 3o36_A            3 NEDWCAVCQNG----GELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSK   53 (184)
T ss_dssp             SCSSCTTTCCC----SSCEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSSS
T ss_pred             CCCccccCCCC----CeeeecCCCCcccCccccCCCCCCCCCCCEECccccCccc
Confidence            45679999744    33566667999999999987665322    5999986543

>2vpb_A Hpygo1, pygopus homolog 1; gene regulation, WNT signaling pathway, WNT signaling complex, chromosomal rearrangement, signaling protein; 1.59A {Homo sapiens} PDB: 2vpd_A 2yyr_A* 2dx8_A* 2vp7_A 2vpg_A* 2vpe_A*

Probab=93.46  E-value=0.064  Score=34.42  Aligned_cols=34  Identities=21%  Similarity=0.457  Sum_probs=28.3

Q ss_pred             CCCcCccccCcccCCCceeecC-CCCccccHhhHH
Q 042698          108 LDNECVICLSDFAPGERVRILP-KCNHGFHVRCID  141 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~-~C~H~FH~~Ci~  141 (203)
                      ....|.+|..++.+++.++... .|.-.||..|+.
T Consensus         7 ~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvg   41 (65)
T 2vpb_A            7 PVYPCGICTNEVNDDQDAILCEASCQKWFHRICTG   41 (65)
T ss_dssp             --CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHT
T ss_pred             CcCcCccCCCccCCCCCeEecccCccccCchhccC
Confidence            3457999999998888888887 799999999984

>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A

Probab=93.05  E-value=0.024  Score=35.89  Aligned_cols=47  Identities=19%  Similarity=0.486  Sum_probs=32.6

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC----CCCccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN----SSCPKCRHCL  157 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~----~~CP~CR~~l  157 (203)
                      ..+..|.||.+.    ..+.....|...||..|+..-+...    =.||.|+...
T Consensus         7 ~~~~~C~vC~~~----g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~   57 (61)
T 1mm2_A            7 HHMEFCRVCKDG----GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC----SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCCCcCCCCCCC----CCEEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCch
Confidence            345679999752    3455556699999999998644332    2499997643

>1wep_A PHF8; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: g.50.1.2

Probab=93.05  E-value=0.075  Score=35.30  Aligned_cols=49  Identities=18%  Similarity=0.390  Sum_probs=34.9

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHh-----cCCCCcccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR-----SNSSCPKCRHCLI  158 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~-----~~~~CP~CR~~l~  158 (203)
                      ...| ||...+.....++....|...||..|+..-..     ..-.||.|+...-
T Consensus        12 ~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~~   65 (79)
T 1wep_A           12 PVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFG   65 (79)
T ss_dssp             CCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSC
T ss_pred             ccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCcccccC
Confidence            3457 99888765566777777999999999953221     2345999987543

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=93.05  E-value=0.013  Score=36.95  Aligned_cols=49  Identities=20%  Similarity=0.674  Sum_probs=34.3

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC----CCCcccccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN----SSCPKCRHCLIES  160 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~----~~CP~CR~~l~~~  160 (203)
                      .+..|.+|...    ..+.....|...||..|+..=+...    -.||.|+......
T Consensus         4 ~~~~C~vC~~~----g~ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~~~   56 (60)
T 2puy_A            4 HEDFCSVCRKS----GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQMLKK   56 (60)
T ss_dssp             CCSSCTTTCCC----SSCEECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHHHHT
T ss_pred             CCCCCcCCCCC----CcEEEcCCCCcCEECCcCCCCcCCCCCCceEChhccChhhch
Confidence            35679999864    3455566799999999998644332    2499997665543

>3u5n_A E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, bromodomain, TGF-beta, epigenetics, methylation, K9ME3, K14AC, transcription; HET: M3L ALY; 1.95A {Homo sapiens} PDB: 3u5m_A* 3u5o_A* 3u5p_A*

Probab=92.80  E-value=0.026  Score=44.50  Aligned_cols=47  Identities=26%  Similarity=0.454  Sum_probs=34.6

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC----CCccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS----SCPKCRHCL  157 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~l  157 (203)
                      ..+..|.+|...    ..+..+..|...||..|+...+....    .||.|+..-
T Consensus         5 ~~~~~C~~C~~~----g~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A            5 PNEDWCAVCQNG----GDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             SSCSSBTTTCCC----EEEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCCCCCCCCC----CceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            345679999743    34667778999999999987665332    599998643

>2kgg_A Histone demethylase jarid1A; PHD finger, histone modification, leukemia, alternative splicing, chromatin regulator, developmental protein; NMR {Homo sapiens} PDB: 2kgi_A* 3gl6_A*

Probab=92.34  E-value=0.048  Score=33.28  Aligned_cols=44  Identities=16%  Similarity=0.280  Sum_probs=32.1

Q ss_pred             cCccccCcccCCCceeecC-CCCccccHhhHHHHH----hcCCCCcccc
Q 042698          111 ECVICLSDFAPGERVRILP-KCNHGFHVRCIDKWL----RSNSSCPKCR  154 (203)
Q Consensus       111 ~CaICl~~~~~~~~v~~l~-~C~H~FH~~Ci~~Wl----~~~~~CP~CR  154 (203)
                      .|.+|...+.+++.++... .|...||..|+..-.    ..+-.||.|+
T Consensus         4 ~cc~C~~p~~~~~~mI~Cd~~C~~WfH~~Cvgl~~~~~~~~~~~C~~C~   52 (52)
T 2kgg_A            4 AAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA   52 (52)
T ss_dssp             SCTTCCCCCCTTCCEEECTTTTCCEEETTTTTCCHHHHHHSCCCCSCC-
T ss_pred             cCCCCcCccCCCCcEEEeCCCCCccCcccccCCCccccCCCCEECCCCC
Confidence            4779998887666677776 699999999985422    2455699885

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=92.29  E-value=0.074  Score=32.10  Aligned_cols=44  Identities=25%  Similarity=0.677  Sum_probs=30.3

Q ss_pred             cCccccCcccCCCceeecCCCCccccHhhHHHHHhcC----CCCccccc
Q 042698          111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN----SSCPKCRH  155 (203)
Q Consensus       111 ~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~----~~CP~CR~  155 (203)
                      .|.||...-.. +.+.....|...||..|+..=+...    -.||.|+.
T Consensus         2 ~C~vC~~~~~~-~~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGED-DKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCC-SCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCC-CCEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            48899865433 3455666799999999997544322    24999965

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=91.93  E-value=0.03  Score=35.99  Aligned_cols=45  Identities=24%  Similarity=0.621  Sum_probs=32.1

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC----CCCccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN----SSCPKCRH  155 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~----~~CP~CR~  155 (203)
                      ..+..|.||.+.    ..+.....|...||..|+..-+...    -.||.|+.
T Consensus         6 ~~~~~C~vC~~~----g~ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~   54 (66)
T 1xwh_A            6 KNEDECAVCRDG----GELICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQ   54 (66)
T ss_dssp             SCCCSBSSSSCC----SSCEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHH
T ss_pred             CCCCCCccCCCC----CCEEEcCCCChhhcccccCCCcCcCCCCCeECccccC
Confidence            346789999864    3455666799999999998644332    24999964

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=91.79  E-value=0.029  Score=34.81  Aligned_cols=45  Identities=24%  Similarity=0.776  Sum_probs=31.5

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC----CCccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS----SCPKCRH  155 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~----~CP~CR~  155 (203)
                      ..+..|.+|.+.    ..+.....|...||..|+..=+....    .||.|+.
T Consensus         7 ~~~~~C~vC~~~----g~ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            7 GHEDFCSVCRKS----GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             SSCCSCSSSCCS----SCCEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCccCCCC----CeEEEcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            345679999864    34555667999999999986443322    4888854

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=91.68  E-value=0.071  Score=34.83  Aligned_cols=49  Identities=20%  Similarity=0.409  Sum_probs=34.2

Q ss_pred             CCCCcCccccCcc-cCCCceeecCCCCccccHhhHHHHHh--cCCCCccccc
Q 042698          107 GLDNECVICLSDF-APGERVRILPKCNHGFHVRCIDKWLR--SNSSCPKCRH  155 (203)
Q Consensus       107 ~~~~~CaICl~~~-~~~~~v~~l~~C~H~FH~~Ci~~Wl~--~~~~CP~CR~  155 (203)
                      ..+..|.||.+.- .+++.+.....|.-.||..|+..-..  ..=.||.|+.
T Consensus        14 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~   65 (71)
T 2ku3_A           14 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQ   65 (71)
T ss_dssp             CSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcC
Confidence            4567899998753 34456777778999999999975321  1224888865

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=91.46  E-value=0.12  Score=35.24  Aligned_cols=46  Identities=24%  Similarity=0.550  Sum_probs=33.3

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC----CCcccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS----SCPKCRHC  156 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~  156 (203)
                      .++..|.+|.+.   + .+.....|.-.||..|+..=+....    .||.|+..
T Consensus        23 ~n~~~C~vC~~~---g-~LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~   72 (88)
T 1fp0_A           23 DSATICRVCQKP---G-DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   72 (88)
T ss_dssp             SSSSCCSSSCSS---S-CCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCC
T ss_pred             CCCCcCcCcCCC---C-CEEECCCCCCceecccCCCCCCCCcCCCcCCccccCC
Confidence            456789999864   2 4556667999999999977554322    59999764

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=91.26  E-value=0.069  Score=36.36  Aligned_cols=51  Identities=20%  Similarity=0.379  Sum_probs=35.2

Q ss_pred             CCCCcCccccCcc-cCCCceeecCCCCccccHhhHHHHHh--cCCCCccccccc
Q 042698          107 GLDNECVICLSDF-APGERVRILPKCNHGFHVRCIDKWLR--SNSSCPKCRHCL  157 (203)
Q Consensus       107 ~~~~~CaICl~~~-~~~~~v~~l~~C~H~FH~~Ci~~Wl~--~~~~CP~CR~~l  157 (203)
                      +++..|.||.+.- ...+.+.....|.-.||..|+..-+.  ..-.||.|+...
T Consensus        23 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~   76 (88)
T 2l43_A           23 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSR   76 (88)
T ss_dssp             CCCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHT
T ss_pred             CCCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCcc
Confidence            4567899998753 23346677777999999999986321  122599996543

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=90.81  E-value=0.071  Score=37.84  Aligned_cols=45  Identities=27%  Similarity=0.597  Sum_probs=32.3

Q ss_pred             cCccccCcccCCCceeecCCCCccccHhhHHHHHhcC----CCCccccc
Q 042698          111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN----SSCPKCRH  155 (203)
Q Consensus       111 ~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~----~~CP~CR~  155 (203)
                      .|.||.+.-.+++.+.....|...||..|++.-+...    =.||.||.
T Consensus        63 ~C~vC~~~~~~~~~ll~Cd~C~~~yH~~Cl~p~l~~~P~~~W~C~~C~~  111 (112)
T 3v43_A           63 TCSSCRDQGKNADNMLFCDSCDRGFHMECCDPPLTRMPKGMWICQICRP  111 (112)
T ss_dssp             CBTTTCCCCCTTCCCEECTTTCCEECGGGCSSCCSSCCSSCCCCTTTSC
T ss_pred             ccccccCcCCCccceEEcCCCCCeeecccCCCCCCCCCCCCeECCCCCC
Confidence            6889986544445666666799999999997655432    25999974

>1wem_A Death associated transcription factor 1; structural genomics, PHD domain, death inducer- obliterator 1(DIO-1); NMR {Mus musculus} SCOP: g.50.1.2

Probab=90.40  E-value=0.16  Score=33.39  Aligned_cols=47  Identities=21%  Similarity=0.440  Sum_probs=32.3

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHH---------hcCCCCccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWL---------RSNSSCPKCRHCL  157 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl---------~~~~~CP~CR~~l  157 (203)
                      ...| ||...+. +..++....|...||..|+..-.         ..+-.||.|+..-
T Consensus        16 ~~~C-~C~~~~~-~~~MI~Cd~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~~   71 (76)
T 1wem_A           16 ALYC-ICRQPHN-NRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS   71 (76)
T ss_dssp             CCCS-TTCCCCC-SSCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHS
T ss_pred             CCEE-ECCCccC-CCCEEEeCCCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCcc
Confidence            3457 8988765 34566666799999999994321         2355799997543

>2ri7_A Nucleosome-remodeling factor subunit BPTF; zinc finger, alpha-helical bundle, dimethyl-lysine, bromodom chromatin regulator, metal-binding, nucleus; HET: MLY; 1.45A {Homo sapiens} PDB: 2fsa_A* 2f6n_A 2f6j_A* 3qzv_A* 3uv2_A* 3qzt_A* 3qzs_A* 2fui_A 2fuu_A*

Probab=90.04  E-value=0.069  Score=40.67  Aligned_cols=48  Identities=21%  Similarity=0.463  Sum_probs=34.7

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHH-----hcCCCCcccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWL-----RSNSSCPKCRHC  156 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl-----~~~~~CP~CR~~  156 (203)
                      ....| +|......+..++.+..|...||..|+..-.     ...-.||.|+..
T Consensus         7 ~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~~   59 (174)
T 2ri7_A            7 TKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQST   59 (174)
T ss_dssp             CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHHH
T ss_pred             CCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcch
Confidence            34579 9998876566677777899999999995321     123469999764

>2xb1_A Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro; fusion protein, signal transduction, transcription, metal BI WNT proteins; 1.90A {Homo sapiens}

Probab=89.99  E-value=0.19  Score=35.25  Aligned_cols=48  Identities=19%  Similarity=0.377  Sum_probs=35.5

Q ss_pred             CcCccccCcccCCCceeecC-CCCccccHhhHHHHH---h-------cCCCCccccccc
Q 042698          110 NECVICLSDFAPGERVRILP-KCNHGFHVRCIDKWL---R-------SNSSCPKCRHCL  157 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~-~C~H~FH~~Ci~~Wl---~-------~~~~CP~CR~~l  157 (203)
                      ..|.||...+.++..++... .|...||..|+..=-   +       .+-.||.|+..-
T Consensus         4 ~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~   62 (105)
T 2xb1_A            4 YPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTK   62 (105)
T ss_dssp             CBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTT
T ss_pred             CCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcC
Confidence            46999999987776777775 699999999995321   0       233599998653

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=89.61  E-value=0.12  Score=36.36  Aligned_cols=47  Identities=21%  Similarity=0.519  Sum_probs=31.7

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc----CCCCcccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS----NSSCPKCR  154 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR  154 (203)
                      .++..|.||.+.-...+ +.....|+..||..|+...+..    .-.||.|+
T Consensus         5 ~~~~~C~~C~~~g~~~~-ll~C~~C~~~~H~~Cl~~~~~~~~~~~W~C~~C~   55 (111)
T 2ysm_A            5 SSGANCAVCDSPGDLLD-QFFCTTCGQHYHGMCLDIAVTPLKRAGWQCPECK   55 (111)
T ss_dssp             CCCSCBTTTCCCCCTTT-SEECSSSCCEECTTTTTCCCCTTTSTTCCCTTTC
T ss_pred             CCCCCCcCCCCCCCCcC-CeECCCCCCCcChHHhCCccccccccCccCCcCC
Confidence            35678999987643322 3444569999999999887642    22477664

>3o70_A PHD finger protein 13; PHF13, structural genomics consortium, SGC, structural genom type zinc finger, protein binding, zinc ION binding; 1.85A {Homo sapiens}

Probab=89.25  E-value=0.11  Score=33.65  Aligned_cols=46  Identities=26%  Similarity=0.535  Sum_probs=31.8

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHh---cCCCCccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR---SNSSCPKCRH  155 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~---~~~~CP~CR~  155 (203)
                      +...| ||..... ++.++....|...||..|+..--.   ..-.||.|+.
T Consensus        18 ~~~~C-iC~~~~~-~~~MIqCd~C~~WfH~~Cvgi~~~~~~~~~~C~~C~~   66 (68)
T 3o70_A           18 GLVTC-FCMKPFA-GRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRD   66 (68)
T ss_dssp             TCCCS-TTCCCCT-TCCEEECTTTCCEEETTTTTCCTTSCCSSCCCHHHHT
T ss_pred             CceEe-ECCCcCC-CCCEEECCCCCccccccccCcCcccCCCcEECCCCCC
Confidence            34568 9987665 445666667999999999975321   2335999865

>1wee_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=89.08  E-value=0.076  Score=34.60  Aligned_cols=47  Identities=28%  Similarity=0.449  Sum_probs=33.2

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHH----hcCCCCcccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWL----RSNSSCPKCRHC  156 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl----~~~~~CP~CR~~  156 (203)
                      ...| ||......++.++....|...||..|+..--    ..+-.||.|+..
T Consensus        16 ~~~C-~C~~~~~~g~~mI~Cd~C~~W~H~~Cvg~~~~~~~~~~~~C~~C~~~   66 (72)
T 1wee_A           16 KVDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIEL   66 (72)
T ss_dssp             EECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHH
T ss_pred             ceEe-eCCCccCCCCcEEECCCCCCccCCeeeccCccccCCCcEECCCccCC
Confidence            3458 7988765555567777799999999997532    123359999754

>1wen_A Inhibitor of growth family, member 4; ING1-like protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.50.1.2 PDB: 1wes_A

Probab=89.08  E-value=0.32  Score=31.65  Aligned_cols=45  Identities=24%  Similarity=0.582  Sum_probs=29.9

Q ss_pred             CCCCcCccccCcccCCCceeecCC--CC-ccccHhhHHHHHhcC----CCCcccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPK--CN-HGFHVRCIDKWLRSN----SSCPKCRHC  156 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~--C~-H~FH~~Ci~~Wl~~~----~~CP~CR~~  156 (203)
                      .+...| ||..... + .++....  |. ..||..|+.  |...    -.||.|+..
T Consensus        14 ~~~~~C-~C~~~~~-g-~MI~CD~~~C~~~wfH~~Cvg--l~~~p~g~w~Cp~C~~~   65 (71)
T 1wen_A           14 NEPTYC-LCHQVSY-G-EMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQE   65 (71)
T ss_dssp             TSCCCS-TTCCCSC-S-SEECCSCSSCSCCCEETTTTT--CSSCCSSCCCCTTTSSC
T ss_pred             CCCCEE-ECCCCCC-C-CEeEeeCCCCCCccEecccCC--cCcCCCCCEECCCCCcc
Confidence            344568 8987642 3 4666666  66 799999998  4332    259999764

>2yt5_A Metal-response element-binding transcription factor 2; zinc-regulated factor 1, ZIRF1, metal-response element DNA-binding protein M96; NMR {Mus musculus}

Probab=88.46  E-value=0.27  Score=31.14  Aligned_cols=50  Identities=24%  Similarity=0.652  Sum_probs=35.2

Q ss_pred             CCCCcCccccCccc-CCCceeecCCCCccccHhhHHHHHh-------cCCCCcccccc
Q 042698          107 GLDNECVICLSDFA-PGERVRILPKCNHGFHVRCIDKWLR-------SNSSCPKCRHC  156 (203)
Q Consensus       107 ~~~~~CaICl~~~~-~~~~v~~l~~C~H~FH~~Ci~~Wl~-------~~~~CP~CR~~  156 (203)
                      .++..|.||..... .+..+.....|...||..|+..=+.       ..-.||.|+..
T Consensus         4 ~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~   61 (66)
T 2yt5_A            4 GSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFA   61 (66)
T ss_dssp             CCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHT
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCc
Confidence            45678999997643 3346667777999999999986332       12259999654

>1weu_A Inhibitor of growth family, member 4; structural genomics, PHD domain, ING1-like protein, DNA binding protein, NPPSFA; NMR {Mus musculus} SCOP: g.50.1.2

Probab=88.39  E-value=0.29  Score=33.51  Aligned_cols=44  Identities=25%  Similarity=0.592  Sum_probs=29.3

Q ss_pred             CCCcCccccCcccCCCceeecCC--CC-ccccHhhHHHHHhc----CCCCcccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPK--CN-HGFHVRCIDKWLRS----NSSCPKCRHC  156 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~--C~-H~FH~~Ci~~Wl~~----~~~CP~CR~~  156 (203)
                      +...| ||..... + .++....  |. ..||..|+.  |..    +-.||.|+..
T Consensus        35 e~~yC-iC~~~~~-g-~MI~CD~~dC~~~WfH~~CVg--l~~~p~g~W~Cp~C~~~   85 (91)
T 1weu_A           35 EPTYC-LCHQVSY-G-EMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQE   85 (91)
T ss_dssp             CCBCS-TTCCBCC-S-CCCCCSCSSCSCCCCCSTTTT--CSSCCCSSCCCTTTCCC
T ss_pred             CCcEE-ECCCCCC-C-CEeEecCCCCCCCCEecccCC--cCcCCCCCEECcCccCc
Confidence            34568 9987643 3 4555556  55 789999998  332    2359999764

>2knc_A Integrin alpha-IIB; transmembrane signaling, protein structure, cell A cleavage on PAIR of basic residues, disease mutation, disul bond, glycoprotein; NMR {Homo sapiens}

Probab=88.31  E-value=2.5  Score=25.86  Aligned_cols=30  Identities=7%  Similarity=-0.006  Sum_probs=15.8

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 042698           35 SNAVIVLSVLVCGIICSLGLHFLIRCILVS   64 (203)
Q Consensus        35 ~~~iiii~il~~~~i~~l~~~~~~~~~~rr   64 (203)
                      ++++++++++...+++++++..++.|-+-+
T Consensus        11 p~wiIi~svl~GLllL~li~~~LwK~GFFk   40 (54)
T 2knc_A           11 PIWWVLVGVLGGLLLLTILVLAMWKVGFFK   40 (54)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHcCccc
Confidence            445555555555555555555555554333

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=88.06  E-value=0.12  Score=40.22  Aligned_cols=44  Identities=25%  Similarity=0.562  Sum_probs=31.3

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC----CCCcccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN----SSCPKCRHC  156 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~----~~CP~CR~~  156 (203)
                      +..|.+|.+.   + .+..+..|...||..|+..=+...    -.||.|+..
T Consensus         2 ~~~C~~C~~~---g-~ll~Cd~C~~~~H~~Cl~p~l~~~p~g~W~C~~C~~~   49 (189)
T 2ro1_A            2 ATICRVCQKP---G-DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   49 (189)
T ss_dssp             CCCBTTTCCC---S-SCCCCTTTCCBCCSTTSTTCCSSCCCTTCCTTTTSCS
T ss_pred             CCcCccCCCC---C-ceeECCCCCchhccccCCCCcccCCCCCCCCcCccCC
Confidence            4579999854   3 345556699999999997644322    259999866

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=87.27  E-value=0.27  Score=33.96  Aligned_cols=45  Identities=22%  Similarity=0.459  Sum_probs=30.7

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhc---CCCCcccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS---NSSCPKCRHC  156 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~---~~~CP~CR~~  156 (203)
                      ..| ||-.....+ .++....|...||..|+..=+..   .-.||.|+..
T Consensus        29 vrC-iC~~~~~~~-~mi~Cd~C~~w~H~~C~~~~~~~~p~~w~C~~C~~~   76 (98)
T 2lv9_A           29 TRC-ICGFTHDDG-YMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQPR   76 (98)
T ss_dssp             CCC-TTSCCSCSS-CEEEBTTTCBEEETTTTTCCTTSCCSSBCCTTTSSS
T ss_pred             EEe-ECCCccCCC-cEEEcCCCCCcCcCcCCCCCccCCCCCEECCCCcCC
Confidence            458 887665444 55666679999999999753221   2359999743

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=86.99  E-value=1.1  Score=31.44  Aligned_cols=46  Identities=20%  Similarity=0.431  Sum_probs=30.6

Q ss_pred             CCcCccccCcc-----cCCCceeecCCCCccccHhhHHHH------Hh-cCCCCcccc
Q 042698          109 DNECVICLSDF-----APGERVRILPKCNHGFHVRCIDKW------LR-SNSSCPKCR  154 (203)
Q Consensus       109 ~~~CaICl~~~-----~~~~~v~~l~~C~H~FH~~Ci~~W------l~-~~~~CP~CR  154 (203)
                      ...|.+|+..-     ..++.+.....|+..||..|+..+      +. ..=.||.|+
T Consensus         5 ~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   62 (112)
T 3v43_A            5 IPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLKFSPELTVRVKALRWQCIECK   62 (112)
T ss_dssp             CSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHTCCHHHHHHHHTSCCCCTTTC
T ss_pred             CccccccCCchhhCcCCCchhceEhhhcCCCCCCchhcCCHHHHHHhhccccccccCC
Confidence            46799998763     223456666679999999999532      22 223577775

>2l8s_A Integrin alpha-1; transmembrane region, detergent micelle, CE adhesion; NMR {Homo sapiens}

Probab=86.63  E-value=2.7  Score=25.71  Aligned_cols=30  Identities=20%  Similarity=0.084  Sum_probs=16.2

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 042698           35 SNAVIVLSVLVCGIICSLGLHFLIRCILVS   64 (203)
Q Consensus        35 ~~~iiii~il~~~~i~~l~~~~~~~~~~rr   64 (203)
                      ++++|+++++...+++++++..++++-+-+
T Consensus         8 p~WiIi~svl~GLLLL~Lii~~LwK~GFFK   37 (54)
T 2l8s_A            8 PLWVILLSAFAGLLLLMLLILALWKIGFFK   37 (54)
T ss_dssp             CTHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHcCccc
Confidence            445556666655555555555555554433

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=86.31  E-value=0.93  Score=33.55  Aligned_cols=46  Identities=24%  Similarity=0.527  Sum_probs=33.5

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHh-----------cCCCCcccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR-----------SNSSCPKCRHC  156 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~-----------~~~~CP~CR~~  156 (203)
                      +.++.|.+|-+-    -.+.....|-..||..||..=+.           ..=.||+|+..
T Consensus        61 g~~d~C~vC~~G----G~LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~~  117 (142)
T 2lbm_A           61 GMDEQCRWCAEG----GNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPE  117 (142)
T ss_dssp             SCBCSCSSSCCC----SSEEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCCC
T ss_pred             CCCCeecccCCC----CcEEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccCc
Confidence            456789999754    34556667999999999997652           12259999754

>4gne_A Histone-lysine N-methyltransferase NSD3; zinc finger, transcription, nuclear protein, transf nuclear protein complex; 1.47A {Homo sapiens} PDB: 4gnd_A 4gnf_A 4gng_A*

Probab=85.46  E-value=0.69  Score=32.56  Aligned_cols=46  Identities=20%  Similarity=0.515  Sum_probs=31.1

Q ss_pred             CCCCcCccccCcccCCCceeecC--CCCccccHhhHHHHHhcCC----CCcccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILP--KCNHGFHVRCIDKWLRSNS----SCPKCRHCLI  158 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~--~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~l~  158 (203)
                      ..+..|.+|.+    +..+....  .|...||..|+.  |....    .||.|+..+-
T Consensus        13 ~~~~~C~~C~~----~G~ll~CD~~~Cp~~fH~~Cl~--L~~~P~g~W~Cp~c~C~~C   64 (107)
T 4gne_A           13 MHEDYCFQCGD----GGELVMCDKKDCPKAYHLLCLN--LTQPPYGKWECPWHQCDEC   64 (107)
T ss_dssp             SSCSSCTTTCC----CSEEEECCSTTCCCEECTGGGT--CSSCCSSCCCCGGGBCTTT
T ss_pred             CCCCCCCcCCC----CCcEeEECCCCCCcccccccCc--CCcCCCCCEECCCCCCCcC
Confidence            45678999983    23455655  598999999998  44322    4887765444

>1wew_A DNA-binding family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=84.99  E-value=0.41  Score=31.56  Aligned_cols=47  Identities=19%  Similarity=0.435  Sum_probs=31.6

Q ss_pred             CCCcCccccCcccCCCceeecC--CCCccccHhhHHHHHh---------cCCCCcccccc
Q 042698          108 LDNECVICLSDFAPGERVRILP--KCNHGFHVRCIDKWLR---------SNSSCPKCRHC  156 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~--~C~H~FH~~Ci~~Wl~---------~~~~CP~CR~~  156 (203)
                      ....| ||-..... ..++...  .|...||..|+..--.         .+-.||.|+..
T Consensus        15 ~~~~C-iC~~~~~~-g~MI~CD~~~C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~~   72 (78)
T 1wew_A           15 IKVRC-VCGNSLET-DSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLT   72 (78)
T ss_dssp             CCCCC-SSCCCCCC-SCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHC
T ss_pred             CCEEe-ECCCcCCC-CCEEEECCccCCccccCEEEccccccccccccCCCCEECCCCCcc
Confidence            34568 79877433 3556666  6999999999964221         23459999764

>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=84.95  E-value=0.19  Score=34.44  Aligned_cols=48  Identities=21%  Similarity=0.515  Sum_probs=33.5

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC----CCcccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS----SCPKCRHC  156 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~  156 (203)
                      ++..|.||...-. .+.+.....|...||..|+..=+....    .||.|+..
T Consensus        15 ~~~~C~vC~~~~~-~~~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~~   66 (92)
T 2e6r_A           15 DSYICQVCSRGDE-DDKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILA   66 (92)
T ss_dssp             CCCCCSSSCCSGG-GGGCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHHH
T ss_pred             CCCCCccCCCcCC-CCCEEEcCCCCchhccccCCCCcccCCCCCcCCccCcCc
Confidence            4457999987643 345666667999999999985333222    49999764

>3c6w_A P28ING5, inhibitor of growth protein 5; chromatin, PHD, ING, epigenetics, alternative splicing, metal-binding, phosphoprotein, zinc; HET: M3L; 1.75A {Homo sapiens} PDB: 2pnx_A*

Probab=84.82  E-value=0.23  Score=31.07  Aligned_cols=43  Identities=26%  Similarity=0.572  Sum_probs=28.8

Q ss_pred             CCCcCccccCcccCCCceeecCC--CC-ccccHhhHHHHHhcC----CCCccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPK--CN-HGFHVRCIDKWLRSN----SSCPKCRH  155 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~--C~-H~FH~~Ci~~Wl~~~----~~CP~CR~  155 (203)
                      +...| ||.... . ..++....  |. ..||..|+.  +...    -.||.|+.
T Consensus         8 e~~yC-~C~~~~-~-g~mi~CD~~~C~~~wfH~~Cvg--l~~~p~~~w~Cp~C~~   57 (59)
T 3c6w_A            8 EPTYC-LCHQVS-Y-GEMIGCDNPDCPIEWFHFACVD--LTTKPKGKWFCPRCVQ   57 (59)
T ss_dssp             CCEET-TTTEEC-C-SEEEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CCcEE-ECCCCC-C-CCeeEeeCCCCCCCCEecccCC--cccCCCCCEECcCccC
Confidence            34567 898764 2 34666666  66 799999998  4332    25999964

>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine trimethylation, protein, histone-binding protein, transcription-structural complex; HET: M3L; 0.93A {Homo sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A

Probab=84.57  E-value=1.5  Score=31.85  Aligned_cols=46  Identities=24%  Similarity=0.514  Sum_probs=32.9

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHH------hc-----CCCCcccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWL------RS-----NSSCPKCRHC  156 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl------~~-----~~~CP~CR~~  156 (203)
                      +.++.|.||-+-    ..+.....|-..||..||..-+      +.     .=.|++|+..
T Consensus        55 g~~~~C~vC~dG----G~LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~~  111 (129)
T 3ql9_A           55 GMDEQCRWCAEG----GNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPE  111 (129)
T ss_dssp             SCBSSCTTTCCC----SEEEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCCG
T ss_pred             CCCCcCeecCCC----CeeEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCCH
Confidence            456789999854    3455666799999999999752      11     1259999764

>2klu_A T-cell surface glycoprotein CD4; cell membrane, disulfide bond, HOST- virus interaction, immune response, immunoglobulin domain, lipoprotein; NMR {Homo sapiens}

Probab=84.51  E-value=1.3  Score=28.30  Aligned_cols=25  Identities=20%  Similarity=-0.194  Sum_probs=11.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhccc
Q 042698           44 LVCGIICSLGLHFLIRCILVSWSRL   68 (203)
Q Consensus        44 l~~~~i~~l~~~~~~~~~~rr~~~~   68 (203)
                      +..++.+++++.+.+.|..|+|+|+
T Consensus        14 lGg~~~lll~~glcI~ccvkcrhRr   38 (70)
T 2klu_A           14 LGGVAGLLLFIGLGIFFSVRSRHRR   38 (70)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCS
T ss_pred             HhHHHHHHHHHHHHHHHhhHHHHHH
Confidence            3333334444445555555554443

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=82.69  E-value=1  Score=31.85  Aligned_cols=45  Identities=22%  Similarity=0.493  Sum_probs=29.9

Q ss_pred             CcCccccCccc------CCCceeecCCCCccccHhhHHHHH------h-cCCCCcccc
Q 042698          110 NECVICLSDFA------PGERVRILPKCNHGFHVRCIDKWL------R-SNSSCPKCR  154 (203)
Q Consensus       110 ~~CaICl~~~~------~~~~v~~l~~C~H~FH~~Ci~~Wl------~-~~~~CP~CR  154 (203)
                      +.|.||+..-.      .++.+.....|+..||..|+..+.      . ..=.||.|+
T Consensus         2 ~~C~~C~~~~~~n~k~g~~~~Li~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   59 (114)
T 2kwj_A            2 SYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFTLNMTEAVKTYKWQCIECK   59 (114)
T ss_dssp             CCCSSSCCBTTBCTTTCCCCCCEECSSSCCEECTTTTTCCHHHHHHHHHTTCCCGGGC
T ss_pred             CcCccCCCCccccccCCCCCCCeEeCCCCCccchhhCCChhhhhhccCCCccCccccC
Confidence            46999987542      224566666799999999997652      1 233577764

>2vnf_A ING 4, P29ING4, inhibitor of growth protein 4; acetylation, alternative splicing, anti-oncogene, cell cycle, coiled C nucleus, zinc, zinc-finger, ING4; HET: M3L; 1.76A {Homo sapiens} SCOP: g.50.1.2 PDB: 2k1j_A 2jmq_A 2qic_A*

Probab=81.99  E-value=0.33  Score=30.41  Aligned_cols=42  Identities=24%  Similarity=0.607  Sum_probs=27.9

Q ss_pred             CCcCccccCcccCCCceeecCC--CC-ccccHhhHHHHHhcC----CCCccccc
Q 042698          109 DNECVICLSDFAPGERVRILPK--CN-HGFHVRCIDKWLRSN----SSCPKCRH  155 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~--C~-H~FH~~Ci~~Wl~~~----~~CP~CR~  155 (203)
                      ...| ||.....  ..++....  |. ..||..|+.  +...    -.||.|+.
T Consensus        10 ~~~C-~C~~~~~--g~mi~CD~cdC~~~wfH~~Cvg--l~~~p~g~w~C~~C~~   58 (60)
T 2vnf_A           10 PTYC-LCHQVSY--GEMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQ   58 (60)
T ss_dssp             CEET-TTTEECC--SEEEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CCEE-ECCCcCC--CCEEEeCCCCCCCceEehhcCC--CCcCCCCCEECcCccC
Confidence            4567 8987632  34666666  55 789999998  4332    25999964

>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2

Probab=81.84  E-value=0.47  Score=32.09  Aligned_cols=50  Identities=18%  Similarity=0.468  Sum_probs=35.8

Q ss_pred             CCcCccccCcccC-CCceeecCCCCccccHhhHHHHHhc--------CCCCcccccccc
Q 042698          109 DNECVICLSDFAP-GERVRILPKCNHGFHVRCIDKWLRS--------NSSCPKCRHCLI  158 (203)
Q Consensus       109 ~~~CaICl~~~~~-~~~v~~l~~C~H~FH~~Ci~~Wl~~--------~~~CP~CR~~l~  158 (203)
                      +..|.||...-.. +..+.....|...||..|+..=+..        .=.|+.|+....
T Consensus        16 ~~~C~vC~~~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~~~~~p~g~W~C~~C~~~~~   74 (88)
T 1wev_A           16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMK   74 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHC
T ss_pred             CCcCCCCCCCCCCCCCceEECCCCCCeEcCccCCCcccccccCCCCCCeeCccccchhh
Confidence            4579999876432 3467777789999999999875431        225999976554

>3o7a_A PHD finger protein 13 variant; PHF13, zinc finger, PHD domain, nuclear protein, structural structural genomics consortium, SGC, protein binding; HET: M3L; 1.67A {Homo sapiens}

Probab=80.55  E-value=0.34  Score=29.32  Aligned_cols=42  Identities=26%  Similarity=0.581  Sum_probs=28.0

Q ss_pred             cccCcccCCCceeecCCCCccccHhhHHHHHh---cCCCCcccccc
Q 042698          114 ICLSDFAPGERVRILPKCNHGFHVRCIDKWLR---SNSSCPKCRHC  156 (203)
Q Consensus       114 ICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~---~~~~CP~CR~~  156 (203)
                      ||..... +..++....|+..||..|+..--.   .+-.||.|+.+
T Consensus         8 ~C~~~~~-~~~MI~Cd~C~~W~H~~Cvgi~~~~~~~~~~C~~C~~S   52 (52)
T 3o7a_A            8 FCMKPFA-GRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRDS   52 (52)
T ss_dssp             TTCCBCT-TCCEEECTTTCCEEETTTTTCCGGGCCSSCCCHHHHTC
T ss_pred             EeCCcCC-CCCEEEcCCCCccccccccCCCcccCCCcEECcCCCCc
Confidence            6766544 445666667999999999964321   23359999753

---

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	203
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	2e-18
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	4e-12
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	2e-10
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	3e-09
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	4e-09
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-08
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	3e-07
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	8e-07
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	8e-07
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	4e-05
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	8e-05
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	1e-04
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	2e-04
d1fp0a1	70	g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-	0.001

>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 = 73.4 bits (180), Expect = 2e-18
 Identities = 24/50 (48%), Positives = 33/50 (66%)

Query: 109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI 158
             EC +CL++   GE  R LP+C HGFH  C+D WL S+S+CP CR  ++
Sbjct: 5   GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

>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 = 56.9 bits (137), Expect = 4e-12
 Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 3/59 (5%)

Query: 111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESCKKIEGSTQ 169
            C ICL D         LP C H F   CI +W+R N +CP C+  +      IE  ++
Sbjct: 7   RCPICLEDP--SNYSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVESVVHTIESDSE 62

>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 = 52.0 bits (124), Expect = 2e-10
 Identities = 10/46 (21%), Positives = 15/46 (32%), Gaps = 1/46 (2%)

Query: 111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR-SNSSCPKCRH 155
           EC +C+      +       C +     C  +     N  CP CR 
Sbjct: 2   ECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRK 47

>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 = 49.7 bits (118), Expect = 3e-09
 Identities = 14/60 (23%), Positives = 19/60 (31%), Gaps = 14/60 (23%)

Query: 109 DNECVICLSDFAPGE--------------RVRILPKCNHGFHVRCIDKWLRSNSSCPKCR 154
            + C IC +                           CNH FH  CI +WL++   CP   
Sbjct: 21  VDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 80

>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 = 49.0 bits (116), Expect = 4e-09
 Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 2/54 (3%)

Query: 109 DNECVICLSDFAPGERVRILP-KCNHGFHVRCIDKWLRSNS-SCPKCRHCLIES 160
           D  C  C +       ++++   C H     C+D      + +CP+C   L +S
Sbjct: 3   DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKS 56

>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 = 48.1 bits (114), Expect = 1e-08
 Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 5/47 (10%)

Query: 112 CVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSS-CPKCRHCL 157
           C IC  +    + V+I P C H     C+  W  S    CP CR  +
Sbjct: 26  CKICAEND---KDVKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEI 68

>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 = 45.4 bits (106), Expect = 3e-07
 Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 20/79 (25%)

Query: 95  TIVKYSGELKLPGLDNECVICL--------------SDFAPGERVRILPKCNHGFHVRCI 140
            I KY+ ELK+   + +C+IC+              S       V  L KC+H FH+ C+
Sbjct: 12  VIRKYTEELKVAP-EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCL 70

Query: 141 DKWLRS-----NSSCPKCR 154
                +     +  CP C+
Sbjct: 71  LAMYCNGNKDGSLQCPSCK 89

>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 = 42.6 bits (100), Expect = 8e-07
 Identities = 10/45 (22%), Positives = 18/45 (40%), Gaps = 7/45 (15%)

Query: 111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRH 155
            C  C ++    +  ++LP C H     C++        CP C+ 
Sbjct: 8   RCQQCQAEA---KCPKLLP-CLHTLCSGCLEAS---GMQCPICQA 45

>d1vyxa_ g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal domain {Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]} Length = 60

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: IE1B protein (ORF K3), N-terminal domain
species: Kaposi's sarcoma-associated herpesvirus, KSHV, HHV8 [TaxId: 37296]

 Score = 42.5 bits (99), Expect = 8e-07
 Identities = 9/51 (17%), Positives = 14/51 (27%), Gaps = 3/51 (5%)

Query: 109 DNECVICLSDFAPGERVRILPK-CNHGFHVRCIDKWLRSN--SSCPKCRHC 156
              C IC  +                  H  C+  WL  +  ++C  C   
Sbjct: 6   VPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVV 56

>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 = 38.9 bits (90), Expect = 4e-05
 Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 7/50 (14%)

Query: 111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS---SCPKCRHCL 157
           EC ICL      +       C+H F   C+ K L        CP C++ +
Sbjct: 23  ECPICLELI---KEPVSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDI 68

>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 = 38.2 bits (88), Expect = 8e-05
 Identities = 15/78 (19%), Positives = 23/78 (29%), Gaps = 19/78 (24%)

Query: 111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHC-------------- 156
            C  C +          L  C H F   C+   +   + CP C                 
Sbjct: 24  RCSRCTNIL---REPVCLGGCEHIFCSNCVSDCI--GTGCPVCYTPAWIQDLKINRQLDS 78

Query: 157 LIESCKKIEGSTQPSSLS 174
           +I+ C K+      + LS
Sbjct: 79  MIQLCSKLRNLLHDNELS 96

>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 = 37.2 bits (86), Expect = 1e-04
 Identities = 14/47 (29%), Positives = 18/47 (38%), Gaps = 5/47 (10%)

Query: 112 CVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS-NSSCPKCRHCL 157
           C IC           +   C H F   CI + L+   S CP CR+  
Sbjct: 26  CQICEHIL----ADPVETSCKHLFCRICILRCLKVMGSYCPSCRYPC 68

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 2e-04
 Identities = 10/54 (18%), Positives = 19/54 (35%), Gaps = 9/54 (16%)

Query: 109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS--------NSSCPKCR 154
            + C +CL ++   +   I   C   F   C+ +++            SCP   
Sbjct: 5   SSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAA 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 = 0.001
 Identities = 17/71 (23%), Positives = 26/71 (36%), Gaps = 7/71 (9%)

Query: 108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSS----CPKCRHCLIESCKK 163
           LD+   IC     PG+ V +  +C   FH+ C    L+        C  C        K+
Sbjct: 3   LDDSATICRVCQKPGDLV-MCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL--PDLKE 59

Query: 164 IEGSTQPSSLS 174
            +   Q   L+
Sbjct: 60  EDVDLQACKLN 70

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	203
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.77
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.62
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.55
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.54
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.54
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.46
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.46
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.35
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.26
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.25
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.21
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.19
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.04
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	98.96
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	98.95
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.75
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.67
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	95.5
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	94.99
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	94.62
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	94.35
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	93.99
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	93.09
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	91.99
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	90.77
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	90.29
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	89.9
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	86.66
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	86.16
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	85.63
d2co8a2	36	Nedd9 interacting protein with calponin homology,	84.1
d2pnxa1	51	Inhibitor of growth protein 4, Ing4 {Homo sapiens	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=99.77  E-value=8e-20  Score=115.32  Aligned_cols=51  Identities=47%  Similarity=1.171  Sum_probs=46.5

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  158 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  158 (203)
                      ++.+|+||+++|..++.+..++.|+|.||..||..|++++.+||+||++++
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            456799999999999999887669999999999999999999999999875

>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=99.62  E-value=2.1e-16  Score=103.63  Aligned_cols=49  Identities=37%  Similarity=0.854  Sum_probs=42.6

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      .++|+||++.+.+  .++.++ |||.||..||..|++.+.+||+||..+...
T Consensus         5 ~d~C~IC~~~~~~--~~~~~~-C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~~   53 (68)
T d1chca_           5 AERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVESV   53 (68)
T ss_dssp             CCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCCE
T ss_pred             CCCCccCCcCccC--CcEEeC-CCCcCcHHHHHHHHHhCCcCCCCCcchHhh
Confidence            4679999999965  356677 999999999999999999999999987644

>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=99.55  E-value=2.4e-15  Score=108.01  Aligned_cols=51  Identities=27%  Similarity=0.720  Sum_probs=40.7

Q ss_pred             CCcCccccCcccCC---------------CceeecCCCCccccHhhHHHHHhcC-----CCCcccccccccc
Q 042698          109 DNECVICLSDFAPG---------------ERVRILPKCNHGFHVRCIDKWLRSN-----SSCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~~~~~~---------------~~v~~l~~C~H~FH~~Ci~~Wl~~~-----~~CP~CR~~l~~~  160 (203)
                      ++.|+||++++...               ..+..++ |+|+||..||..|++.+     .+||+||+.+...
T Consensus        25 ~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~-CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T d1v87a_          25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             cccccchhheecccccccccccccccccccceEECC-CCChhhHHHHHHHHHhcCcCCCCccccccchhccC
Confidence            46799999998542               2456677 99999999999999753     3799999988655

>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=99.54  E-value=6.5e-16  Score=95.97  Aligned_cols=48  Identities=21%  Similarity=0.454  Sum_probs=40.3

Q ss_pred             cCccccCcccCCCce-eecCCCCccccHhhHHHHHhcC-CCCccccccccc
Q 042698          111 ECVICLSDFAPGERV-RILPKCNHGFHVRCIDKWLRSN-SSCPKCRHCLIE  159 (203)
Q Consensus       111 ~CaICl~~~~~~~~v-~~l~~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~l~~  159 (203)
                      +|+||+++|..++.. ..++ |||.||.+||..|++.+ ..||+||+++.+
T Consensus         2 eCpICl~~~~~~~~~~~~~~-CgH~~c~~C~~~w~~~~~~~CP~CR~~~~~   51 (52)
T d1ur6b_           2 ECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPE   51 (52)
T ss_dssp             EETTTTEECCGGGTTCCSSS-SSCCCCHHHHHHHTTTSCCBCTTTCCBCSC
T ss_pred             CCcCCChhhhCCCceEEecC-CCCccchHHHHHHHhhcCCCCCccCCcCCC
Confidence            699999999877654 4456 99999999999999864 469999998764

>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=99.54  E-value=2.1e-15  Score=103.61  Aligned_cols=50  Identities=30%  Similarity=0.625  Sum_probs=41.9

Q ss_pred             CCcCccccCcccCCC---------------ceeecCCCCccccHhhHHHHHhcCCCCccccccccc
Q 042698          109 DNECVICLSDFAPGE---------------RVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  159 (203)
Q Consensus       109 ~~~CaICl~~~~~~~---------------~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  159 (203)
                      ++.|+||++++....               .+..++ |||+||.+||..||+.+.+||+||+...-
T Consensus        21 ~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   85 (88)
T d3dplr1          21 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEF   85 (88)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCCE
T ss_pred             CCcCEEccchhhCccccccccccccccccCCeEEcc-ccCcccHHHHHHHHHHCCcCCCCCCcccc
Confidence            457999999987532               356677 99999999999999999999999998753

>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=99.46  E-value=1.9e-14  Score=93.30  Aligned_cols=51  Identities=24%  Similarity=0.544  Sum_probs=40.1

Q ss_pred             CCcCccccCcccCC-C-ceeecCCCCccccHhhHHHHHhc-CCCCcccccccccc
Q 042698          109 DNECVICLSDFAPG-E-RVRILPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIES  160 (203)
Q Consensus       109 ~~~CaICl~~~~~~-~-~v~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~  160 (203)
                      +.+|+||++++..+ + .+.+++ |||.||..||..|+.. +.+||+||..+...
T Consensus         3 d~~CpIC~~~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~   56 (65)
T d1g25a_           3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCCCcCCceeecCCceEEEeCc-cChHhhHHHHHHHhCcCcCCCCCCCcCcccc
Confidence            56899999986433 3 345566 9999999999999965 45799999987544

>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=99.46  E-value=2.9e-14  Score=95.92  Aligned_cols=51  Identities=29%  Similarity=0.633  Sum_probs=42.3

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc-CCCCccccccccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIESCKK  163 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~~~~  163 (203)
                      ...|+||++.+..   .++++ |||.||..||..|++. +.+||+||..+......
T Consensus        23 ~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~i   74 (79)
T d1fbva4          23 FQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPI   74 (79)
T ss_dssp             TTBCTTTSSSBCC---EECSS-SCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCCS
T ss_pred             CCCCccCCCcCCC---eEEeC-CCCeeeHHHHHHHHHHCcCcCCCCCcCccCCcee
Confidence            3569999999865   46788 9999999999999975 56799999999765443

>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=99.35  E-value=1.2e-13  Score=86.69  Aligned_cols=47  Identities=13%  Similarity=0.087  Sum_probs=40.4

Q ss_pred             cCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccccc
Q 042698          111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIES  160 (203)
Q Consensus       111 ~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~  160 (203)
                      .|+||++.|+++  +.... |||+|+++||..|++++.+||+||..+...
T Consensus         2 ~C~Ic~~~~~~P--v~~~~-cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~   48 (56)
T d2baya1           2 LCAISGKVPRRP--VLSPK-SRTIFEKSLLEQYVKDTGNDPITNEPLSIE   48 (56)
T ss_dssp             CCTTTCSCCSSE--EEETT-TTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             CCccCCchHHhc--CccCC-CCCcccHHHHHHHHhhccCCCccCCcCCHH
Confidence            599999999764  44444 999999999999999999999999987765

>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=99.26  E-value=1.5e-12  Score=88.56  Aligned_cols=47  Identities=32%  Similarity=0.554  Sum_probs=39.7

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhc-CCCCcccccccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIES  160 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~  160 (203)
                      ..|+||++.+.+.   .+++ |||.|+..||..|++. +.+||+||..+.+.
T Consensus        24 l~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~   71 (86)
T d1rmda2          24 ISCQICEHILADP---VETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (86)
T ss_dssp             TBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             cCCccCCcchhcc---eecC-CCChhhHHHHHHHHhhCCCcCcccCCCCChh
Confidence            4799999998764   5677 9999999999999975 45799999987654

>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=99.25  E-value=5.1e-13  Score=83.79  Aligned_cols=45  Identities=22%  Similarity=0.552  Sum_probs=38.1

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccccccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIESC  161 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~~~  161 (203)
                      .+|+||++.|.+.   ++++ |||.||..||..|   +.+||+||..+....
T Consensus         7 l~C~IC~~~~~~p---~~lp-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T d1bora_           7 LRCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             SSCSSSCSSCBCC---SCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             CCCcccCcccCCC---EEec-CCCHHhHHHHHcC---CCcCcCCCCcccCCC
Confidence            5899999999775   5678 9999999999875   567999999987553

>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=99.21  E-value=3.1e-12  Score=89.87  Aligned_cols=46  Identities=30%  Similarity=0.620  Sum_probs=38.6

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC---CCccccccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS---SCPKCRHCLIE  159 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~---~CP~CR~~l~~  159 (203)
                      .+|+||++.|.++   ..++ |||.||..||..|++.+.   .||+||..+..
T Consensus        22 l~CpIC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (103)
T d1jm7a_          22 LECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (103)
T ss_dssp             TSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             cCCCccCchhCCe---EEcC-CCCchhhHHHHHHHHHCCCCCcCcCCCCcCCh
Confidence            4799999999775   4577 999999999999997653   69999988753

>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=99.19  E-value=5.6e-12  Score=79.96  Aligned_cols=52  Identities=19%  Similarity=0.353  Sum_probs=37.6

Q ss_pred             CCCCcCccccCcccCCCcee-ecCCCCccccHhhHHHHHh--cCCCCcccccccc
Q 042698          107 GLDNECVICLSDFAPGERVR-ILPKCNHGFHVRCIDKWLR--SNSSCPKCRHCLI  158 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~-~l~~C~H~FH~~Ci~~Wl~--~~~~CP~CR~~l~  158 (203)
                      ++...|.||++++....... ...+|+|.||..||..|+.  .+.+||+||+.+.
T Consensus         4 ed~~~C~IC~~~~~~~~~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~   58 (60)
T d1vyxa_           4 EDVPVCWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSCCCCCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCCCccCCccCCCceeEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeee
Confidence            34578999999986542211 1113569999999999995  4557999998753

>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=99.04  E-value=2e-11  Score=84.73  Aligned_cols=44  Identities=23%  Similarity=0.516  Sum_probs=36.5

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCcccccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLI  158 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~  158 (203)
                      .+|+||++.|..+  +...+ |||.||..||..|+.  ..||.||..+.
T Consensus        23 l~C~IC~~~~~~p--v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~   66 (97)
T d1jm7b_          23 LRCSRCTNILREP--VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAW   66 (97)
T ss_dssp             TSCSSSCSCCSSC--BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCS
T ss_pred             CCCccCCchhhcC--ceeCC-CCCchhHHHHHHHHh--ccccccCCcCc
Confidence            5799999999765  44446 999999999999985  35999998764

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.96  E-value=2.9e-10  Score=75.87  Aligned_cols=49  Identities=16%  Similarity=0.091  Sum_probs=41.0

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhc-CCCCcccccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRS-NSSCPKCRHCLIES  160 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~l~~~  160 (203)
                      ++..|+||++-|.++   .+++ |||.|+..||..|+.. +..||.||..+...
T Consensus         6 ~~l~CpIc~~l~~dP---v~~~-cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~   55 (80)
T d2c2la2           6 DYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQE   55 (80)
T ss_dssp             STTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCGG
T ss_pred             ccccCcCcCchhhhh---cccC-CcCeecHHHHHHHHhcCCccCCCcccccccc
Confidence            457899999999875   4677 9999999999999965 55799999987643

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=98.95  E-value=3.5e-10  Score=75.11  Aligned_cols=49  Identities=24%  Similarity=0.482  Sum_probs=41.1

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC-CCCccccccccc
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN-SSCPKCRHCLIE  159 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~l~~  159 (203)
                      .++..|+||++-|.++   .+++ |||.|+..||..|++.+ ..||.|+..+..
T Consensus         6 P~~l~CpIc~~~m~dP---V~~~-cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~   55 (78)
T d1t1ha_           6 PEYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             CccCCCcCcCchhhCc---eEcc-CCCcchHHHHHHHHHHCCCCCCcccccCCc
Confidence            3567899999999876   4567 99999999999999764 569999988754

>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=98.75  E-value=4.2e-09  Score=72.87  Aligned_cols=49  Identities=18%  Similarity=0.068  Sum_probs=41.6

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCCCCccccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNSSCPKCRHCLIE  159 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~l~~  159 (203)
                      .+..|+||++-|.++   .+++.|+|.|.+.||..|++.+..||+||..+..
T Consensus        21 ~~f~CPI~~~lm~dP---V~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~   69 (98)
T d1wgma_          21 DEFLDPIMSTLMCDP---VVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             TTTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             HHhCCcCchhHHHHH---HhcccccchhhHHHHHHHHHhcCCcccccccccc
Confidence            457899999999886   4666356789999999999999999999998764

>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=98.67  E-value=4.8e-09  Score=71.73  Aligned_cols=46  Identities=22%  Similarity=0.602  Sum_probs=36.8

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC--------CCCccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN--------SSCPKCRH  155 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~--------~~CP~CR~  155 (203)
                      ..+|+||++++...+.+..++ |+|.||.+|+..|+..+        -.||.|+.
T Consensus         5 ~~~C~IC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           5 SSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             BCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCcCccCCCcccCCceEEECC-CCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            468999999998777777776 99999999999999521        14998643

>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=95.50  E-value=0.0032  Score=36.90  Aligned_cols=44  Identities=25%  Similarity=0.705  Sum_probs=32.3

Q ss_pred             cCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC----CCccccc
Q 042698          111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS----SCPKCRH  155 (203)
Q Consensus       111 ~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~----~CP~CR~  155 (203)
                      .|.||...-.. +.+.....|+..||..|++.-+....    .||.||.
T Consensus         2 ~C~vC~~~~~~-~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGED-DKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCC-SCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCC-CCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            58899766433 45566777999999999998664322    4999975

>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=94.99  E-value=0.0072  Score=37.04  Aligned_cols=49  Identities=22%  Similarity=0.468  Sum_probs=36.8

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHH---h--cCCCCcccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWL---R--SNSSCPKCRHC  156 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl---~--~~~~CP~CR~~  156 (203)
                      ++..|.+|......++.++....|+..||..|+..=.   .  .+-.||.|+..
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            4568999998887777777777899999999996321   1  23359999753

>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=94.62  E-value=0.0039  Score=38.06  Aligned_cols=46  Identities=20%  Similarity=0.506  Sum_probs=32.7

Q ss_pred             CCCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcC----CCCccccccc
Q 042698          108 LDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSN----SSCPKCRHCL  157 (203)
Q Consensus       108 ~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~----~~CP~CR~~l  157 (203)
                      .++.|.+|.+.    ..+.....|.-.||..|+...+...    -.||.|+..-
T Consensus         8 ~~~~C~~C~~~----g~lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           8 HMEFCRVCKDG----GELLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SCSSCTTTCCC----SSCBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CcCCCcCCCCC----CeEEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            44579999753    3455666799999999998665432    2599997653

>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=94.35  E-value=0.018  Score=37.04  Aligned_cols=37  Identities=19%  Similarity=0.388  Sum_probs=27.0

Q ss_pred             CCCCCCcCccccCcccCCCceeecCCCCccccHhhHHHH
Q 042698          105 LPGLDNECVICLSDFAPGERVRILPKCNHGFHVRCIDKW  143 (203)
Q Consensus       105 ~~~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~W  143 (203)
                      ...++..|.|| +-+...+.. -..-|+.+||..|+.+-
T Consensus        11 ~v~~D~mC~vC-~v~t~~~l~-pCRvCtRv~H~~CL~r~   47 (89)
T d1wila_          11 PVVNDEMCDVC-EVWTAESLF-PCRVCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCCSCCCTTT-CCCCSSCCS-SCSSSSSCCCHHHHHHH
T ss_pred             CCCcCcccccc-Cccccccee-cceeecchhhHHHHHHh
Confidence            34567899999 666665433 22238999999999985

>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=93.99  E-value=0.013  Score=36.57  Aligned_cols=46  Identities=24%  Similarity=0.520  Sum_probs=31.8

Q ss_pred             CCcCccccCcccCCCceeecCCCCccccHhhHHHHHhcCC----CCcccccccc
Q 042698          109 DNECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLRSNS----SCPKCRHCLI  158 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~~~~----~CP~CR~~l~  158 (203)
                      ...|.+|.+.   + .+.....|...||..|+...+....    .||.|+..-.
T Consensus         7 c~~C~~C~~~---~-~ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~   56 (70)
T d1fp0a1           7 ATICRVCQKP---G-DLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPD   56 (70)
T ss_dssp             SSCCSSSCSS---S-CCEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCS
T ss_pred             CCCCCCCCCc---C-EEEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCc
Confidence            3457777543   3 4566667999999999998765433    4999965443

>d1wepa_ g.50.1.2 (A:) PHD finger protein 8 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 8
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.09  E-value=0.25  Score=31.03  Aligned_cols=47  Identities=19%  Similarity=0.422  Sum_probs=34.0

Q ss_pred             cCccccCcccCCCceeecCCCCccccHhhHHH--H-Hhc--CCCCcccccccc
Q 042698          111 ECVICLSDFAPGERVRILPKCNHGFHVRCIDK--W-LRS--NSSCPKCRHCLI  158 (203)
Q Consensus       111 ~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~--W-l~~--~~~CP~CR~~l~  158 (203)
                      .| ||...+..++.++....|+-.||..|+..  . ...  +-.||.|+....
T Consensus        14 ~C-iC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~g   65 (79)
T d1wepa_          14 YC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFG   65 (79)
T ss_dssp             CS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSC
T ss_pred             Ee-ECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCcC
Confidence            45 99988776667777888999999999952  2 122  246999986543

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.99  E-value=0.031  Score=36.23  Aligned_cols=49  Identities=18%  Similarity=0.495  Sum_probs=33.4

Q ss_pred             CCcCccccCcccC-CCceeecCCCCccccHhhHHHHH-----hc---CCCCccccccc
Q 042698          109 DNECVICLSDFAP-GERVRILPKCNHGFHVRCIDKWL-----RS---NSSCPKCRHCL  157 (203)
Q Consensus       109 ~~~CaICl~~~~~-~~~v~~l~~C~H~FH~~Ci~~Wl-----~~---~~~CP~CR~~l  157 (203)
                      ...|.||...... ...+.....|+..||..|+...+     ..   .-.||.|+...
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~   73 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQM   73 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHH
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchH
Confidence            3469999865443 34566677799999999987443     11   23599996543

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.77  E-value=0.041  Score=28.60  Aligned_cols=29  Identities=21%  Similarity=0.500  Sum_probs=24.9

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhH
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCI  140 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci  140 (203)
                      ..|+-|...+...|.|+.-  =+++||-.|+
T Consensus         3 g~Ca~C~~~I~~~e~VmRA--~~~VyHl~CF   31 (31)
T d1rutx3           3 GACSACGQSIPASELVMRA--QGNVYHLKCF   31 (31)
T ss_dssp             EECTTTCCEECTTSEEEEE--TTEEECGGGC
T ss_pred             cccccccCcCChhHhheec--ccceeeeccC
Confidence            3699999999999988875  4799999984

>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {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 At1g33420
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=90.29  E-value=0.029  Score=34.94  Aligned_cols=46  Identities=28%  Similarity=0.457  Sum_probs=32.9

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHHHHHh----cCCCCcccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCIDKWLR----SNSSCPKCRHC  156 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~~Wl~----~~~~CP~CR~~  156 (203)
                      ..| ||......++.++....|...||..|+..=..    ..-.||.|+..
T Consensus        17 ~~C-~C~~~~~~~~~mv~Cd~C~~w~H~~C~g~~~~~~~~~~~~C~~C~~~   66 (72)
T d1weea_          17 VDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIEL   66 (72)
T ss_dssp             ECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHH
T ss_pred             EEe-eCCCCcCCCCeEEEeCCCCCcCchhhcCCccccCCCCcEECcCCcCc
Confidence            358 78877767777777778999999999854211    22359999654

>d1wesa_ g.50.1.2 (A:) PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD Inhibitor of growth protein 2, Ing2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.90  E-value=0.076  Score=33.08  Aligned_cols=43  Identities=33%  Similarity=0.651  Sum_probs=25.1

Q ss_pred             CcCccccCcccCCCceeec-CCC-CccccHhhHHHHHhcC----CCCcccccc
Q 042698          110 NECVICLSDFAPGERVRIL-PKC-NHGFHVRCIDKWLRSN----SSCPKCRHC  156 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l-~~C-~H~FH~~Ci~~Wl~~~----~~CP~CR~~  156 (203)
                      .-| ||..... ++.+... ..| +..||..|+.  |...    -.||.|+..
T Consensus        17 ~~C-iC~~~~~-~~~i~c~~~~C~~~wfH~~Cvg--l~~~p~~~w~C~~C~~~   65 (71)
T d1wesa_          17 TYC-LCNQVSY-GEMIGCDNEQCPIEWFHFSCVS--LTYKPKGKWYCPKCRGD   65 (71)
T ss_dssp             CCS-TTCCCCC-SSEECCSCTTCSCCCEETTTTT--CSSCCSSCCCCTTTSSC
T ss_pred             CEE-EeCCCCC-CCEEEEECCCCCCcCccCccCC--CCcCCCCcEECcCCccc
Confidence            456 9987642 2333321 134 4579999985  3322    249999753

>d1wewa_ g.50.1.2 (A:) Sumoylation ligase E3, SIZ1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Sumoylation ligase E3, SIZ1
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=86.66  E-value=0.35  Score=30.22  Aligned_cols=47  Identities=19%  Similarity=0.387  Sum_probs=30.5

Q ss_pred             CCcCccccCcccCCCceeecC--CCCccccHhhHHH----HHh-----cCCCCccccccc
Q 042698          109 DNECVICLSDFAPGERVRILP--KCNHGFHVRCIDK----WLR-----SNSSCPKCRHCL  157 (203)
Q Consensus       109 ~~~CaICl~~~~~~~~v~~l~--~C~H~FH~~Ci~~----Wl~-----~~~~CP~CR~~l  157 (203)
                      ...| ||......+. ++.+.  .|+..||..|+.-    .-.     .+-.||.|+..-
T Consensus        16 ~~~C-~C~~~~~~~~-~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~   73 (78)
T d1wewa_          16 KVRC-VCGNSLETDS-MIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS   73 (78)
T ss_dssp             CCCC-SSCCCCCCSC-EEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCC
T ss_pred             ccEe-ECCCccCCCc-EEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcC
Confidence            3568 8998776543 44553  4999999999842    101     124599997654

>d1wema_ g.50.1.2 (A:) Death associated transcription factor 1, Datf1 (DIO-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Death associated transcription factor 1, Datf1 (DIO-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.16  E-value=0.46  Score=29.25  Aligned_cols=45  Identities=24%  Similarity=0.558  Sum_probs=30.3

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhHH----HH--H---hcCCCCcccccc
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCID----KW--L---RSNSSCPKCRHC  156 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci~----~W--l---~~~~~CP~CR~~  156 (203)
                      ..| ||..... ++.++....|.-.||..|+.    ..  .   ..+-.||.|+..
T Consensus        17 ~~C-iC~~~~~-~~~mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~   70 (76)
T d1wema_          17 LYC-ICRQPHN-NRFMICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             CCS-TTCCCCC-SSCEEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             CEE-ECCCccC-CCeEEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCc
Confidence            458 8976654 34566777799999999982    11  1   234579999654

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.63  E-value=0.063  Score=28.62  Aligned_cols=27  Identities=26%  Similarity=0.666  Sum_probs=20.9

Q ss_pred             CcCccccCcccCCCceeecCCCCccccHhhH
Q 042698          110 NECVICLSDFAPGERVRILPKCNHGFHVRCI  140 (203)
Q Consensus       110 ~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci  140 (203)
                      +.|++|-..+.+    +++.+.|-.||-.|+
T Consensus         9 EkC~~C~~~I~d----riLrA~Gk~yHP~CF   35 (35)
T d2dloa1           9 EKCATCSQPILD----RILRAMGKAYHPGCF   35 (35)
T ss_dssp             CBCTTTCCBCCS----CCEEETTEEECTTTC
T ss_pred             HHHHHhchHHHH----HHHHHhCCCCCCCCC
Confidence            579999988776    344458899998884

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.10  E-value=0.27  Score=26.28  Aligned_cols=31  Identities=29%  Similarity=0.523  Sum_probs=21.2

Q ss_pred             CCCCcCccccCcccCCCceeecCCCCccccHhhH
Q 042698          107 GLDNECVICLSDFAPGERVRILPKCNHGFHVRCI  140 (203)
Q Consensus       107 ~~~~~CaICl~~~~~~~~v~~l~~C~H~FH~~Ci  140 (203)
                      +..+.|.+|-...-.-+.+   ..=|++||+.|+
T Consensus         6 g~~~~C~~C~K~VY~~Erl---~a~g~~yHk~CF   36 (36)
T d2co8a2           6 GAGDLCALCGEHLYVLERL---CVNGHFFHRSCF   36 (36)
T ss_dssp             CSSCBCSSSCCBCCTTTBC---CBTTBCCBTTTC
T ss_pred             CCCCcccccCCEEeeeeEE---EecCcEeccccC
Confidence            4567899997765443333   225799999984

>d2pnxa1 g.50.1.2 (A:195-245) Inhibitor of growth protein 4, Ing4 {Homo sapiens [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Inhibitor of growth protein 4, Ing4
species: Homo sapiens [TaxId: 9606]

Probab=80.18  E-value=0.24  Score=28.51  Aligned_cols=40  Identities=28%  Similarity=0.693  Sum_probs=23.9

Q ss_pred             cCccccCcccCCCceeecCC--C-CccccHhhHHHHHhcCC----CCccccc
Q 042698          111 ECVICLSDFAPGERVRILPK--C-NHGFHVRCIDKWLRSNS----SCPKCRH  155 (203)
Q Consensus       111 ~CaICl~~~~~~~~v~~l~~--C-~H~FH~~Ci~~Wl~~~~----~CP~CR~  155 (203)
                      -| ||.... .+ .+.....  | .-.||..|+.  +....    .||.|+.
T Consensus         4 yC-~C~~~~-~~-~mi~Cd~~~C~~~WfH~~Cvg--l~~~p~~~w~C~~C~~   50 (51)
T d2pnxa1           4 YC-LCHQVS-YG-EMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQ   50 (51)
T ss_dssp             ET-TTTEEC-CS-EEEECSCTTCSSCEEEGGGGT--CSSCCSSCCCCHHHHC
T ss_pred             EE-EcCCCC-CC-CEEEEecCCCCCCCEeCCccC--CCcCCCCcEECcCCCC
Confidence            47 787664 22 3444432  3 4579999996  33222    4998875