Citrus Sinensis ID: 042990

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-----
Protein Sequence
MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILPNKGIKQKALKTFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETCQKIIGCSQAASSSENPVTAQETIVTITPLEPEGLIRNYRGIS
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHcccEEEEEcccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHccccccHHHHHHccEEEEccccccccccccEEEEEcccccccEEEEcccccccccHHHHHHHHHccccccHHHHHcccccccccccccccccccccccccccEEEEcccccccccccccccc
Coil and Loop (DISEMBL)
MVLSVLLCALICSLGLNSIIRCVVRCSSlvasrsgasnsaailpnkgikqkalktfpvVSYSAELNLAGLDTECVICLsefaagdrlrllpkcnhgfhvrCIDKwlsshsscpkcrhCLIETCQKIigcsqaasssenpvtaqetivtitplepeglirnyrgis
Flexible Loop (DISEMBL)
MVLSVLLCALICSLGLNSIIRCVVRCSSLVAsrsgasnsaailpnkgikQKALKTFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETCQKIIGCSQAASSSENPVTAQEtivtitplepeglirnyrgis
Low Complexity Region (SEG)
MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILPNKGIKQKALKTFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETCQKIIGCSQAASSSENPVTAQETIVTITPLEPEGLIRNYRGIS
Disordered region (IsUnstruct)
**LSVLLCALICSLGLNSIIRCVVRCSSLVASR******AAILPNKGIKQKALKTFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETCQKIIGCSQ*************TIVTITPL*************
Disordered Region (DISOPRED)
MVLSVLLCALICSLGLNSIIRCVVR***************************LKTFPVVSYSAEL***GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCL**********************************************
Disordered Region (DISEMBL)
MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILPNKGIKQKALKTFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETCQKIIGC**************ETIVTITPLEPEGLIRNYRGIS
Disordered Region (DISPRO)
MVLSVLLCALICSLGLNSIIRCVVRCSS*****************KGIKQKALKTFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET***********************IV******************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILPNKGIKQKALKTFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETCQKIIGCSQAASSSENPVTAQETIVTITPLEPEGLIRNYRGIS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	165	2.2.26 [Sep-21-2011]
Q6NQG7	219	RING-H2 finger protein AT	yes	no	0.981	0.739	0.660	1e-57
Q6NML0	225	E3 ubiquitin-protein liga	no	no	0.969	0.711	0.587	7e-50
P0C034	251	RING-H2 finger protein AT	no	no	0.945	0.621	0.590	2e-48
Q94BY6	226	RING-H2 finger protein AT	no	no	0.969	0.707	0.557	2e-46
Q9LS99	220	RING-H2 finger protein AT	no	no	0.939	0.704	0.538	3e-46
Q9FLC6	176	RING-H2 finger protein AT	no	no	0.715	0.670	0.545	3e-33
Q8LC69	185	RING-H2 finger protein AT	no	no	0.757	0.675	0.488	3e-27
Q9SG96	181	RING-H2 finger protein AT	no	no	0.721	0.657	0.480	5e-27
Q9LM69	197	RING-H2 finger protein AT	no	no	0.727	0.609	0.484	9e-27
Q9LZV8	159	RING-H2 finger protein AT	no	no	0.606	0.628	0.528	2e-25

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

 Score =  221 bits (564), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 107/162 (66%), Positives = 124/162 (76%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILPNKGIKQKALKTFPVVS 60
           MVLSVLLCAL+CSLGLNSIIRC +RCS+LV S +G  N    L N G+K+KALK+F  VS
Sbjct: 58  MVLSVLLCALVCSLGLNSIIRCALRCSNLVPSEAGGDNYPVRLTNTGVKRKALKSFQTVS 117

Query: 61  YSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI 120
           YS ELNL GLDTEC ICLSEF A +R++LLP C+HGFHVRCIDKWLSSHSSCP CRHCLI
Sbjct: 118 YSTELNLPGLDTECAICLSEFVAEERVKLLPTCHHGFHVRCIDKWLSSHSSCPTCRHCLI 177

Query: 121 ETCQKIIGCSQAASSSENPVTAQETIVTITPLEPEGLIRNYR 162
           +TC+KI  CSQ +S +         I+ I PLEPE  IR +R
Sbjct: 178 QTCEKIADCSQTSSLNSTQPPQDSIILQIAPLEPERWIRWFR 219

Arabidopsis thaliana (taxid: 3702)

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

 Score =  196 bits (497), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 97/165 (58%), Positives = 122/165 (73%), Gaps = 5/165 (3%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSS--LVASRSGASNSAAILPNKGIKQKALKTFPV 58
           M+LSVL+C +IC LGL+ IIRC  R SS  +++    + ++     NKGIK+KAL+ FPV
Sbjct: 60  MLLSVLICGIICCLGLHYIIRCAFRRSSRFMISEPISSLSTPRSSSNKGIKKKALRMFPV 119

Query: 59  VSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHC 118
           VSYS E+NL G+  ECVICLS+F +G++LRLLPKCNHGFHVRCIDKWL  H +CPKCRHC
Sbjct: 120 VSYSREMNLPGIGEECVICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQHHLTCPKCRHC 179

Query: 119 LIETCQKIIG-CSQAASSSENPVTAQETIVTITPLEPEGLIRNYR 162
           L+ETCQKI+G  SQA S +  P   +  IV I PLEPEG +  +R
Sbjct: 180 LVETCQKILGDFSQADSMASTP--TESVIVRIDPLEPEGRVNTFR 222

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 =  191 bits (484), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 95/161 (59%), Positives = 122/161 (75%), Gaps = 5/161 (3%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSS--LVASRSGASNSAAILPNKGIKQKALKTFPV 58
           M+LS+L+C +IC LGL+ IIRC +R S+  +++    + +S     NKGIK+KAL+ FPV
Sbjct: 60  MLLSILICGIICCLGLHYIIRCALRRSTRFMISEPVPSLSSTRGSSNKGIKKKALRMFPV 119

Query: 59  VSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHC 118
           VSYS E+NL GLD ECVICLS+F +G++LRLLPKCNHGFHVRCIDKWL  H +CPKCR+C
Sbjct: 120 VSYSPEMNLPGLDEECVICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQQHLTCPKCRNC 179

Query: 119 LIETCQKIIG-CSQAASSSENPVTAQETIVTITPLEPEGLI 158
           L+ETCQKI+G  SQA S +  P   +  IVTI PLEP  ++
Sbjct: 180 LVETCQKILGDFSQADSVTAEP--TEIVIVTIVPLEPTEIV 218

Arabidopsis thaliana (taxid: 3702)

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

 Score =  184 bits (468), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 92/165 (55%), Positives = 118/165 (71%), Gaps = 5/165 (3%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSS--LVASRSGASNSAAILPNKGIKQKALKTFPV 58
           M+LSVL+C +IC LGL+ IIRC  R +S  +++      ++     NKGI +KAL+ FPV
Sbjct: 61  MLLSVLICGIICCLGLHYIIRCAFRRTSSFMISEPIAGLSTPCGSSNKGINKKALRMFPV 120

Query: 59  VSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHC 118
           VSYS E+NL GL  ECVICLS+F +G+++R+LPKC+HGFHVRCIDKWL  H +CPKCRHC
Sbjct: 121 VSYSPEMNLPGLGEECVICLSDFVSGEQIRMLPKCHHGFHVRCIDKWLQQHLTCPKCRHC 180

Query: 119 LIETCQKIIG-CSQAASSSENPVTAQETIVTITPLEPEGLIRNYR 162
           L+ETCQKI+G  SQA   +  P  +   IV I PLEPEG +   R
Sbjct: 181 LVETCQKILGDFSQADQVAATPTAS--VIVRIAPLEPEGRVNILR 223

Arabidopsis thaliana (taxid: 3702)

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

 Score =  184 bits (466), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 92/171 (53%), Positives = 121/171 (70%), Gaps = 16/171 (9%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILP--------NKGIKQKA 52
           M+LS+LLC +ICSLGL+ IIRC     + + SRS   +    +P        NKGIK+KA
Sbjct: 54  MLLSILLCGIICSLGLHYIIRC-----AFIRSRSFMISDPISIPSTPRDSSVNKGIKKKA 108

Query: 53  LKTFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSC 112
           LK  PVV+YS E+NL G+  ECVICLS+F AG++LR+LPKCNHGFH+RCIDKWL+ H +C
Sbjct: 109 LKMLPVVNYSPEINLPGVGEECVICLSDFVAGEQLRVLPKCNHGFHLRCIDKWLTQHMTC 168

Query: 113 PKCRHCLIETCQKIIGCSQAASSSENPVTAQETI-VTITPLEPEGLIRNYR 162
           PKCRHCL++TCQK++    AA   +   TA E+I + I+PLEPE  +  +R
Sbjct: 169 PKCRHCLVDTCQKVLSDCDAA--DQVAATATESIDIRISPLEPEARVATFR 217

Arabidopsis thaliana (taxid: 3702)

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

 Score =  140 bits (354), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 66/121 (54%), Positives = 88/121 (72%), Gaps = 3/121 (2%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILPNKGIKQKALKTFPVVS 60
           ++L+ LLCALIC+LG+NS++RCV+RC+          ++ A +  KGIK++ALK  PV S
Sbjct: 43  IILAALLCALICALGINSVLRCVLRCTRRFTPNEDPVDTNANVA-KGIKKRALKVIPVDS 101

Query: 61  YSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI 120
           YS EL +    TEC+ICL +F  G+ +R+LPKCNHGFHV+CID WL SHSSCP CR  L+
Sbjct: 102 YSPELKMKA--TECLICLGDFVEGETVRVLPKCNHGFHVKCIDTWLLSHSSCPTCRQSLL 159

Query: 121 E 121
           E
Sbjct: 160 E 160

Arabidopsis thaliana (taxid: 3702)

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

 Score =  120 bits (302), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 62/127 (48%), Positives = 83/127 (65%), Gaps = 2/127 (1%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILP-NKGIKQKALKTFPVV 59
           ++L+VLLCAL C +GL ++ RC         +RS  ++   +   NKG+K+K L++ P +
Sbjct: 30  LILAVLLCALTCIIGLIAVSRCAWLRRIASRNRSDQTHPPPVAAANKGLKKKVLRSLPKL 89

Query: 60  SYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCL 119
           +YS +   A    EC ICL+EFAAGD LR+LP+C HGFHV CID WL SHSSCP CR  L
Sbjct: 90  TYSPDSPPAEKLVECAICLTEFAAGDELRVLPQCGHGFHVSCIDTWLGSHSSCPSCRQIL 149

Query: 120 IET-CQK 125
           + T C K
Sbjct: 150 VVTRCHK 156

Arabidopsis thaliana (taxid: 3702)

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

 Score =  120 bits (300), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 61/127 (48%), Positives = 83/127 (65%), Gaps = 8/127 (6%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILPN-------KGIKQKAL 53
           ++L+ LLCALIC+L LNS +RCV+R +    S    SN++    N        G+K++AL
Sbjct: 35  IILAALLCALICALSLNSALRCVLRITRRFTSDDQVSNASNANANLGRLAAATGLKKQAL 94

Query: 54  KTFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCP 113
           K  PV  Y + + +    TEC+ICL +F  G+++R+LPKCNHGFHVRCID WL S SSCP
Sbjct: 95  KQIPVGLYGSGI-IDMKATECLICLGDFEDGEKVRVLPKCNHGFHVRCIDTWLLSRSSCP 153

Query: 114 KCRHCLI 120
            CR  L+
Sbjct: 154 TCRQSLL 160

Arabidopsis thaliana (taxid: 3702)

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

 Score =  119 bits (298), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 61/126 (48%), Positives = 84/126 (66%), Gaps = 6/126 (4%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVV--RCSSLVASRSGASNSAAILP----NKGIKQKALK 54
           ++L+ LLCALIC LGL ++ RCV   R ++   + SG+   +   P    NKG+K+K L+
Sbjct: 32  VILAALLCALICVLGLIAVSRCVWLRRLAAGNRTVSGSQTQSPQPPVAAANKGLKKKVLQ 91

Query: 55  TFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPK 114
           + P +++S E   +    EC ICL+EF+AGD LR+LP+C HGFHV CID WL SHSSCP 
Sbjct: 92  SLPKLTFSPESPESEKFAECAICLAEFSAGDELRVLPQCGHGFHVACIDTWLGSHSSCPS 151

Query: 115 CRHCLI 120
           CR  L+
Sbjct: 152 CRQILV 157

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LZV8|ATL74_ARATH RING-H2 finger protein ATL74 OS=Arabidopsis thaliana GN=ATL74 PE=2 SV=1

 Score =  115 bits (287), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 56/106 (52%), Positives = 71/106 (66%), Gaps = 6/106 (5%)

Query: 17  NSIIRCVVRCSSLVASRSGASNSAAILPNKGIKQKALKTFPVVSY-SAELNLAGLDTECV 75
           NSI+RC +RC   ++S + A     +    G+K++ LK FPV  Y S E+ +A   TEC 
Sbjct: 52  NSILRCAMRCGFGLSSSAAA---GTVADRAGLKKRELKKFPVAEYGSGEVKIAA--TECA 106

Query: 76  ICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE 121
           ICL EFA G+R+R+LP CNH FH+ CID WL SHSSCP CRH LIE
Sbjct: 107 ICLGEFADGERVRVLPPCNHSFHMSCIDTWLVSHSSCPNCRHSLIE 152

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	165
255562369	223	RING-H2 finger protein ATL1L, putative [	0.975	0.721	0.793	1e-67
224055977	225	predicted protein [Populus trichocarpa]	0.981	0.72	0.730	1e-64
224116596	225	predicted protein [Populus trichocarpa]	0.969	0.711	0.734	2e-63
225431583	224	PREDICTED: RING-H2 finger protein ATL78	0.975	0.718	0.739	5e-63
388496412	175	unknown [Lotus japonicus]	0.993	0.937	0.664	7e-61
356508999	239	PREDICTED: RING-H2 finger protein ATL78-	1.0	0.690	0.679	2e-60
255636983	239	unknown [Glycine max]	1.0	0.690	0.674	1e-59
356516339	236	PREDICTED: RING-H2 finger protein ATL78-	1.0	0.699	0.695	2e-58
388508514	228	unknown [Medicago truncatula]	0.993	0.719	0.698	6e-58
255635726	236	unknown [Glycine max]	1.0	0.699	0.689	7e-58

>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 =  260 bits (665), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 131/165 (79%), Positives = 143/165 (86%), Gaps = 4/165 (2%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILPNKGIKQKALKTFPVVS 60
           MVLSVLLCALICSLGLNSIIRC +RCSSLVASRS A NS+A L N G+K+KALKTFP V+
Sbjct: 63  MVLSVLLCALICSLGLNSIIRCALRCSSLVASRS-ADNSSAGLANTGVKRKALKTFPTVN 121

Query: 61  YSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI 120
           YS +LNL GLDTEC ICLSEF  G+R+RLLPKCNHGFHVRCIDKWLSSHSSCP CRHCLI
Sbjct: 122 YSTDLNLPGLDTECAICLSEFTPGERVRLLPKCNHGFHVRCIDKWLSSHSSCPTCRHCLI 181

Query: 121 ETCQKIIGCSQAASSSENPVTAQETIVTITPLEPEGLIRNYRGIS 165
           ETCQKI+GCSQ  SSS+ PV  QE+IV I PLEPE LIR+YRG S
Sbjct: 182 ETCQKIVGCSQ-TSSSDPPV--QESIVNIAPLEPEALIRSYRGTS 223

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  250 bits (639), Expect = 1e-64,   Method: Compositional matrix adjust.
 Identities = 119/163 (73%), Positives = 137/163 (84%), Gaps = 1/163 (0%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILPNKGIKQKALKTFPVVS 60
           MVLS+LLCALICSLGLNSIIRC +RCS+LVAS S A+N +    N G+K+KALKTFP+V 
Sbjct: 64  MVLSILLCALICSLGLNSIIRCALRCSNLVASES-AANPSTQAANTGVKRKALKTFPIVK 122

Query: 61  YSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI 120
           YS +LNL GLDT+CVICLSEF  G+ +RLLPKCNHGFHV+CIDKWLSSHSSCP CRHCLI
Sbjct: 123 YSTDLNLPGLDTQCVICLSEFTPGEHVRLLPKCNHGFHVKCIDKWLSSHSSCPTCRHCLI 182

Query: 121 ETCQKIIGCSQAASSSENPVTAQETIVTITPLEPEGLIRNYRG 163
           ETC+KI GCSQA++S    +  QE IV+I PLEPEGLI NYRG
Sbjct: 183 ETCKKIAGCSQASTSGPTSLPVQEAIVSILPLEPEGLISNYRG 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 =  246 bits (628), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 119/162 (73%), Positives = 141/162 (87%), Gaps = 2/162 (1%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILPNKGIKQKALKTFPVVS 60
           MVLSVLLCALICSLGLNSIIRC +RCS++ AS S A+N +    N G+ ++ALK+FPVV+
Sbjct: 63  MVLSVLLCALICSLGLNSIIRCALRCSNIAASES-AANPSTQSANTGVNRRALKSFPVVN 121

Query: 61  YSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI 120
           YS++LNL GLDTECVICLSEF  G+R+RLLPKC+HGFHV+CIDKWLSSHSSCP CRHCLI
Sbjct: 122 YSSDLNLPGLDTECVICLSEFTPGERVRLLPKCHHGFHVKCIDKWLSSHSSCPTCRHCLI 181

Query: 121 ETCQKIIGCSQAASSSENPVTAQETIVTITPLEPEGLIRNYR 162
           ETCQKIIGCSQA++S  + +  QETIV+I PLEPEGLIR+YR
Sbjct: 182 ETCQKIIGCSQASTSGTS-LPVQETIVSILPLEPEGLIRDYR 222

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

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 =  245 bits (625), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 122/165 (73%), Positives = 139/165 (84%), Gaps = 4/165 (2%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILPNKGIKQKALKTFPVVS 60
           MVLSVLLCALICSLGLNSIIRC +RCSSLVAS   + ++   L N G+K+KALKTFP ++
Sbjct: 64  MVLSVLLCALICSLGLNSIIRCALRCSSLVASPGNSPSTR--LANTGVKKKALKTFPTLN 121

Query: 61  YSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI 120
           YSA LNL GLDTECVICLS+F  G+R+R+LPKCNHGFHVRCIDKWL+SHSSCP CRHCLI
Sbjct: 122 YSAGLNLPGLDTECVICLSDFTPGERIRILPKCNHGFHVRCIDKWLNSHSSCPTCRHCLI 181

Query: 121 ETCQKIIGCSQAASSSENPVTAQETIVTITPLEPEGLIRNYRGIS 165
           ETCQKIIGCSQ ASSSE P   QE+++ I PLEPEG  RNYR +S
Sbjct: 182 ETCQKIIGCSQ-ASSSETPPPLQESMI-IVPLEPEGFSRNYREVS 224

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388496412|gb|AFK36272.1| unknown [Lotus japonicus]

 Score =  238 bits (607), Expect = 7e-61,   Method: Compositional matrix adjust.
 Identities = 117/176 (66%), Positives = 139/176 (78%), Gaps = 12/176 (6%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILPNKGIKQKALKTFPVVS 60
           MVLSV+LCALICSLGLNSIIRC +RCS+LV      +NS     N G+K+KALKTFPVVS
Sbjct: 1   MVLSVVLCALICSLGLNSIIRCALRCSNLVVIGDSVTNSPTRAANTGVKKKALKTFPVVS 60

Query: 61  YSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI 120
           YSAELNL  LD+ECVICLSEF  G+++R+LPKCNHGFHVRCIDKWLSSHSSCPKCR CLI
Sbjct: 61  YSAELNLPSLDSECVICLSEFTNGEKVRILPKCNHGFHVRCIDKWLSSHSSCPKCRQCLI 120

Query: 121 ETCQKIIGCSQAASSSE-----------NPVTAQETIVTITPLEPEGLIRNYRGIS 165
           ETC+KI+G + ++S  +           +PV   ET+VTI PLEPEG++R+YRGIS
Sbjct: 121 ETCEKIVGATTSSSQPQLSVVVVTPNLLDPVLL-ETVVTIAPLEPEGMVRSYRGIS 175

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356508999|ref|XP_003523240.1| PREDICTED: RING-H2 finger protein ATL78-like [Glycine max]

 Score =  236 bits (602), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 121/178 (67%), Positives = 139/178 (78%), Gaps = 13/178 (7%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASN-----SAAILPNKGIKQKALKT 55
           MVLSVLLCALICSLGLNSIIRC +RCS+ V S S A+N     +AA + N G+K+KALKT
Sbjct: 62  MVLSVLLCALICSLGLNSIIRCALRCSNFVVSDSVATNNNNPPAAARVANTGVKKKALKT 121

Query: 56  FPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKC 115
           FP VSYSAELNL  LD+ECVICLSEF +GD++R+LPKCNH FHVRCIDKWLSSHSSCPKC
Sbjct: 122 FPTVSYSAELNLPSLDSECVICLSEFTSGDKVRILPKCNHRFHVRCIDKWLSSHSSCPKC 181

Query: 116 RHCLIETCQKIIGCSQ-------AASSSENPVTAQETIVTIT-PLEPEGLIRNYRGIS 165
           R CLIETCQKI+GCS             ++ +   ETIVTI  PLEPEGL+RNYR +S
Sbjct: 182 RQCLIETCQKIVGCSTQQASSSQQQQQQQHVLAVPETIVTIVAPLEPEGLVRNYRELS 239

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255636983|gb|ACU18824.1| unknown [Glycine max]

 Score =  234 bits (597), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 120/178 (67%), Positives = 138/178 (77%), Gaps = 13/178 (7%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASN-----SAAILPNKGIKQKALKT 55
           MVLSVLLCALICSLGLNSIIRC +RCS+ V S S A+N     +AA + N G+K+KALKT
Sbjct: 62  MVLSVLLCALICSLGLNSIIRCALRCSNFVVSDSVATNNNNPPAAARVANTGVKKKALKT 121

Query: 56  FPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKC 115
           FP VSYSAELNL  LD+ECVICLSEF +GD++R+LPKCNH FHVRCIDKWLSSHSSCPKC
Sbjct: 122 FPTVSYSAELNLPSLDSECVICLSEFTSGDKVRILPKCNHRFHVRCIDKWLSSHSSCPKC 181

Query: 116 RHCLIETCQKIIGCSQ-------AASSSENPVTAQETIVTIT-PLEPEGLIRNYRGIS 165
           R CLIETCQKI+GCS             ++ +   ETIVTI  PLEPE L+RNYR +S
Sbjct: 182 RQCLIETCQKIVGCSTQQASSSQQQQQQQHVLAVPETIVTIVAPLEPESLVRNYRELS 239

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356516339|ref|XP_003526853.1| PREDICTED: RING-H2 finger protein ATL78-like [Glycine max]

 Score =  229 bits (585), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 121/174 (69%), Positives = 141/174 (81%), Gaps = 9/174 (5%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILP------NKGIKQKALK 54
           MVLSVLLCALICSLGLNSIIRC +RCS+ V S S A+N+    P      N G+K+KALK
Sbjct: 63  MVLSVLLCALICSLGLNSIIRCALRCSNFVVSDSVATNNNNNNPPAARVANTGVKKKALK 122

Query: 55  TFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPK 114
           TF  VSYSAELNL  LD+ECVICLSEF +G+++R+LPKCNHGFH+RCIDKWLSSHSSCPK
Sbjct: 123 TFTTVSYSAELNLPSLDSECVICLSEFTSGEKVRILPKCNHGFHIRCIDKWLSSHSSCPK 182

Query: 115 CRHCLIETCQKIIGC--SQAASSSENPVTAQETIVT-ITPLEPEGLIRNYRGIS 165
           CR CLIETCQKI+GC   QA+SS ++ +   ETIVT I PLEPEGL+RNYR +S
Sbjct: 183 CRQCLIETCQKIVGCSTQQASSSQQHVLAVPETIVTIIAPLEPEGLVRNYRELS 236

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  228 bits (581), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 118/169 (69%), Positives = 131/169 (77%), Gaps = 5/169 (2%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSG--ASNSAAILPNKGIKQKALKTFPV 58
           MVLSVLLCALICSL LNSIIRC ++CS+LV  R    A+N      N GIK+KALK F  
Sbjct: 61  MVLSVLLCALICSLCLNSIIRCALKCSNLVVMRGDRSANNIPVRAANTGIKKKALKKFTT 120

Query: 59  VSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHC 118
           VSYS EL L  LD+ECVICLSEF  GD++RLLPKCNHGFHVRCIDKWLSSHSSCPKCR C
Sbjct: 121 VSYSDELKLLSLDSECVICLSEFTNGDKVRLLPKCNHGFHVRCIDKWLSSHSSCPKCRQC 180

Query: 119 LIETCQKIIGCSQAASSSENPV--TAQETIVTITPLEPEGLIRNYRGIS 165
           LIETC KI+G SQ +SS   P+     ETIVTI PLEPEGL+RNYR +S
Sbjct: 181 LIETCNKIVG-SQGSSSQPQPMLFPVPETIVTIAPLEPEGLVRNYREVS 228

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255635726|gb|ACU18212.1| unknown [Glycine max]

 Score =  228 bits (581), Expect = 7e-58,   Method: Compositional matrix adjust.
 Identities = 120/174 (68%), Positives = 140/174 (80%), Gaps = 9/174 (5%)

Query: 1   MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILP------NKGIKQKALK 54
           MVLSVLLC LICSLGLNSIIRC +RCS+ V S S A+N+    P      N G+K+KALK
Sbjct: 63  MVLSVLLCVLICSLGLNSIIRCALRCSNFVVSDSVATNNNNNNPPAARVANTGVKKKALK 122

Query: 55  TFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPK 114
           TF  VSYSAELNL  LD+ECVICLSEF +G+++R+LPKCNHGFH+RCIDKWLSSHSSCPK
Sbjct: 123 TFTTVSYSAELNLPSLDSECVICLSEFTSGEKVRILPKCNHGFHIRCIDKWLSSHSSCPK 182

Query: 115 CRHCLIETCQKIIGC--SQAASSSENPVTAQETIVT-ITPLEPEGLIRNYRGIS 165
           CR CLIETCQKI+GC   QA+SS ++ +   ETIVT I PLEPEGL+RNYR +S
Sbjct: 183 CRQCLIETCQKIVGCSTQQASSSQQHVLAVPETIVTIIAPLEPEGLVRNYRELS 236

Source: Glycine max

Species: Glycine max

Genus: Glycine

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	165
TAIR|locus:2028436	219	AT1G49230 [Arabidopsis thalian	0.981	0.739	0.660	1.4e-55
TAIR|locus:2028406	225	AT1G49210 [Arabidopsis thalian	0.969	0.711	0.587	4.1e-49
TAIR|locus:2028506	251	AT1G49220 [Arabidopsis thalian	0.945	0.621	0.590	1.6e-47
TAIR|locus:2028411	226	AT1G49200 [Arabidopsis thalian	0.969	0.707	0.593	1.8e-46
TAIR|locus:2830088	220	AT3G18773 [Arabidopsis thalian	0.969	0.727	0.560	1e-45
TAIR|locus:2153554	176	DAF "DEFECTIVE IN ANTHER DEHIS	0.715	0.670	0.545	3.2e-33
TAIR|locus:2181032	159	DAFL2 "DAF-Like gene 2" [Arabi	0.703	0.729	0.557	7.7e-32
TAIR|locus:2011686	185	ATL8 [Arabidopsis thaliana (ta	0.854	0.762	0.468	1.8e-30
TAIR|locus:2825708	197	AT1G20823 [Arabidopsis thalian	0.818	0.685	0.464	1.5e-28
TAIR|locus:2103162	181	DAFL1 "DAF-Like gene 1" [Arabi	0.721	0.657	0.503	1.3e-27

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

 Score = 573 (206.8 bits), Expect = 1.4e-55, P = 1.4e-55
 Identities = 107/162 (66%), Positives = 124/162 (76%)

Query:     1 MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILPNKGIKQKALKTFPVVS 60
             MVLSVLLCAL+CSLGLNSIIRC +RCS+LV S +G  N    L N G+K+KALK+F  VS
Sbjct:    58 MVLSVLLCALVCSLGLNSIIRCALRCSNLVPSEAGGDNYPVRLTNTGVKRKALKSFQTVS 117

Query:    61 YSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI 120
             YS ELNL GLDTEC ICLSEF A +R++LLP C+HGFHVRCIDKWLSSHSSCP CRHCLI
Sbjct:   118 YSTELNLPGLDTECAICLSEFVAEERVKLLPTCHHGFHVRCIDKWLSSHSSCPTCRHCLI 177

Query:   121 ETCQKIIGCSQAASSSENPVTAQETIVTITPLEPEGLIRNYR 162
             +TC+KI  CSQ +S +         I+ I PLEPE  IR +R
Sbjct:   178 QTCEKIADCSQTSSLNSTQPPQDSIILQIAPLEPERWIRWFR 219

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

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

 Score = 512 (185.3 bits), Expect = 4.1e-49, P = 4.1e-49
 Identities = 97/165 (58%), Positives = 122/165 (73%)

Query:     1 MVLSVLLCALICSLGLNSIIRCVVRCSS--LVASRSGASNSAAILPNKGIKQKALKTFPV 58
             M+LSVL+C +IC LGL+ IIRC  R SS  +++    + ++     NKGIK+KAL+ FPV
Sbjct:    60 MLLSVLICGIICCLGLHYIIRCAFRRSSRFMISEPISSLSTPRSSSNKGIKKKALRMFPV 119

Query:    59 VSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHC 118
             VSYS E+NL G+  ECVICLS+F +G++LRLLPKCNHGFHVRCIDKWL  H +CPKCRHC
Sbjct:   120 VSYSREMNLPGIGEECVICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQHHLTCPKCRHC 179

Query:   119 LIETCQKIIG-CSQAASSSENPVTAQETIVTITPLEPEGLIRNYR 162
             L+ETCQKI+G  SQA S +  P   +  IV I PLEPEG +  +R
Sbjct:   180 LVETCQKILGDFSQADSMASTPT--ESVIVRIDPLEPEGRVNTFR 222

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

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

 Score = 497 (180.0 bits), Expect = 1.6e-47, P = 1.6e-47
 Identities = 95/161 (59%), Positives = 122/161 (75%)

Query:     1 MVLSVLLCALICSLGLNSIIRCVVRCSS--LVASRSGASNSAAILPNKGIKQKALKTFPV 58
             M+LS+L+C +IC LGL+ IIRC +R S+  +++    + +S     NKGIK+KAL+ FPV
Sbjct:    60 MLLSILICGIICCLGLHYIIRCALRRSTRFMISEPVPSLSSTRGSSNKGIKKKALRMFPV 119

Query:    59 VSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHC 118
             VSYS E+NL GLD ECVICLS+F +G++LRLLPKCNHGFHVRCIDKWL  H +CPKCR+C
Sbjct:   120 VSYSPEMNLPGLDEECVICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQQHLTCPKCRNC 179

Query:   119 LIETCQKIIG-CSQAASSSENPVTAQETIVTITPLEPEGLI 158
             L+ETCQKI+G  SQA S +  P   +  IVTI PLEP  ++
Sbjct:   180 LVETCQKILGDFSQADSVTAEPT--EIVIVTIVPLEPTEIV 218

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

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

 Score = 487 (176.5 bits), Expect = 1.8e-46, P = 1.8e-46
 Identities = 98/165 (59%), Positives = 118/165 (71%)

Query:     1 MVLSVLLCALICSLGLNSIIRCVVR-CSSLVASRSGASNSAAI-LPNKGIKQKALKTFPV 58
             M+LSVL+C +IC LGL+ IIRC  R  SS + S   A  S      NKGI +KAL+ FPV
Sbjct:    61 MLLSVLICGIICCLGLHYIIRCAFRRTSSFMISEPIAGLSTPCGSSNKGINKKALRMFPV 120

Query:    59 VSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHC 118
             VSYS E+NL GL  ECVICLS+F +G+++R+LPKC+HGFHVRCIDKWL  H +CPKCRHC
Sbjct:   121 VSYSPEMNLPGLGEECVICLSDFVSGEQIRMLPKCHHGFHVRCIDKWLQQHLTCPKCRHC 180

Query:   119 LIETCQKIIG-CSQAASSSENPVTAQETIVTITPLEPEGLIRNYR 162
             L+ETCQKI+G  SQA   +  P TA   IV I PLEPEG +   R
Sbjct:   181 LVETCQKILGDFSQADQVAATP-TAS-VIVRIAPLEPEGRVNILR 223

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

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

 Score = 480 (174.0 bits), Expect = 1.0e-45, P = 1.0e-45
 Identities = 93/166 (56%), Positives = 120/166 (72%)

Query:     1 MVLSVLLCALICSLGLNSIIRCV-VRCSSLVASR--SGASNSAAILPNKGIKQKALKTFP 57
             M+LS+LLC +ICSLGL+ IIRC  +R  S + S   S  S       NKGIK+KALK  P
Sbjct:    54 MLLSILLCGIICSLGLHYIIRCAFIRSRSFMISDPISIPSTPRDSSVNKGIKKKALKMLP 113

Query:    58 VVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRH 117
             VV+YS E+NL G+  ECVICLS+F AG++LR+LPKCNHGFH+RCIDKWL+ H +CPKCRH
Sbjct:   114 VVNYSPEINLPGVGEECVICLSDFVAGEQLRVLPKCNHGFHLRCIDKWLTQHMTCPKCRH 173

Query:   118 CLIETCQKIIGCSQAASSSENPVTAQETI-VTITPLEPEGLIRNYR 162
             CL++TCQK++    AA   +   TA E+I + I+PLEPE  +  +R
Sbjct:   174 CLVDTCQKVLSDCDAAD--QVAATATESIDIRISPLEPEARVATFR 217

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

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

 Score = 362 (132.5 bits), Expect = 3.2e-33, P = 3.2e-33
 Identities = 66/121 (54%), Positives = 88/121 (72%)

Query:     1 MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILPNKGIKQKALKTFPVVS 60
             ++L+ LLCALIC+LG+NS++RCV+RC+          ++ A +  KGIK++ALK  PV S
Sbjct:    43 IILAALLCALICALGINSVLRCVLRCTRRFTPNEDPVDTNANVA-KGIKKRALKVIPVDS 101

Query:    61 YSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI 120
             YS EL +    TEC+ICL +F  G+ +R+LPKCNHGFHV+CID WL SHSSCP CR  L+
Sbjct:   102 YSPELKMKA--TECLICLGDFVEGETVRVLPKCNHGFHVKCIDTWLLSHSSCPTCRQSLL 159

Query:   121 E 121
             E
Sbjct:   160 E 160

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

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

 Score = 349 (127.9 bits), Expect = 7.7e-32, P = 7.7e-32
 Identities = 68/122 (55%), Positives = 87/122 (71%)

Query:     1 MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILPNKGIKQKALKTFPVVS 60
             ++L+ LLCALI +LGLNSI+RC +RC   ++S S A+ + A     G+K++ LK FPV  
Sbjct:    36 IILAALLCALILALGLNSILRCAMRCGFGLSS-SAAAGTVA--DRAGLKKRELKKFPVAE 92

Query:    61 Y-SAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCL 119
             Y S E+ +A   TEC ICL EFA G+R+R+LP CNH FH+ CID WL SHSSCP CRH L
Sbjct:    93 YGSGEVKIAA--TECAICLGEFADGERVRVLPPCNHSFHMSCIDTWLVSHSSCPNCRHSL 150

Query:   120 IE 121
             IE
Sbjct:   151 IE 152

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

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

 Score = 336 (123.3 bits), Expect = 1.8e-30, P = 1.8e-30
 Identities = 67/143 (46%), Positives = 90/143 (62%)

Query:     1 MVLSVLLCALICSLGLNSIIRCVVRCSSLVASRSGASNSAAILP-NKGIKQKALKTFPVV 59
             ++L+VLLCAL C +GL ++ RC         +RS  ++   +   NKG+K+K L++ P +
Sbjct:    30 LILAVLLCALTCIIGLIAVSRCAWLRRIASRNRSDQTHPPPVAAANKGLKKKVLRSLPKL 89

Query:    60 SYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCL 119
             +YS +   A    EC ICL+EFAAGD LR+LP+C HGFHV CID WL SHSSCP CR  L
Sbjct:    90 TYSPDSPPAEKLVECAICLTEFAAGDELRVLPQCGHGFHVSCIDTWLGSHSSCPSCRQIL 149

Query:   120 IET-CQKIIGCSQAASSSENPVT 141
             + T C K  G   ++SS   P T
Sbjct:   150 VVTRCHKCGGLPGSSSSGPEPDT 172

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

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

 Score = 318 (117.0 bits), Expect = 1.5e-28, P = 1.5e-28
 Identities = 66/142 (46%), Positives = 89/142 (62%)

Query:     1 MVLSVLLCALICSLGLNSIIRCVVRCSSLVASR--SGASNSAAILP----NKGIKQKALK 54
             ++L+ LLCALIC LGL ++ RCV        +R  SG+   +   P    NKG+K+K L+
Sbjct:    32 VILAALLCALICVLGLIAVSRCVWLRRLAAGNRTVSGSQTQSPQPPVAAANKGLKKKVLQ 91

Query:    55 TFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPK 114
             + P +++S E   +    EC ICL+EF+AGD LR+LP+C HGFHV CID WL SHSSCP 
Sbjct:    92 SLPKLTFSPESPESEKFAECAICLAEFSAGDELRVLPQCGHGFHVACIDTWLGSHSSCPS 151

Query:   115 CRHCLIET-CQKIIGCSQAASS 135
             CR  L+   C K  G   ++SS
Sbjct:   152 CRQILVVARCHKCGGLPGSSSS 173

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

GO:0009507 "chloroplast" evidence=ISM

GO:0010200 "response to chitin" evidence=IEP

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

 Score = 309 (113.8 bits), Expect = 1.3e-27, P = 1.3e-27
 Identities = 64/127 (50%), Positives = 85/127 (66%)

Query:     1 MVLSVLLCALICSLGLNSIIRCVVRCSSLVASR---SGASNSAAILPN----KGIKQKAL 53
             ++L+ LLCALIC+L LNS +RCV+R +    S    S ASN+ A L       G+K++AL
Sbjct:    35 IILAALLCALICALSLNSALRCVLRITRRFTSDDQVSNASNANANLGRLAAATGLKKQAL 94

Query:    54 KTFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCP 113
             K  PV  Y + + +    TEC+ICL +F  G+++R+LPKCNHGFHVRCID WL S SSCP
Sbjct:    95 KQIPVGLYGSGI-IDMKATECLICLGDFEDGEKVRVLPKCNHGFHVRCIDTWLLSRSSCP 153

Query:   114 KCRHCLI 120
              CR  L+
Sbjct:   154 TCRQSLL 160

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

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q6NQG7	ATL78_ARATH	No assigned EC number	0.6604	0.9818	0.7397	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!

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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.

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	165
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	6e-14
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	5e-12
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	3e-08
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	2e-07
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	4e-07
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	3e-06
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	5e-06
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	9e-06
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	2e-04
COG5432	391	COG5432, RAD18, RING-finger-containing E3 ubiquiti	4e-04
TIGR00599	397	TIGR00599, rad18, DNA repair protein rad18	7e-04
smart00184	40	smart00184, RING, Ring finger	0.001
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	0.001

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

 Score = 67.7 bits (165), Expect = 6e-14
 Identities = 35/97 (36%), Positives = 46/97 (47%), Gaps = 7/97 (7%)

Query: 21  RCVVRCSSLVASRSGASNSAAILPNKGIKQKALKTFPVVSYSAELNLAGLDTECVICLSE 80
           R  +     +    G  +S+  +P    K   LK   +         A    EC IC+S 
Sbjct: 278 RFNIILEIQINFDVGFYSSSEAIPTTTTKGS-LKPLSIERAVE----ADKGVECAICMSN 332

Query: 81  FAAGDRLRLLPKCNHGFHVRCIDKWLSSHS-SCPKCR 116
           F   DRLR+LP C+H FHV C+DKWL  +S  CP CR
Sbjct: 333 FIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCR 368

Length = 374

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

 Score = 57.0 bits (138), Expect = 5e-12
 Identities = 24/45 (53%), Positives = 30/45 (66%), Gaps = 1/45 (2%)

Query: 73  ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRH 117
           EC ICL EF  G+ + +LP C H FH  C+DKWL S ++CP CR 
Sbjct: 2   ECPICLDEFEPGEEVVVLP-CGHVFHKECLDKWLRSSNTCPLCRA 45

Length = 46

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

 Score = 47.4 bits (113), Expect = 3e-08
 Identities = 22/48 (45%), Positives = 26/48 (54%), Gaps = 4/48 (8%)

Query: 73  ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWL-SSHSSCPKCRHCL 119
           EC ICL EF       +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 = 48.2 bits (115), Expect = 2e-07
 Identities = 26/71 (36%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 51  KALKTFPVVSYSAE-LNLAGLDTECVICLSEFAAGD----RLRLLPKCNHGFHVRCIDKW 105
           K LKT P V    E L     D EC IC+ +    +       +L  CNH F + CID W
Sbjct: 153 KFLKTIPSVLSEYEKLYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIW 212

Query: 106 LSSHSSCPKCR 116
               ++CP CR
Sbjct: 213 KKEKNTCPVCR 223

Length = 238

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

 Score = 44.7 bits (106), Expect = 4e-07
 Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 9/55 (16%)

Query: 71  DTECVICLSEFAA--------GDRLRL-LPKCNHGFHVRCIDKWLSSHSSCPKCR 116
           D  C IC + F          GD   +   +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|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

 Score = 45.8 bits (108), Expect = 3e-06
 Identities = 20/49 (40%), Positives = 25/49 (51%), Gaps = 5/49 (10%)

Query: 73   ECVICLSEFAAGDRL---RLLPKCNHGFHVRCIDKWL--SSHSSCPKCR 116
            EC IC S     DR    +    C + FH RC+ KW   S+ S+CP CR
Sbjct: 1471 ECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCR 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 = 42.5 bits (100), Expect = 5e-06
 Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 74  CVICLSEFAAGDRLRLL-PKCNHGFHVRCIDKWLSSHSSCPKCR 116
           C  C      GD   ++   CNH FH  CI +WL +   CP  R
Sbjct: 34  CPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDR 77

Length = 88

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

 Score = 44.2 bits (104), Expect = 9e-06
 Identities = 28/107 (26%), Positives = 40/107 (37%), Gaps = 20/107 (18%)

Query: 54  KTFPVVSYSAELNLAGLDTECVICLSEFAAGDR------LRLLPK---CNHGFHVRCIDK 104
             +P  +   E  L   D  C IC+ E    D       L + PK   C H  H+ C+  
Sbjct: 273 AMYPTAT---EEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKN 329

Query: 105 WLSSHSSCPKCRHCLIETCQKIIGCSQAASSSENPVTAQETIVTITP 151
           WL    +CP CR  +I          Q++ +  +P      I T  P
Sbjct: 330 WLERQQTCPICRRPVI--------FDQSSPTPASPNVRNTQIATQVP 368

Length = 491

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

 Score = 36.7 bits (85), Expect = 2e-04
 Identities = 19/47 (40%), Positives = 23/47 (48%), Gaps = 3/47 (6%)

Query: 71  DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRH 117
           + EC ICL      D + L P C H F   CI ++L   S CP CR 
Sbjct: 2   ELECPICLDLLR--DPVVLTP-CGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

 Score = 39.3 bits (91), Expect = 4e-04
 Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 6/53 (11%)

Query: 66  NLAGLDT--ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCR 116
           +L GLD+   C IC         +     C H F   CI + L +   CP CR
Sbjct: 18  SLKGLDSMLRCRICDCRI----SIPCETTCGHTFCSLCIRRHLGTQPFCPVCR 66

Length = 391

>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18

 Score = 38.4 bits (89), Expect = 7e-04
 Identities = 20/52 (38%), Positives = 25/52 (48%), Gaps = 6/52 (11%)

Query: 67  LAGLDT--ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCR 116
           L  LDT   C IC   F     + +L  C+H F   CI + LS+   CP CR
Sbjct: 20  LYPLDTSLRCHICKDFF----DVPVLTSCSHTFCSLCIRRCLSNQPKCPLCR 67

All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 397

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

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

Query: 74  CVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHS-SCPKC 115
           C ICL E+       +LP C H F   CI KWL S + +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 = 35.9 bits (83), Expect = 0.001
 Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 3/31 (9%)

Query: 89  LLPKCNHGFHVRCIDKWLSSHSS---CPKCR 116
           +  KC H FH+ CI KWL++ +S   CP CR
Sbjct: 48  VWGKCKHNFHMHCILKWLATETSKGLCPMCR 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	165
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.82
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.64
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.46
PHA02929	238	N1R/p28-like protein; Provisional	99.45
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.38
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.31
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.27
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.23
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.22
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	99.17
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.15
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.1
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.08
PHA02926	242	zinc finger-like protein; Provisional	98.99
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	98.96
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	98.93
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	98.93
PF14634	44	zf-RING_5: zinc-RING finger domain	98.92
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	98.9
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.89
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.86
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	98.86
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	98.85
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	98.78
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	98.69
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.62
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.57
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	98.57
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.47
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.41
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.37
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.34
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.27
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.26
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.25
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.24
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.24
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.22
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.22
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.11
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	98.06
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.05
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	97.93
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	97.89
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	97.78
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.72
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	97.72
KOG0825	1134	consensus PHD Zn-finger protein [General function	97.65
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	97.63
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.62
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.48
KOG4445	368	consensus Uncharacterized conserved protein, conta	97.47
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	97.44
PHA02862	156	5L protein; Provisional	97.39
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	97.38
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	97.35
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.21
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.17
PHA02825	162	LAP/PHD finger-like protein; Provisional	97.12
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.12
COG5236	493	Uncharacterized conserved protein, contains RING Z	96.98
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	96.9
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	96.86
COG5152	259	Uncharacterized conserved protein, contains RING a	96.85
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	96.83
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	96.6
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	96.56
KOG1002	791	consensus Nucleotide excision repair protein RAD16	96.52
KOG2660	331	consensus Locus-specific chromosome binding protei	96.49
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	96.33
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	96.28
KOG3039	303	consensus Uncharacterized conserved protein [Funct	96.17
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	96.13
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	95.68
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	95.66
PHA03096	284	p28-like protein; Provisional	95.56
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	95.27
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	95.21
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	95.05
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	95.02
KOG3053	293	consensus Uncharacterized conserved protein [Funct	94.93
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	94.92
COG5175	480	MOT2 Transcriptional repressor [Transcription]	94.85
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	94.68
COG5222	427	Uncharacterized conserved protein, contains RING Z	94.64
PF04641	260	Rtf2: Rtf2 RING-finger	94.63
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	94.54
KOG4739	233	consensus Uncharacterized protein involved in syna	94.49
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	94.32
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	94.26
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	94.24
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	94.08
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	93.97
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	93.75
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	93.55
KOG1940	276	consensus Zn-finger protein [General function pred	93.39
KOG1609	323	consensus Protein involved in mRNA turnover and st	92.31
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	91.71
KOG1001	674	consensus Helicase-like transcription factor HLTF/	91.25
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	90.9
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	90.07
KOG0298	1394	consensus DEAD box-containing helicase-like transc	89.92
KOG3899	381	consensus Uncharacterized conserved protein [Funct	89.67
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	89.3
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	89.03
PF01102	122	Glycophorin_A: Glycophorin A; InterPro: IPR001195	88.55
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	87.96
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	87.21
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	87.05
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	86.34
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	86.31
KOG1829	580	consensus Uncharacterized conserved protein, conta	85.63
PF12273	130	RCR: Chitin synthesis regulation, resistance to Co	85.41
KOG3002	299	consensus Zn finger protein [General function pred	85.25
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	84.78
KOG0269	839	consensus WD40 repeat-containing protein [Function	83.6
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	83.18
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	81.95
KOG3113	293	consensus Uncharacterized conserved protein [Funct	81.76
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	80.49

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

Probab=99.82  E-value=3.3e-20  Score=152.26  Aligned_cols=79  Identities=34%  Similarity=0.841  Sum_probs=67.1

Q ss_pred             CCCCCCHHHhhcCCeEeeccccccCCCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc-CCCCCCCCcccccc
Q 042990           44 PNKGIKQKALKTFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS-HSSCPKCRHCLIET  122 (165)
Q Consensus        44 ~~~~~~~~~~~~lp~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~~  122 (165)
                      ...+..+..++++|...|......... +.|+||+|+|+.|+++|.|| |+|.||..||+.||.. +..||+||.++...
T Consensus       203 ~~~r~~k~~l~~~p~~~f~~~~~~~~~-~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~~~  280 (348)
T KOG4628|consen  203 RRNRLIKRLLKKLPVRTFTKGDDEDAT-DTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIRTD  280 (348)
T ss_pred             hhhhhHHHHHhhCCcEEeccccccCCC-ceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCCCC
Confidence            456778899999999999986554433 79999999999999999999 9999999999999955 56699999988765


Q ss_pred             cc
Q 042990          123 CQ  124 (165)
Q Consensus       123 ~~  124 (165)
                      ..
T Consensus       281 ~~  282 (348)
T KOG4628|consen  281 SG  282 (348)
T ss_pred             CC
Confidence            43

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

Probab=99.64  E-value=6e-17  Score=96.10  Aligned_cols=44  Identities=52%  Similarity=1.235  Sum_probs=40.2

Q ss_pred             CcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCC
Q 042990           72 TECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCR  116 (165)
Q Consensus        72 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR  116 (165)
                      ++|+||+++|.+++.+..++ |+|.||.+||..|++++.+||+||
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            47999999999999999998 999999999999999899999997

...

>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=99.46  E-value=5.9e-14  Score=92.02  Aligned_cols=47  Identities=34%  Similarity=0.877  Sum_probs=36.1

Q ss_pred             CCCcCccccccccCC---------CeeeecCCCCccccHhhHHHHHhcCCCCCCCC
Q 042990           70 LDTECVICLSEFAAG---------DRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCR  116 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~---------~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR  116 (165)
                      .++.|+||+++|.+.         +....+..|||.||..||.+|++.+.+||+||
T Consensus        18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence            456799999999331         23333334999999999999999999999998

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=99.45  E-value=6.6e-14  Score=110.51  Aligned_cols=76  Identities=36%  Similarity=0.673  Sum_probs=57.0

Q ss_pred             CCCCHHHhhcCCeEeeccc-cccCCCCCcCccccccccCCCe----eeecCCCCccccHhhHHHHHhcCCCCCCCCcccc
Q 042990           46 KGIKQKALKTFPVVSYSAE-LNLAGLDTECVICLSEFAAGDR----LRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI  120 (165)
Q Consensus        46 ~~~~~~~~~~lp~~~~~~~-~~~~~~~~~C~ICl~~~~~~~~----~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  120 (165)
                      .+..+..++.+|....... ......+.+|+||++.+.+.+.    ...++.|+|.||.+||.+|++.+.+||+||..+.
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            4556778888888765542 2223457899999999876431    2344459999999999999999999999999876


Q ss_pred             c
Q 042990          121 E  121 (165)
Q Consensus       121 ~  121 (165)
                      .
T Consensus       228 ~  228 (238)
T PHA02929        228 S  228 (238)
T ss_pred             E
Confidence            4

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

Probab=99.38  E-value=1.4e-12  Score=107.21  Aligned_cols=71  Identities=27%  Similarity=0.665  Sum_probs=54.2

Q ss_pred             HHHhhcCCeEeeccccccCCCCCcCccccccc-cCC---------CeeeecCCCCccccHhhHHHHHhcCCCCCCCCccc
Q 042990           50 QKALKTFPVVSYSAELNLAGLDTECVICLSEF-AAG---------DRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCL  119 (165)
Q Consensus        50 ~~~~~~lp~~~~~~~~~~~~~~~~C~ICl~~~-~~~---------~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~  119 (165)
                      ++..+.++.++..+.   ..+|..|+||||++ ..+         .++..+| |||+||-+|++-|+.++.+||.||.++
T Consensus       269 kdl~~~~~t~t~eql---~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~  344 (491)
T COG5243         269 KDLNAMYPTATEEQL---TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPV  344 (491)
T ss_pred             hHHHhhcchhhhhhh---cCCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCcc
Confidence            455555665555543   23678999999994 433         3567898 999999999999999999999999996


Q ss_pred             ccccc
Q 042990          120 IETCQ  124 (165)
Q Consensus       120 ~~~~~  124 (165)
                      +-...
T Consensus       345 ifd~~  349 (491)
T COG5243         345 IFDQS  349 (491)
T ss_pred             ccccC
Confidence            65433

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

Probab=99.31  E-value=1.1e-12  Score=105.25  Aligned_cols=51  Identities=51%  Similarity=1.158  Sum_probs=46.6

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHh-cCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS-SHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~~~~  121 (165)
                      .+.+|+|||+.|..+++++.+| |.|.||..|++.|+. -+..||+||..+++
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            4589999999999999999999 999999999999996 57789999998875

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

Probab=99.27  E-value=6.3e-12  Score=100.36  Aligned_cols=50  Identities=30%  Similarity=0.713  Sum_probs=44.8

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      +....|.+||+..++   +..+| |||+||..||..|...+..||+||..+.++
T Consensus       237 ~a~~kC~LCLe~~~~---pSaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~ps  286 (293)
T KOG0317|consen  237 EATRKCSLCLENRSN---PSATP-CGHIFCWSCILEWCSEKAECPLCREKFQPS  286 (293)
T ss_pred             CCCCceEEEecCCCC---CCcCc-CcchHHHHHHHHHHccccCCCcccccCCCc
Confidence            466899999999877   67888 999999999999999999999999988764

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

Probab=99.23  E-value=7.7e-12  Score=83.42  Aligned_cols=52  Identities=42%  Similarity=0.839  Sum_probs=41.5

Q ss_pred             CCCcCccccccccC--------C-CeeeecCCCCccccHhhHHHHHhc---CCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAA--------G-DRLRLLPKCNHGFHVRCIDKWLSS---HSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~--------~-~~~~~l~~C~H~FH~~Ci~~Wl~~---~~~CP~CR~~~~~  121 (165)
                      .|+.|.||+..|+.        + +.+.++..|+|.||.+||.+|+..   +..||+||+.+..
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            48899999999963        2 234455679999999999999964   5679999998753

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.22  E-value=3.2e-11  Score=92.02  Aligned_cols=49  Identities=35%  Similarity=0.746  Sum_probs=40.3

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc----------------CCCCCCCCccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS----------------HSSCPKCRHCLIE  121 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----------------~~~CP~CR~~~~~  121 (165)
                      +.+.+|+||++.+++   ...++ |||.||..||..|+..                ...||+||..+..
T Consensus        16 ~~~~~CpICld~~~d---PVvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~   80 (193)
T PLN03208         16 GGDFDCNICLDQVRD---PVVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE   80 (193)
T ss_pred             CCccCCccCCCcCCC---cEEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence            356899999999876   46676 9999999999999842                3479999998865

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

Probab=99.17  E-value=1.6e-11  Score=80.13  Aligned_cols=53  Identities=30%  Similarity=0.632  Sum_probs=38.8

Q ss_pred             CcCccccccccCCC-eeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccccc
Q 042990           72 TECVICLSEFAAGD-RLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETCQ  124 (165)
Q Consensus        72 ~~C~ICl~~~~~~~-~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~~  124 (165)
                      +.|+-|...+.+++ .+.....|+|.||.+||.+||..+..||++|+.+.-++.
T Consensus        32 ~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~~~~   85 (88)
T COG5194          32 GTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQTWVLADG   85 (88)
T ss_pred             CcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhCCCCCCCCceeEEecc
Confidence            33444444333433 455566799999999999999999999999998876543

>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=99.15  E-value=3.3e-11  Score=73.13  Aligned_cols=46  Identities=37%  Similarity=0.843  Sum_probs=39.8

Q ss_pred             CCcCccccccccCCCeeeecCCCCcc-ccHhhHHHHHhcCCCCCCCCcccc
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHG-FHVRCIDKWLSSHSSCPKCRHCLI  120 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~  120 (165)
                      +..|.||++...+   +..+| |||. |+..|+.+|++.+..||+||.++.
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            5789999999766   77888 9999 999999999999999999999875

...

>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=99.10  E-value=8.6e-11  Score=68.49  Aligned_cols=44  Identities=55%  Similarity=1.194  Sum_probs=36.1

Q ss_pred             cCccccccccCCCeeeecCCCCccccHhhHHHHHhc-CCCCCCCCccc
Q 042990           73 ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS-HSSCPKCRHCL  119 (165)
Q Consensus        73 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~  119 (165)
                      +|+||++.+.  +.....+ |+|.||..|+..|++. +..||+||..+
T Consensus         1 ~C~iC~~~~~--~~~~~~~-C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEFR--EPVVLLP-CGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhhh--CceEecC-CCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            5999999983  2355555 9999999999999976 77899998764

>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=99.08  E-value=9.8e-11  Score=67.48  Aligned_cols=39  Identities=41%  Similarity=1.063  Sum_probs=32.5

Q ss_pred             CccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCC
Q 042990           74 CVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKC  115 (165)
Q Consensus        74 C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~C  115 (165)
                      |+||++.+.+  .+..++ |||.|+.+||.+|++++..||+|
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            7999999887  335676 99999999999999888899998

>PHA02926 zinc finger-like protein; Provisional

Probab=98.99  E-value=3.1e-10  Score=87.96  Aligned_cols=53  Identities=32%  Similarity=0.741  Sum_probs=39.9

Q ss_pred             CCCCCcCccccccccCC-----CeeeecCCCCccccHhhHHHHHhcC------CCCCCCCcccc
Q 042990           68 AGLDTECVICLSEFAAG-----DRLRLLPKCNHGFHVRCIDKWLSSH------SSCPKCRHCLI  120 (165)
Q Consensus        68 ~~~~~~C~ICl~~~~~~-----~~~~~l~~C~H~FH~~Ci~~Wl~~~------~~CP~CR~~~~  120 (165)
                      .+.+.+|+||||..-..     .....++.|+|.||..||..|.+.+      .+||+||..+.
T Consensus       167 ~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        167 VSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             ccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            34678999999986332     1234565699999999999998643      35999998765

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

Probab=98.96  E-value=2e-10  Score=100.83  Aligned_cols=50  Identities=40%  Similarity=1.012  Sum_probs=44.6

Q ss_pred             CCCcCccccccccCCCe--eeecCCCCccccHhhHHHHHhcCCCCCCCCcccc
Q 042990           70 LDTECVICLSEFAAGDR--LRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI  120 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~--~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  120 (165)
                      .+..|+||+|++..+..  +..++ |+|+||..|+..|++++.+||+||..+.
T Consensus       290 ~~~~C~IC~e~l~~~~~~~~~rL~-C~Hifh~~CL~~W~er~qtCP~CR~~~~  341 (543)
T KOG0802|consen  290 SDELCIICLEELHSGHNITPKRLP-CGHIFHDSCLRSWFERQQTCPTCRTVLY  341 (543)
T ss_pred             cCCeeeeechhhccccccccceee-cccchHHHHHHHHHHHhCcCCcchhhhh
Confidence            47899999999987654  77888 9999999999999999999999999444

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

Probab=98.93  E-value=5.9e-10  Score=83.52  Aligned_cols=50  Identities=30%  Similarity=0.620  Sum_probs=41.0

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI  120 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  120 (165)
                      +.-..|+|||+.+..... ... +|||+||+.||..-++....||+|+..+.
T Consensus       129 ~~~~~CPiCl~~~sek~~-vsT-kCGHvFC~~Cik~alk~~~~CP~C~kkIt  178 (187)
T KOG0320|consen  129 EGTYKCPICLDSVSEKVP-VST-KCGHVFCSQCIKDALKNTNKCPTCRKKIT  178 (187)
T ss_pred             ccccCCCceecchhhccc-ccc-ccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence            344789999999987433 234 59999999999999999999999997554

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

Probab=98.93  E-value=7.8e-10  Score=64.78  Aligned_cols=38  Identities=39%  Similarity=0.955  Sum_probs=29.5

Q ss_pred             CccccccccCCCeeeecCCCCccccHhhHHHHHhcC----CCCCCC
Q 042990           74 CVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSH----SSCPKC  115 (165)
Q Consensus        74 C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~----~~CP~C  115 (165)
                      |+||++-|.+   +..++ |||.|+..||.+|++..    ..||.|
T Consensus         1 CpiC~~~~~~---Pv~l~-CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKD---PVSLP-CGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SS---EEE-S-SSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCC---ccccC-CcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            8999999988   78888 99999999999999543    469987

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=98.92  E-value=9.3e-10  Score=65.04  Aligned_cols=44  Identities=34%  Similarity=0.850  Sum_probs=38.3

Q ss_pred             cCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCc
Q 042990           73 ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRH  117 (165)
Q Consensus        73 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~  117 (165)
                      .|.||+++|.+.....+++ |||+|+..|+..+......||+||+
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            4999999996666788887 9999999999999866778999984

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

Probab=98.90  E-value=7.5e-10  Score=86.16  Aligned_cols=50  Identities=28%  Similarity=0.594  Sum_probs=40.9

Q ss_pred             CCCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc---CCCCCCCCccccc
Q 042990           68 AGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS---HSSCPKCRHCLIE  121 (165)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~---~~~CP~CR~~~~~  121 (165)
                      .....+|.||||.-++   ++++. |||.||+-||.+|+..   .+.||+||..+-.
T Consensus        44 ~~~~FdCNICLd~akd---PVvTl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~   96 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKD---PVVTL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI   96 (230)
T ss_pred             CCCceeeeeeccccCC---CEEee-cccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence            3567899999999766   56666 9999999999999954   4569999987764

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

Probab=98.89  E-value=2.8e-10  Score=73.77  Aligned_cols=51  Identities=37%  Similarity=0.799  Sum_probs=40.4

Q ss_pred             CCCcCccccccccC---------CCeeeecCCCCccccHhhHHHHHhc---CCCCCCCCcccc
Q 042990           70 LDTECVICLSEFAA---------GDRLRLLPKCNHGFHVRCIDKWLSS---HSSCPKCRHCLI  120 (165)
Q Consensus        70 ~~~~C~ICl~~~~~---------~~~~~~l~~C~H~FH~~Ci~~Wl~~---~~~CP~CR~~~~  120 (165)
                      .++.|.||+-.|+.         ++.+.++..|.|.||.+||.+|+..   +..||+||+.+.
T Consensus        19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~   81 (84)
T KOG1493|consen   19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQ   81 (84)
T ss_pred             CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeE
Confidence            56799999999853         3345566679999999999999954   456999998765

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

Probab=98.86  E-value=6.4e-10  Score=76.12  Aligned_cols=53  Identities=26%  Similarity=0.633  Sum_probs=41.2

Q ss_pred             CCcCccccccc-------------cCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccccc
Q 042990           71 DTECVICLSEF-------------AAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETC  123 (165)
Q Consensus        71 ~~~C~ICl~~~-------------~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~  123 (165)
                      -+.|+||+.-+             ..++.......|+|.||.+||.+|++++..||+|..+..-+.
T Consensus        46 vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrWlktr~vCPLdn~eW~~qr  111 (114)
T KOG2930|consen   46 VDNCAICRNHIMDLCIECQANQSATSEECTVAWGVCNHAFHFHCISRWLKTRNVCPLDNKEWVFQR  111 (114)
T ss_pred             echhHHHHHHHHHHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHHHhhcCcCCCcCcceeEee
Confidence            35677776543             234556667779999999999999999999999988876544

>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=98.86  E-value=2.3e-09  Score=62.14  Aligned_cols=39  Identities=46%  Similarity=1.145  Sum_probs=32.9

Q ss_pred             CccccccccCCCeeeecCCCCccccHhhHHHHHh--cCCCCCCC
Q 042990           74 CVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS--SHSSCPKC  115 (165)
Q Consensus        74 C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~--~~~~CP~C  115 (165)
                      |+||++.+...  ...++ |||.|+..|+..|++  ....||+|
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            78999998773  24676 999999999999997  56679988

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

>smart00184 RING Ring finger

Probab=98.85  E-value=2.5e-09  Score=60.07  Aligned_cols=38  Identities=47%  Similarity=1.164  Sum_probs=32.1

Q ss_pred             CccccccccCCCeeeecCCCCccccHhhHHHHHh-cCCCCCCC
Q 042990           74 CVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS-SHSSCPKC  115 (165)
Q Consensus        74 C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~C  115 (165)
                      |+||++...   ....++ |+|.||..|+..|++ .+..||+|
T Consensus         1 C~iC~~~~~---~~~~~~-C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEELK---DPVVLP-CGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccCCC---CcEEec-CCChHHHHHHHHHHHhCcCCCCCC
Confidence            789999843   367777 999999999999997 66779987

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

>smart00504 Ubox Modified RING finger domain

Probab=98.78  E-value=7.6e-09  Score=65.21  Aligned_cols=46  Identities=30%  Similarity=0.512  Sum_probs=40.1

Q ss_pred             CcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           72 TECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        72 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      ..|+||++.+++   +..++ |||.|.+.||..|++.+..||.|+..+..
T Consensus         2 ~~Cpi~~~~~~~---Pv~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~~   47 (63)
T smart00504        2 FLCPISLEVMKD---PVILP-SGQTYERRAIEKWLLSHGTDPVTGQPLTH   47 (63)
T ss_pred             cCCcCCCCcCCC---CEECC-CCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence            469999999987   46677 99999999999999888899999987743

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

>TIGR00599 rad18 DNA repair protein rad18

Probab=98.69  E-value=1.3e-08  Score=85.96  Aligned_cols=49  Identities=35%  Similarity=0.654  Sum_probs=42.3

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      +....|+||++.|.+   +..++ |||.||..||..|+.....||+||..+..
T Consensus        24 e~~l~C~IC~d~~~~---Pvitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~   72 (397)
T TIGR00599        24 DTSLRCHICKDFFDV---PVLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQE   72 (397)
T ss_pred             ccccCCCcCchhhhC---ccCCC-CCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence            456899999999976   45677 99999999999999888889999997654

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

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

Probab=98.62  E-value=7.7e-09  Score=82.16  Aligned_cols=50  Identities=30%  Similarity=0.707  Sum_probs=41.6

Q ss_pred             CCCcCccccccccCCC-------eeeecCCCCccccHhhHHHHH--hcCCCCCCCCcccc
Q 042990           70 LDTECVICLSEFAAGD-------RLRLLPKCNHGFHVRCIDKWL--SSHSSCPKCRHCLI  120 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~-------~~~~l~~C~H~FH~~Ci~~Wl--~~~~~CP~CR~~~~  120 (165)
                      +|..|+||-..+....       ....+. |+|+||..||.-|-  .++.+||+|+..+-
T Consensus       223 ~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVd  281 (328)
T KOG1734|consen  223 SDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVD  281 (328)
T ss_pred             CcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhh
Confidence            5789999999986544       566787 99999999999995  67889999987554

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

Probab=98.57  E-value=2.7e-08  Score=78.83  Aligned_cols=50  Identities=30%  Similarity=0.680  Sum_probs=42.1

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHH-HHhcCCC-CCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDK-WLSSHSS-CPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~-Wl~~~~~-CP~CR~~~~~~  122 (165)
                      ..|..|+||++....   ...++ |||+|+..||.. |=+++.. ||+||+...+.
T Consensus       213 ~~d~kC~lC~e~~~~---ps~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk  264 (271)
T COG5574         213 LADYKCFLCLEEPEV---PSCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPK  264 (271)
T ss_pred             ccccceeeeecccCC---ccccc-ccchhhHHHHHHHHHhhccccCchhhhhccch
Confidence            357899999999766   67777 999999999999 8766555 99999988764

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

Probab=98.57  E-value=6.5e-08  Score=82.49  Aligned_cols=51  Identities=33%  Similarity=0.831  Sum_probs=38.8

Q ss_pred             CCCcCccccccccCCC----------ee----eecCCCCccccHhhHHHHHhc-CCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGD----------RL----RLLPKCNHGFHVRCIDKWLSS-HSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~----------~~----~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~  121 (165)
                      ...+|+|||..+.--.          .+    ..+| |.|+||..|+.+|... +-.||+||.++++
T Consensus       570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tP-C~HifH~~CL~~WMd~ykl~CPvCR~pLPp  635 (636)
T KOG0828|consen  570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTP-CHHIFHRQCLLQWMDTYKLICPVCRCPLPP  635 (636)
T ss_pred             ccccceEeccccceeeccCcchhhhhhhhccccccc-hHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence            3468999999975311          11    1346 9999999999999984 5589999998864

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

Probab=98.47  E-value=1.6e-07  Score=56.81  Aligned_cols=42  Identities=26%  Similarity=0.783  Sum_probs=31.7

Q ss_pred             cCccccccccCCCeeeecCCCC-----ccccHhhHHHHHhc--CCCCCCCC
Q 042990           73 ECVICLSEFAAGDRLRLLPKCN-----HGFHVRCIDKWLSS--HSSCPKCR  116 (165)
Q Consensus        73 ~C~ICl~~~~~~~~~~~l~~C~-----H~FH~~Ci~~Wl~~--~~~CP~CR  116 (165)
                      .|.||++..++ +.....| |.     |.+|..|+.+|+..  +.+||+|+
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            48999994434 3444677 75     89999999999943  55899995

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

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

Probab=98.41  E-value=6.2e-08  Score=62.89  Aligned_cols=50  Identities=32%  Similarity=0.786  Sum_probs=23.1

Q ss_pred             CCcCcccccccc-CCCeee-ec--CCCCccccHhhHHHHHhc---CC--------CCCCCCcccc
Q 042990           71 DTECVICLSEFA-AGDRLR-LL--PKCNHGFHVRCIDKWLSS---HS--------SCPKCRHCLI  120 (165)
Q Consensus        71 ~~~C~ICl~~~~-~~~~~~-~l--~~C~H~FH~~Ci~~Wl~~---~~--------~CP~CR~~~~  120 (165)
                      +.+|.||.+.+. .++.+. ..  +.|++.||..|+.+||+.   .+        .||.|+..+.
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~   66 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS   66 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence            468999999865 333322 22  269999999999999953   11        3999998775

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

Probab=98.37  E-value=2.9e-07  Score=54.04  Aligned_cols=33  Identities=33%  Similarity=0.768  Sum_probs=21.6

Q ss_pred             CccccccccC-CCeeeecCCCCccccHhhHHHHHhc
Q 042990           74 CVICLSEFAA-GDRLRLLPKCNHGFHVRCIDKWLSS  108 (165)
Q Consensus        74 C~ICl~~~~~-~~~~~~l~~C~H~FH~~Ci~~Wl~~  108 (165)
                      |+||++ |.. ...+.+|+ |||.|+++|+.+|+++
T Consensus         1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~   34 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKK   34 (43)
T ss_dssp             -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH
T ss_pred             CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhc
Confidence            899999 754 44678898 9999999999999964

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

Probab=98.34  E-value=2.6e-07  Score=79.24  Aligned_cols=47  Identities=32%  Similarity=0.622  Sum_probs=38.5

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcC-----CCCCCCCccccc
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSH-----SSCPKCRHCLIE  121 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~-----~~CP~CR~~~~~  121 (165)
                      +..|+||++....   ...+. |||+||..||.++|...     ..||+||..+-.
T Consensus       186 ~~~CPICL~~~~~---p~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~  237 (513)
T KOG2164|consen  186 DMQCPICLEPPSV---PVRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL  237 (513)
T ss_pred             CCcCCcccCCCCc---ccccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence            7899999998654   44555 99999999999998543     469999998776

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

Probab=98.27  E-value=3.6e-07  Score=75.99  Aligned_cols=49  Identities=31%  Similarity=0.800  Sum_probs=37.1

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc---CCCCCCCCccc
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS---HSSCPKCRHCL  119 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~---~~~CP~CR~~~  119 (165)
                      .-.|.||-+-+.....+.....|||+||..|+.+||..   ++.||.|+-.+
T Consensus         4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~   55 (465)
T KOG0827|consen    4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKL   55 (465)
T ss_pred             cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecc
Confidence            34799995555555556556579999999999999965   45799998333

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

Probab=98.26  E-value=3.3e-07  Score=73.78  Aligned_cols=52  Identities=27%  Similarity=0.502  Sum_probs=44.2

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETCQ  124 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~~  124 (165)
                      +....|-||.+.+..   +..++ |||-||.-||...|..+..||+||.+.-+...
T Consensus        23 Ds~lrC~IC~~~i~i---p~~Tt-CgHtFCslCIR~hL~~qp~CP~Cr~~~~esrl   74 (391)
T COG5432          23 DSMLRCRICDCRISI---PCETT-CGHTFCSLCIRRHLGTQPFCPVCREDPCESRL   74 (391)
T ss_pred             hhHHHhhhhhheeec---ceecc-cccchhHHHHHHHhcCCCCCccccccHHhhhc
Confidence            345789999999877   45666 99999999999999999999999998776544

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

Probab=98.25  E-value=3.2e-07  Score=77.48  Aligned_cols=48  Identities=38%  Similarity=0.888  Sum_probs=39.4

Q ss_pred             CCCcCccccccccCCC-eeeecCCCCccccHhhHHHHHhcCCCCCCCCcccc
Q 042990           70 LDTECVICLSEFAAGD-RLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI  120 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~-~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  120 (165)
                      +-..|+||||.|...- .++... |.|.||..|+..|  ...+||+||....
T Consensus       174 ELPTCpVCLERMD~s~~gi~t~~-c~Hsfh~~cl~~w--~~~scpvcR~~q~  222 (493)
T KOG0804|consen  174 ELPTCPVCLERMDSSTTGILTIL-CNHSFHCSCLMKW--WDSSCPVCRYCQS  222 (493)
T ss_pred             cCCCcchhHhhcCccccceeeee-cccccchHHHhhc--ccCcChhhhhhcC
Confidence            3478999999998754 344455 9999999999999  6778999998765

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

Probab=98.24  E-value=2.3e-07  Score=84.32  Aligned_cols=52  Identities=37%  Similarity=0.809  Sum_probs=39.2

Q ss_pred             CCCCcCccccccccCCC---eeeecCCCCccccHhhHHHHHhc--CCCCCCCCcccc
Q 042990           69 GLDTECVICLSEFAAGD---RLRLLPKCNHGFHVRCIDKWLSS--HSSCPKCRHCLI  120 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~---~~~~l~~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~~~  120 (165)
                      +..++|+||...+..-+   .-...+.|.|.||..|+..|++.  +.+||+||.++.
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            46689999998875211   12334569999999999999954  567999997764

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.24  E-value=1.1e-06  Score=71.75  Aligned_cols=52  Identities=25%  Similarity=0.598  Sum_probs=38.1

Q ss_pred             CCcCcccccc-ccCCC-eeeecCCCCccccHhhHHHHH-hcCCCCCCCCccccccc
Q 042990           71 DTECVICLSE-FAAGD-RLRLLPKCNHGFHVRCIDKWL-SSHSSCPKCRHCLIETC  123 (165)
Q Consensus        71 ~~~C~ICl~~-~~~~~-~~~~l~~C~H~FH~~Ci~~Wl-~~~~~CP~CR~~~~~~~  123 (165)
                      +..|++|+.. |-+.+ ..-..+ |||.||..|++..| .....||.|+..+....
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            5689999996 33323 223334 99999999999977 44568999998877643

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=98.22  E-value=1.1e-06  Score=57.41  Aligned_cols=49  Identities=24%  Similarity=0.403  Sum_probs=38.2

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc-CCCCCCCCcccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS-HSSCPKCRHCLIET  122 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~~  122 (165)
                      +...|+|+.+-|.+   +..++ +||.|.+.+|..|++. +..||.|+..+...
T Consensus         3 ~~f~CpIt~~lM~d---PVi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~   52 (73)
T PF04564_consen    3 DEFLCPITGELMRD---PVILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSES   52 (73)
T ss_dssp             GGGB-TTTSSB-SS---EEEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SGG
T ss_pred             cccCCcCcCcHhhC---ceeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCcc
Confidence            35689999999998   77888 9999999999999977 88999998877653

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=98.22  E-value=3.8e-07  Score=74.76  Aligned_cols=51  Identities=33%  Similarity=0.698  Sum_probs=44.5

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccccccc
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETCQK  125 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~~~  125 (165)
                      -..|.||.+-|..   +..+| |+|.||.-||..+|+.+..||.|+..+-+.+.+
T Consensus        23 lLRC~IC~eyf~i---p~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr   73 (442)
T KOG0287|consen   23 LLRCGICFEYFNI---PMITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLR   73 (442)
T ss_pred             HHHHhHHHHHhcC---ceecc-ccchHHHHHHHHHhccCCCCCceecccchhhhh
Confidence            4689999999887   56777 999999999999999999999999988776543

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

Probab=98.11  E-value=7.7e-07  Score=56.22  Aligned_cols=50  Identities=26%  Similarity=0.491  Sum_probs=24.8

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccccccc
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETCQK  125 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~~~  125 (165)
                      -..|++|.+-++.   +..+..|.|+|++.||..-+..  .||+|+.+.-.++-+
T Consensus         7 lLrCs~C~~~l~~---pv~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD~~   56 (65)
T PF14835_consen    7 LLRCSICFDILKE---PVCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQDIQ   56 (65)
T ss_dssp             TTS-SSS-S--SS----B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS--
T ss_pred             hcCCcHHHHHhcC---CceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHHHH
Confidence            3579999999877   4555569999999999885543  499999887665443

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

Probab=98.06  E-value=2.9e-06  Score=71.07  Aligned_cols=49  Identities=37%  Similarity=0.866  Sum_probs=39.3

Q ss_pred             CCCcCcccccccc-CCCeeeecCCCCccccHhhHHHHHh--cCCCCCCCCcc
Q 042990           70 LDTECVICLSEFA-AGDRLRLLPKCNHGFHVRCIDKWLS--SHSSCPKCRHC  118 (165)
Q Consensus        70 ~~~~C~ICl~~~~-~~~~~~~l~~C~H~FH~~Ci~~Wl~--~~~~CP~CR~~  118 (165)
                      ....|+||+++|. .+++....++|||.|..+||..|+-  ....||.|...
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            3578999999997 4566666667999999999999993  24469999764

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

Probab=98.05  E-value=1.7e-06  Score=68.45  Aligned_cols=44  Identities=39%  Similarity=0.834  Sum_probs=39.1

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCC
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCR  116 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR  116 (165)
                      .....|+||++.|...   ..++ |+|.|+..|+..++.....||.||
T Consensus        11 ~~~~~C~iC~~~~~~p---~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr   54 (386)
T KOG2177|consen   11 QEELTCPICLEYFREP---VLLP-CGHNFCRACLTRSWEGPLSCPVCR   54 (386)
T ss_pred             cccccChhhHHHhhcC---cccc-ccchHhHHHHHHhcCCCcCCcccC
Confidence            3567999999999985   7887 999999999999988667899999

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

Probab=97.93  E-value=1.2e-06  Score=72.25  Aligned_cols=55  Identities=33%  Similarity=0.593  Sum_probs=45.0

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHH-hcCCCCCCCCcccccccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWL-SSHSSCPKCRHCLIETCQKI  126 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl-~~~~~CP~CR~~~~~~~~~~  126 (165)
                      ..+..|+|||+-++.   .+..+.|.|-||.+||..-+ ..++.||.||..+.......
T Consensus        41 ~~~v~c~icl~llk~---tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~SkrsLr   96 (381)
T KOG0311|consen   41 DIQVICPICLSLLKK---TMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRSLR   96 (381)
T ss_pred             hhhhccHHHHHHHHh---hcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccccCC
Confidence            457899999999877   45555799999999999998 46889999999998754433

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

Probab=97.89  E-value=8.2e-06  Score=67.41  Aligned_cols=50  Identities=36%  Similarity=0.693  Sum_probs=42.2

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCc-cccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNH-GFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H-~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      ++..+|.|||.+-.+   +.+|| |.| -.|..|-+..--..+.||+||+++.+.
T Consensus       288 ~~gkeCVIClse~rd---t~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~l  338 (349)
T KOG4265|consen  288 ESGKECVICLSESRD---TVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIEEL  338 (349)
T ss_pred             cCCCeeEEEecCCcc---eEEec-chhhehhHhHHHHHHHhhcCCCccccchHhh
Confidence            346799999999877   78999 999 689999998655677899999998764

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

Probab=97.78  E-value=1.6e-05  Score=62.08  Aligned_cols=58  Identities=28%  Similarity=0.667  Sum_probs=47.2

Q ss_pred             cccccCCCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc--------CCCCCCCCcccccc
Q 042990           63 AELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS--------HSSCPKCRHCLIET  122 (165)
Q Consensus        63 ~~~~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~--------~~~CP~CR~~~~~~  122 (165)
                      +...+.+.+..|..|-..+..++.+|..  |-|.||..|+++|-..        +..||.|..++++.
T Consensus        42 qWL~DsDY~pNC~LC~t~La~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp  107 (299)
T KOG3970|consen   42 QWLQDSDYNPNCRLCNTPLASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPP  107 (299)
T ss_pred             HHHhhcCCCCCCceeCCccccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCC
Confidence            3444455678999999999999998875  9999999999999633        44699999988854

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

Probab=97.72  E-value=3e-05  Score=65.14  Aligned_cols=51  Identities=29%  Similarity=0.662  Sum_probs=40.3

Q ss_pred             CcCccccccccCCCeeeecCCCCccccHhhHHHHH-h-cCCCCCCCCcccccccccc
Q 042990           72 TECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWL-S-SHSSCPKCRHCLIETCQKI  126 (165)
Q Consensus        72 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl-~-~~~~CP~CR~~~~~~~~~~  126 (165)
                      ..|-||-|.=++   +..-| |||..|..|+..|- . .+.+||.||..+.-.+.-+
T Consensus       370 eLCKICaendKd---vkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIKGte~vi  422 (563)
T KOG1785|consen  370 ELCKICAENDKD---VKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIKGTEPVI  422 (563)
T ss_pred             HHHHHhhccCCC---ccccc-ccchHHHHHHHhhcccCCCCCCCceeeEecccccee
Confidence            469999887444   78888 99999999999996 2 3778999999887554433

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

Probab=97.72  E-value=1.5e-05  Score=64.46  Aligned_cols=48  Identities=29%  Similarity=0.542  Sum_probs=39.9

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhHHHHH-hcCCCCCCCCcccccc
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWL-SSHSSCPKCRHCLIET  122 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl-~~~~~CP~CR~~~~~~  122 (165)
                      +.+|+||+....-   +..++ |+|.|+-.||.--+ +.+.+|++||.++.+.
T Consensus         7 ~~eC~IC~nt~n~---Pv~l~-C~HkFCyiCiKGsy~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    7 KKECLICYNTGNC---PVNLY-CFHKFCYICIKGSYKNDKKTCAVCRFPIDST   55 (324)
T ss_pred             CCcceeeeccCCc---Ccccc-ccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence            5799999998654   57787 99999999999876 4566799999998864

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

Probab=97.65  E-value=8.7e-06  Score=73.06  Aligned_cols=49  Identities=22%  Similarity=0.400  Sum_probs=37.6

Q ss_pred             CcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           72 TECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        72 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      ..|++|+..+.++.....-+ |+|.||.+||..|-+...+||+||..+.+
T Consensus       124 ~~CP~Ci~s~~DqL~~~~k~-c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~  172 (1134)
T KOG0825|consen  124 NQCPNCLKSCNDQLEESEKH-TAHYFCEECVGSWSRCAQTCPVDRGEFGE  172 (1134)
T ss_pred             hhhhHHHHHHHHHhhccccc-cccccHHHHhhhhhhhcccCchhhhhhhe
Confidence            34666666655544343444 99999999999999999999999987764

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

Probab=97.63  E-value=3e-05  Score=64.56  Aligned_cols=51  Identities=39%  Similarity=0.914  Sum_probs=38.6

Q ss_pred             CCCCcCccccccccCCC----eeeecCCCCccccHhhHHHHH--hc-----CCCCCCCCccc
Q 042990           69 GLDTECVICLSEFAAGD----RLRLLPKCNHGFHVRCIDKWL--SS-----HSSCPKCRHCL  119 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~----~~~~l~~C~H~FH~~Ci~~Wl--~~-----~~~CP~CR~~~  119 (165)
                      ..+.+|.|||+...+..    ....+|+|.|.|+..||..|-  ++     .+.||.||...
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s  220 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPS  220 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCcc
Confidence            35789999999976533    122346799999999999997  33     36799999853

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

Probab=97.62  E-value=2.8e-05  Score=65.07  Aligned_cols=46  Identities=39%  Similarity=0.936  Sum_probs=37.7

Q ss_pred             CCCcCccccccccCC-CeeeecCCCCccccHhhHHHHHhc--CCCCCCCC
Q 042990           70 LDTECVICLSEFAAG-DRLRLLPKCNHGFHVRCIDKWLSS--HSSCPKCR  116 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~-~~~~~l~~C~H~FH~~Ci~~Wl~~--~~~CP~CR  116 (165)
                      -+..|..|-+.+... +..-.+| |.|+||..|+...+.+  .++||.||
T Consensus       364 ~~L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~Cr  412 (518)
T KOG1941|consen  364 TELYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCR  412 (518)
T ss_pred             HhhhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHH
Confidence            456799999998643 4566788 9999999999999944  55899998

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

Probab=97.48  E-value=6.8e-05  Score=46.63  Aligned_cols=42  Identities=24%  Similarity=0.592  Sum_probs=27.3

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc--CCCCCC
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS--HSSCPK  114 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~--~~~CP~  114 (165)
                      ....|+|.+..|++  .++... |+|.|-++.|.+|+++  ...||+
T Consensus        10 ~~~~CPiT~~~~~~--PV~s~~-C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen   10 ISLKCPITLQPFED--PVKSKK-CGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             --SB-TTTSSB-SS--EEEESS-S--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             eccCCCCcCChhhC--CcCcCC-CCCeecHHHHHHHHHhcCCCCCCC
Confidence            45789999999987  244444 9999999999999943  446998

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

Probab=97.47  E-value=2.6e-05  Score=63.19  Aligned_cols=53  Identities=30%  Similarity=0.770  Sum_probs=43.6

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc-----------------------CCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS-----------------------HSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-----------------------~~~CP~CR~~~~~~  122 (165)
                      .....|.|||--|.+++....+. |.|.||..|+.++|..                       +..||+||..+.-.
T Consensus       113 ~p~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e  188 (368)
T KOG4445|consen  113 HPNGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIE  188 (368)
T ss_pred             CCCCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhcccc
Confidence            35678999999999999888888 9999999999988622                       11399999988754

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

Probab=97.44  E-value=5e-05  Score=68.06  Aligned_cols=49  Identities=22%  Similarity=0.603  Sum_probs=39.3

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHH-hcCCCCCCCCcccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWL-SSHSSCPKCRHCLIET  122 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl-~~~~~CP~CR~~~~~~  122 (165)
                      .-..|+.|-+..++   .... .|+|+||..|+..-+ -+++.||.|-..+-..
T Consensus       642 ~~LkCs~Cn~R~Kd---~vI~-kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFgan  691 (698)
T KOG0978|consen  642 ELLKCSVCNTRWKD---AVIT-KCGHVFCEECVQTRYETRQRKCPKCNAAFGAN  691 (698)
T ss_pred             hceeCCCccCchhh---HHHH-hcchHHHHHHHHHHHHHhcCCCCCCCCCCCcc
Confidence            34679999988777   4444 499999999999999 4577899998877654

>PHA02862 5L protein; Provisional

Probab=97.39  E-value=0.00014  Score=53.19  Aligned_cols=48  Identities=19%  Similarity=0.535  Sum_probs=35.3

Q ss_pred             CCcCccccccccCCCeeeecCCC---CccccHhhHHHHHh--cCCCCCCCCccccc
Q 042990           71 DTECVICLSEFAAGDRLRLLPKC---NHGFHVRCIDKWLS--SHSSCPKCRHCLIE  121 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C---~H~FH~~Ci~~Wl~--~~~~CP~CR~~~~~  121 (165)
                      ++.|-||+++-++.  ..-.. |   ...-|.+|+.+|++  ++..|+.|+.++.-
T Consensus         2 ~diCWIC~~~~~e~--~~PC~-C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~I   54 (156)
T PHA02862          2 SDICWICNDVCDER--NNFCG-CNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNI   54 (156)
T ss_pred             CCEEEEecCcCCCC--ccccc-ccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEE
Confidence            46899999986443  22222 4   26899999999994  46689999998764

>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=97.38  E-value=5.8e-05  Score=54.56  Aligned_cols=35  Identities=23%  Similarity=0.581  Sum_probs=29.9

Q ss_pred             CCcCccccccccCCCeeeecCCCC------ccccHhhHHHHH
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCN------HGFHVRCIDKWL  106 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~------H~FH~~Ci~~Wl  106 (165)
                      ..+|.||++.+.+++.++.++ ||      |+||.+|+.+|-
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            579999999999866666666 66      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=97.35  E-value=5.2e-05  Score=46.31  Aligned_cols=47  Identities=28%  Similarity=0.568  Sum_probs=33.8

Q ss_pred             CCCcCccccccccCCCeeeecCCCCcc-ccHhhHHHHHh-cCCCCCCCCcccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHG-FHVRCIDKWLS-SHSSCPKCRHCLI  120 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~-~~~~CP~CR~~~~  120 (165)
                      -+++|.||+|.--+  .  ++-.|||+ .+-.|-.+.++ .+..||.||+++.
T Consensus         6 ~~dECTICye~pvd--s--VlYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    6 WSDECTICYEHPVD--S--VLYTCGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             cccceeeeccCcch--H--HHHHcchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            35899999987443  1  23349995 56778766655 6788999999874

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

Probab=97.21  E-value=0.00017  Score=61.19  Aligned_cols=49  Identities=33%  Similarity=0.825  Sum_probs=42.8

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      ..+.+|.||+.-+.+   +..+| |||.|+..||.+-+.....||.||..+.+
T Consensus        82 ~sef~c~vc~~~l~~---pv~tp-cghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   82 RSEFECCVCSRALYP---PVVTP-CGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cchhhhhhhHhhcCC---Ccccc-ccccccHHHHHHHhccCCCCccccccccc
Confidence            456899999888877   67777 99999999999987878889999999986

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

Probab=97.17  E-value=0.00028  Score=67.35  Aligned_cols=64  Identities=27%  Similarity=0.599  Sum_probs=45.9

Q ss_pred             CCeEeeccccccCCCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCC----------CCCCCCcccc
Q 042990           56 FPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHS----------SCPKCRHCLI  120 (165)
Q Consensus        56 lp~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~----------~CP~CR~~~~  120 (165)
                      +|-+.-.......+.|+.|-||..+--.....+.+. |+|+||.+|..+-|.++.          +||+|+..+.
T Consensus      3471 LPCl~Cdks~tkQD~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~In 3544 (3738)
T KOG1428|consen 3471 LPCLHCDKSATKQDADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKIN 3544 (3738)
T ss_pred             ccccccChhhhhcccCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchhh
Confidence            343333333334467899999998865555677887 999999999988764432          5999998765

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=97.12  E-value=0.00049  Score=51.10  Aligned_cols=50  Identities=24%  Similarity=0.581  Sum_probs=36.2

Q ss_pred             CCCCcCccccccccCCCeeeecC-CCCc---cccHhhHHHHHh--cCCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLP-KCNH---GFHVRCIDKWLS--SHSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~-~C~H---~FH~~Ci~~Wl~--~~~~CP~CR~~~~~~  122 (165)
                      ..+..|-||+++..+  ..  .| .|..   ..|.+|+.+|+.  +...|+.|+..+.-.
T Consensus         6 ~~~~~CRIC~~~~~~--~~--~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~   61 (162)
T PHA02825          6 LMDKCCWICKDEYDV--VT--NYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIK   61 (162)
T ss_pred             CCCCeeEecCCCCCC--cc--CCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEE
Confidence            357899999998543  22  24 2443   669999999994  355799999887654

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

Probab=97.12  E-value=0.00026  Score=60.19  Aligned_cols=51  Identities=31%  Similarity=0.654  Sum_probs=42.3

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      +.+..|++|+..+.+.-..  . +|||.|+..|+..|+..+..||.|+..+...
T Consensus        19 ~~~l~C~~C~~vl~~p~~~--~-~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~   69 (391)
T KOG0297|consen   19 DENLLCPICMSVLRDPVQT--T-TCGHRFCAGCLLESLSNHQKCPVCRQELTQA   69 (391)
T ss_pred             cccccCccccccccCCCCC--C-CCCCcccccccchhhccCcCCcccccccchh
Confidence            4678999999999874221  3 4999999999999998899999998877754

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

Probab=96.98  E-value=0.00098  Score=55.30  Aligned_cols=70  Identities=23%  Similarity=0.404  Sum_probs=51.1

Q ss_pred             CCCHHHhhcCCeEeeccccccCCCCCcCccccccccCCCeeeecCCCCccccHhhHHHH--HhcCCCCCCCCcccc
Q 042990           47 GIKQKALKTFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKW--LSSHSSCPKCRHCLI  120 (165)
Q Consensus        47 ~~~~~~~~~lp~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~W--l~~~~~CP~CR~~~~  120 (165)
                      ...+-.+..-|.........+.++...|-||-+.+.-   ..++| |+|..+--|--+.  |-+++.||.||...-
T Consensus        37 kqkKNnlsaEPnlttsSaddtDEen~~C~ICA~~~TY---s~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE~e  108 (493)
T COG5236          37 KQKKNNLSAEPNLTTSSADDTDEENMNCQICAGSTTY---SARYP-CGHQICHACAVRLRALYMQKGCPLCRTETE  108 (493)
T ss_pred             hccccccccCCccccccccccccccceeEEecCCceE---EEecc-CCchHHHHHHHHHHHHHhccCCCccccccc
Confidence            3444455556666666655566677899999988654   56788 9999998887765  356889999998654

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

Probab=96.90  E-value=0.0007  Score=40.35  Aligned_cols=41  Identities=27%  Similarity=0.853  Sum_probs=26.0

Q ss_pred             CccccccccCCCeeeecC-CCC---ccccHhhHHHHHh--cCCCCCCC
Q 042990           74 CVICLSEFAAGDRLRLLP-KCN---HGFHVRCIDKWLS--SHSSCPKC  115 (165)
Q Consensus        74 C~ICl~~~~~~~~~~~l~-~C~---H~FH~~Ci~~Wl~--~~~~CP~C  115 (165)
                      |-||+++-+.++ ....| .|.   ...|..|+.+|+.  ++..|++|
T Consensus         1 CrIC~~~~~~~~-~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            679999877665 23344 244   3889999999995  45678887

>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=96.86  E-value=0.00048  Score=47.44  Aligned_cols=34  Identities=26%  Similarity=0.694  Sum_probs=27.9

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHH
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDK  104 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~  104 (165)
                      ..+..|++|...+.. ......| |||+||..|+.+
T Consensus        76 ~~~~~C~vC~k~l~~-~~f~~~p-~~~v~H~~C~~r  109 (109)
T PF10367_consen   76 TESTKCSVCGKPLGN-SVFVVFP-CGHVVHYSCIKR  109 (109)
T ss_pred             CCCCCccCcCCcCCC-ceEEEeC-CCeEEecccccC
Confidence            356789999999987 5566777 999999999753

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 [].

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

Probab=96.85  E-value=0.00039  Score=53.46  Aligned_cols=44  Identities=20%  Similarity=0.503  Sum_probs=37.7

Q ss_pred             CcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccc
Q 042990           72 TECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCL  119 (165)
Q Consensus        72 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~  119 (165)
                      ..|.||..+|+.   +++.. |||.||..|...-++....|-+|-...
T Consensus       197 F~C~iCKkdy~s---pvvt~-CGH~FC~~Cai~~y~kg~~C~~Cgk~t  240 (259)
T COG5152         197 FLCGICKKDYES---PVVTE-CGHSFCSLCAIRKYQKGDECGVCGKAT  240 (259)
T ss_pred             eeehhchhhccc---hhhhh-cchhHHHHHHHHHhccCCcceecchhh
Confidence            479999999987   55665 999999999999889999999996543

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

Probab=96.83  E-value=0.00036  Score=51.96  Aligned_cols=30  Identities=43%  Similarity=0.855  Sum_probs=27.2

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHh
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVR  100 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~  100 (165)
                      ..-+|.||||+++.++++..+| |-.+||+.
T Consensus       176 dkGECvICLEdL~~GdtIARLP-CLCIYHK~  205 (205)
T KOG0801|consen  176 DKGECVICLEDLEAGDTIARLP-CLCIYHKQ  205 (205)
T ss_pred             cCCcEEEEhhhccCCCceeccc-eEEEeecC
Confidence            4578999999999999999999 99999973

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

Probab=96.60  E-value=0.0018  Score=38.70  Aligned_cols=45  Identities=24%  Similarity=0.553  Sum_probs=22.4

Q ss_pred             CccccccccCCC-eeeecCCCCccccHhhHHHHHh-cCCCCCCCCccc
Q 042990           74 CVICLSEFAAGD-RLRLLPKCNHGFHVRCIDKWLS-SHSSCPKCRHCL  119 (165)
Q Consensus        74 C~ICl~~~~~~~-~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~~  119 (165)
                      |++|.+++...+ ...-.+ |++.++..|...-+. .+..||-||.++
T Consensus         1 cp~C~e~~d~~d~~~~PC~-Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDKDFYPCE-CGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCTT--SST-TS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCCccccCc-CCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            789999994433 333344 889999999988775 477899999864

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

Probab=96.56  E-value=0.0012  Score=60.12  Aligned_cols=51  Identities=31%  Similarity=0.711  Sum_probs=38.5

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc-------CCCCCCCCccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS-------HSSCPKCRHCL  119 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-------~~~CP~CR~~~  119 (165)
                      ...++|.||.+.+.....+-....|-|+||..||..|-++       ...||.|....
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            3558999999999876544444458899999999999743       12499997433

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

Probab=96.52  E-value=0.001  Score=57.98  Aligned_cols=48  Identities=27%  Similarity=0.596  Sum_probs=37.5

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc-----CCCCCCCCcccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS-----HSSCPKCRHCLI  120 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-----~~~CP~CR~~~~  120 (165)
                      ....+|.+|.++-++   .+... |.|.||+-||.+++..     +.+||+|-..+.
T Consensus       534 k~~~~C~lc~d~aed---~i~s~-ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~Ls  586 (791)
T KOG1002|consen  534 KGEVECGLCHDPAED---YIESS-CHHKFCRLCIKEYVESFMENNNVTCPVCHIGLS  586 (791)
T ss_pred             cCceeecccCChhhh---hHhhh-hhHHHHHHHHHHHHHhhhcccCCCCcccccccc
Confidence            345789999998665   56666 9999999999998732     568999966554

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

Probab=96.49  E-value=0.0008  Score=55.27  Aligned_cols=51  Identities=25%  Similarity=0.601  Sum_probs=41.6

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      .....|.+|..=|-+..++.   .|-|-||+.||...|....+||+|...+...
T Consensus        13 n~~itC~LC~GYliDATTI~---eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t   63 (331)
T KOG2660|consen   13 NPHITCRLCGGYLIDATTIT---ECLHTFCKSCIVKYLEESKYCPTCDIVIHKT   63 (331)
T ss_pred             ccceehhhccceeecchhHH---HHHHHHHHHHHHHHHHHhccCCccceeccCc
Confidence            45689999988777643332   3999999999999998899999998877755

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

Probab=96.33  E-value=0.0022  Score=48.59  Aligned_cols=29  Identities=31%  Similarity=0.925  Sum_probs=23.7

Q ss_pred             CCCccccHhhHHHHHhcC----C-------CCCCCCcccc
Q 042990           92 KCNHGFHVRCIDKWLSSH----S-------SCPKCRHCLI  120 (165)
Q Consensus        92 ~C~H~FH~~Ci~~Wl~~~----~-------~CP~CR~~~~  120 (165)
                      +||.-||.-|+..||+.-    .       .||+|..++.
T Consensus       189 qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia  228 (234)
T KOG3268|consen  189 QCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA  228 (234)
T ss_pred             ccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence            599999999999999652    1       3999987764

>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=96.28  E-value=0.0028  Score=37.07  Aligned_cols=41  Identities=32%  Similarity=0.765  Sum_probs=23.5

Q ss_pred             CccccccccCCCeeeecCCCCccccHhhHHHHHhcCC--CCCCC
Q 042990           74 CVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHS--SCPKC  115 (165)
Q Consensus        74 C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~--~CP~C  115 (165)
                      |.+|.+-...|....... |+-.+|..|+..+++.+.  .||.|
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            667777776665554444 999999999999996655  69987

; PDB: 3NW0_A 2CT0_A.

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.17  E-value=0.0049  Score=49.00  Aligned_cols=52  Identities=13%  Similarity=0.208  Sum_probs=45.6

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      .-+.|++|.+.+.+.-.+..+..|||+|..+|+...++....||+|-.++.+
T Consensus       220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkd  271 (303)
T KOG3039|consen  220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKD  271 (303)
T ss_pred             cceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcc
Confidence            3468999999999987777777799999999999999999999999877765

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

Probab=96.13  E-value=0.021  Score=47.11  Aligned_cols=48  Identities=19%  Similarity=0.274  Sum_probs=37.2

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCL  119 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~  119 (165)
                      .....|++|+..-.++..+   .--|-+||-.||..+++++..||+--.+.
T Consensus       298 ~~~~~CpvClk~r~Nptvl---~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~  345 (357)
T KOG0826|consen  298 PDREVCPVCLKKRQNPTVL---EVSGYVFCYPCIFSYVVNYGHCPVTGYPA  345 (357)
T ss_pred             CccccChhHHhccCCCceE---EecceEEeHHHHHHHHHhcCCCCccCCcc
Confidence            3567899999998774222   22689999999999999999999864443

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

Probab=95.68  E-value=0.0068  Score=50.45  Aligned_cols=46  Identities=28%  Similarity=0.566  Sum_probs=34.5

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      ...+.|.||+++.++   ...+| |||+-+  |..-- +...+||+||..+..
T Consensus       303 ~~p~lcVVcl~e~~~---~~fvp-cGh~cc--ct~cs-~~l~~CPvCR~rI~~  348 (355)
T KOG1571|consen  303 PQPDLCVVCLDEPKS---AVFVP-CGHVCC--CTLCS-KHLPQCPVCRQRIRL  348 (355)
T ss_pred             CCCCceEEecCCccc---eeeec-CCcEEE--chHHH-hhCCCCchhHHHHHH
Confidence            356899999999877   67788 999965  55443 445569999987753

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=95.66  E-value=0.015  Score=35.64  Aligned_cols=35  Identities=29%  Similarity=0.765  Sum_probs=30.6

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHH
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDK  104 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~  104 (165)
                      ....|.+|-++|.+++.+.+.+.||-.+|++|...
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            35689999999998888889999999999999654

>PHA03096 p28-like protein; Provisional

Probab=95.56  E-value=0.0071  Score=49.36  Aligned_cols=48  Identities=23%  Similarity=0.557  Sum_probs=33.8

Q ss_pred             CcCccccccccCCC----eeeecCCCCccccHhhHHHHHhc---CCC---CCCCCccc
Q 042990           72 TECVICLSEFAAGD----RLRLLPKCNHGFHVRCIDKWLSS---HSS---CPKCRHCL  119 (165)
Q Consensus        72 ~~C~ICl~~~~~~~----~~~~l~~C~H~FH~~Ci~~Wl~~---~~~---CP~CR~~~  119 (165)
                      ..|.||++......    .-..++.|.|.|+..||..|...   ...   ||.|+..+
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~~~~~~~  236 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRLNTVI  236 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCccccchhhHH
Confidence            68999999976432    23356679999999999999743   223   55555544

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

Probab=95.27  E-value=0.0065  Score=49.36  Aligned_cols=45  Identities=24%  Similarity=0.403  Sum_probs=38.2

Q ss_pred             CcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccc
Q 042990           72 TECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI  120 (165)
Q Consensus        72 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  120 (165)
                      ..|-||...|..   +++.. |+|.|+..|...=+++...|.+|-+...
T Consensus       242 f~c~icr~~f~~---pVvt~-c~h~fc~~ca~~~~qk~~~c~vC~~~t~  286 (313)
T KOG1813|consen  242 FKCFICRKYFYR---PVVTK-CGHYFCEVCALKPYQKGEKCYVCSQQTH  286 (313)
T ss_pred             cccccccccccc---chhhc-CCceeehhhhccccccCCcceecccccc
Confidence            459999999987   56665 9999999999998888889999976544

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

Probab=95.21  E-value=0.014  Score=47.57  Aligned_cols=48  Identities=35%  Similarity=0.719  Sum_probs=39.2

Q ss_pred             CCcCccccccccCCC---eeeecCCCCccccHhhHHHHHh-cCCCCCCCCccc
Q 042990           71 DTECVICLSEFAAGD---RLRLLPKCNHGFHVRCIDKWLS-SHSSCPKCRHCL  119 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~---~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~~  119 (165)
                      -..|-||-++|+.++   .++.+. |||.|+..|+..-+. ....||.||...
T Consensus         3 ~~~c~~c~~~~s~~~~~~~p~~l~-c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    3 FPECEICNEDYSSEDGDHIPRVLK-CGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CCceeecCccccccCcccCCcccc-cCceehHhHHHHHhcCceeeccCCCCcc
Confidence            358999999998653   566776 999999999998774 455799999985

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

Probab=95.05  E-value=0.031  Score=46.96  Aligned_cols=52  Identities=21%  Similarity=0.535  Sum_probs=33.9

Q ss_pred             CCCCcCccccccccCCC-------------------eeeecCCCCccccHhhHHHHHhcCC-------------CCCCCC
Q 042990           69 GLDTECVICLSEFAAGD-------------------RLRLLPKCNHGFHVRCIDKWLSSHS-------------SCPKCR  116 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~-------------------~~~~l~~C~H~FH~~Ci~~Wl~~~~-------------~CP~CR  116 (165)
                      ++.+.|.-|+..-.+-.                   ...... |.-++|.+|+.+||..+.             .||+||
T Consensus       269 ~e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~-CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCR  347 (358)
T PF10272_consen  269 QELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCY-CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCR  347 (358)
T ss_pred             cccCCccccccCCCCcEEEeccCCcccCCcccccCCCCcccc-ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCc
Confidence            45678999998743210                   111222 556788899999993322             499999


Q ss_pred             ccccc
Q 042990          117 HCLIE  121 (165)
Q Consensus       117 ~~~~~  121 (165)
                      +.+--
T Consensus       348 a~FCi  352 (358)
T PF10272_consen  348 AKFCI  352 (358)
T ss_pred             cccee
Confidence            97653

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

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

Probab=95.02  E-value=0.013  Score=49.64  Aligned_cols=37  Identities=27%  Similarity=0.736  Sum_probs=31.9

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHh
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS  107 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~  107 (165)
                      .-..|.||+++.........+| |+|+|++.|...++.
T Consensus       183 slf~C~ICf~e~~G~~c~~~lp-C~Hv~Ck~C~kdY~~  219 (445)
T KOG1814|consen  183 SLFDCCICFEEQMGQHCFKFLP-CSHVFCKSCLKDYFT  219 (445)
T ss_pred             hcccceeeehhhcCcceeeecc-cchHHHHHHHHHHHH
Confidence            3578999999976667788888 999999999999983

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.93  E-value=0.011  Score=47.16  Aligned_cols=55  Identities=25%  Similarity=0.681  Sum_probs=37.4

Q ss_pred             CCCCcCccccccccCCCee-eecC-CCC---ccccHhhHHHHHhcCC--------CCCCCCccccccc
Q 042990           69 GLDTECVICLSEFAAGDRL-RLLP-KCN---HGFHVRCIDKWLSSHS--------SCPKCRHCLIETC  123 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~-~~l~-~C~---H~FH~~Ci~~Wl~~~~--------~CP~CR~~~~~~~  123 (165)
                      +.+..|-||...=+++..- =+-| +|.   |..|..|+.+|+..+.        +||.|++.+...-
T Consensus        18 e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~   85 (293)
T KOG3053|consen   18 ELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVF   85 (293)
T ss_pred             ccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeec
Confidence            4578899999886554321 1122 243   8999999999993322        4999999877543

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

Probab=94.92  E-value=0.034  Score=44.90  Aligned_cols=50  Identities=26%  Similarity=0.409  Sum_probs=37.3

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc--CCCCCCCCccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS--HSSCPKCRHCLIE  121 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~~~~  121 (165)
                      ..+.+|++|.+.=...  -... .|+|+||=.||..-+..  ..+||.|-.+..+
T Consensus       237 t~~~~C~~Cg~~PtiP--~~~~-~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~  288 (298)
T KOG2879|consen  237 TSDTECPVCGEPPTIP--HVIG-KCGHIYCYYCIATSRLWDASFTCPLCGENVEP  288 (298)
T ss_pred             cCCceeeccCCCCCCC--eeec-cccceeehhhhhhhhcchhhcccCccCCCCcc
Confidence            4678999998874432  2233 49999999999987643  4689999777763

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=94.85  E-value=0.02  Score=47.54  Aligned_cols=52  Identities=19%  Similarity=0.468  Sum_probs=37.0

Q ss_pred             CCCCcCccccccccCCCeee-ecCCCCccccHhhHHHHHh-cCCCCCCCCccccc
Q 042990           69 GLDTECVICLSEFAAGDRLR-LLPKCNHGFHVRCIDKWLS-SHSSCPKCRHCLIE  121 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~-~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~~~~  121 (165)
                      ++++.|+.|+|++...++-- -.+ ||...|.-|...--. -+..||-||+-+-+
T Consensus        12 deed~cplcie~mditdknf~pc~-cgy~ic~fc~~~irq~lngrcpacrr~y~d   65 (480)
T COG5175          12 DEEDYCPLCIEPMDITDKNFFPCP-CGYQICQFCYNNIRQNLNGRCPACRRKYDD   65 (480)
T ss_pred             cccccCcccccccccccCCcccCC-cccHHHHHHHHHHHhhccCCChHhhhhccc
Confidence            34566999999998665433 344 998888888766432 25579999987653

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=94.68  E-value=0.019  Score=35.25  Aligned_cols=43  Identities=28%  Similarity=0.544  Sum_probs=30.9

Q ss_pred             cCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           73 ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        73 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      .|-.|...   +.+-..++ |+|+....|+..+  +...||.|-+++..
T Consensus         9 ~~~~~~~~---~~~~~~~p-CgH~I~~~~f~~~--rYngCPfC~~~~~~   51 (55)
T PF14447_consen    9 PCVFCGFV---GTKGTVLP-CGHLICDNCFPGE--RYNGCPFCGTPFEF   51 (55)
T ss_pred             eEEEcccc---cccccccc-ccceeeccccChh--hccCCCCCCCcccC
Confidence            44444443   33356777 9999999998875  67779999877654

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

Probab=94.64  E-value=0.02  Score=46.79  Aligned_cols=43  Identities=30%  Similarity=0.673  Sum_probs=33.6

Q ss_pred             CcCccccccccCCCeeeecCCCCccccHhhHHHHH-hcCCCCCCCCc
Q 042990           72 TECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWL-SSHSSCPKCRH  117 (165)
Q Consensus        72 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl-~~~~~CP~CR~  117 (165)
                      ..|+.|..-+.+.   ..++-|+|.|+.+||..-| .....||.|.+
T Consensus       275 LkCplc~~Llrnp---~kT~cC~~~fc~eci~~al~dsDf~CpnC~r  318 (427)
T COG5222         275 LKCPLCHCLLRNP---MKTPCCGHTFCDECIGTALLDSDFKCPNCSR  318 (427)
T ss_pred             ccCcchhhhhhCc---ccCccccchHHHHHHhhhhhhccccCCCccc
Confidence            5799998877663   2334499999999999877 67889999944

>PF04641 Rtf2: Rtf2 RING-finger

Probab=94.63  E-value=0.047  Score=43.91  Aligned_cols=52  Identities=19%  Similarity=0.403  Sum_probs=41.0

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      .....|+|...+|........+..|||+|-..++.+- +....||+|-.++.+
T Consensus       111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-k~~~~Cp~c~~~f~~  162 (260)
T PF04641_consen  111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-KKSKKCPVCGKPFTE  162 (260)
T ss_pred             CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-cccccccccCCcccc
Confidence            4567899999999766655555559999999999996 335679999887764

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

Probab=94.54  E-value=0.016  Score=53.29  Aligned_cols=36  Identities=22%  Similarity=0.567  Sum_probs=29.0

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHH
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWL  106 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl  106 (165)
                      +.++.|.+|.-.+-.. .-.+.+ |||.||++|+.+-.
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            5789999999987653 345666 99999999998765

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

Probab=94.49  E-value=0.013  Score=46.32  Aligned_cols=44  Identities=27%  Similarity=0.609  Sum_probs=30.9

Q ss_pred             cCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccc
Q 042990           73 ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI  120 (165)
Q Consensus        73 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  120 (165)
                      -|.-|.-.-. ++....+. |+|+||..|...-  ....||+|+.++-
T Consensus         5 hCn~C~~~~~-~~~f~LTa-C~HvfC~~C~k~~--~~~~C~lCkk~ir   48 (233)
T KOG4739|consen    5 HCNKCFRFPS-QDPFFLTA-CRHVFCEPCLKAS--SPDVCPLCKKSIR   48 (233)
T ss_pred             EeccccccCC-CCceeeee-chhhhhhhhcccC--Cccccccccceee
Confidence            3665654433 55666775 9999999997663  2338999999844

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

Probab=94.32  E-value=0.049  Score=45.59  Aligned_cols=49  Identities=27%  Similarity=0.556  Sum_probs=40.4

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      .+|..|+||...--.   -...| |+|.=|..||.+-+.+.+.|=.|+..+..
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            467899999776322   34566 99999999999999999999999998873

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

Probab=94.26  E-value=0.0024  Score=53.68  Aligned_cols=50  Identities=26%  Similarity=0.616  Sum_probs=43.1

Q ss_pred             CCcCccccccccCC-CeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           71 DTECVICLSEFAAG-DRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        71 ~~~C~ICl~~~~~~-~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      ...|+||.+.|+.. +.+.... |||.+|..|+..|+.+...||.||+.+..
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            46799999999876 5677776 99999999999999888889999998763

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

Probab=94.24  E-value=0.0061  Score=49.55  Aligned_cols=43  Identities=26%  Similarity=0.686  Sum_probs=32.1

Q ss_pred             CCcCccccccccCCCeeeecCCCCcc-ccHhhHHHHHhcCCCCCCCCccccc
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHG-FHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      +..|+||++.-.+   ...|+ |||. -+..|-++.    ..||+||+-+..
T Consensus       300 ~~LC~ICmDaP~D---CvfLe-CGHmVtCt~CGkrm----~eCPICRqyi~r  343 (350)
T KOG4275|consen  300 RRLCAICMDAPRD---CVFLE-CGHMVTCTKCGKRM----NECPICRQYIVR  343 (350)
T ss_pred             HHHHHHHhcCCcc---eEEee-cCcEEeehhhcccc----ccCchHHHHHHH
Confidence            6789999998555   77887 9995 456775552    379999987654

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

Probab=94.08  E-value=0.028  Score=51.15  Aligned_cols=23  Identities=30%  Similarity=0.902  Sum_probs=21.3

Q ss_pred             CCCccccHhhHHHHHhcCCCCCC
Q 042990           92 KCNHGFHVRCIDKWLSSHSSCPK  114 (165)
Q Consensus        92 ~C~H~FH~~Ci~~Wl~~~~~CP~  114 (165)
                      .|+|+.|.+|...||+.+..||.
T Consensus      1047 ~C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1047 TCGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             cccccccHHHHHHHHhcCCcCCC
Confidence            49999999999999999999983

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

Probab=93.97  E-value=0.026  Score=51.77  Aligned_cols=41  Identities=24%  Similarity=0.755  Sum_probs=32.3

Q ss_pred             CcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcc
Q 042990           72 TECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHC  118 (165)
Q Consensus        72 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~  118 (165)
                      ..|..|-..++-.  .+-. .|||.||.+|+.   .+...||.|+..
T Consensus       841 skCs~C~~~LdlP--~VhF-~CgHsyHqhC~e---~~~~~CP~C~~e  881 (933)
T KOG2114|consen  841 SKCSACEGTLDLP--FVHF-LCGHSYHQHCLE---DKEDKCPKCLPE  881 (933)
T ss_pred             eeecccCCccccc--eeee-ecccHHHHHhhc---cCcccCCccchh
Confidence            5899999887752  3333 499999999988   467789999883

>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=93.75  E-value=0.079  Score=39.48  Aligned_cols=36  Identities=25%  Similarity=0.538  Sum_probs=22.0

Q ss_pred             CCcCccccccccCCC---------eeeecCCCCc-cccHhhHHHHHh
Q 042990           71 DTECVICLSEFAAGD---------RLRLLPKCNH-GFHVRCIDKWLS  107 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~---------~~~~l~~C~H-~FH~~Ci~~Wl~  107 (165)
                      +..|+||||---+.-         ..|-- -|+- .-|..|++++-+
T Consensus         2 d~~CpICme~PHNAVLLlCSS~~kgcRpy-mc~Ts~rhSNCLdqfkk   47 (162)
T PF07800_consen    2 DVTCPICMEHPHNAVLLLCSSHEKGCRPY-MCDTSYRHSNCLDQFKK   47 (162)
T ss_pred             CccCceeccCCCceEEEEeccccCCcccc-ccCCccchhHHHHHHHH
Confidence            568999999744321         11111 1553 457899999753

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.

>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=93.55  E-value=0.033  Score=44.21  Aligned_cols=47  Identities=28%  Similarity=0.716  Sum_probs=36.0

Q ss_pred             CCCcCccccccc--cCCCeeeecCCCCccccHhhHHHHHh-cCCCCC--CCC
Q 042990           70 LDTECVICLSEF--AAGDRLRLLPKCNHGFHVRCIDKWLS-SHSSCP--KCR  116 (165)
Q Consensus        70 ~~~~C~ICl~~~--~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP--~CR  116 (165)
                      .|..|++|..+-  .++-+.-.-|.|-|-.|.+|+++-|. ....||  -|-
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~   60 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCG   60 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHH
Confidence            456899999873  34445555667999999999999995 566899  663

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

Probab=93.39  E-value=0.05  Score=44.16  Aligned_cols=46  Identities=26%  Similarity=0.652  Sum_probs=37.7

Q ss_pred             CCcCccccccccCCC-eeeecCCCCccccHhhHHHHHhcCCCCCCCCc
Q 042990           71 DTECVICLSEFAAGD-RLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRH  117 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~-~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~  117 (165)
                      ...|+||.+.+-... .+..++ |||.-|..|+......+.+||+|..
T Consensus       158 ~~ncPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  158 EFNCPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             cCCCchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccc
Confidence            345999999876654 455666 9999999999999877799999977

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

Probab=92.31  E-value=0.082  Score=42.98  Aligned_cols=52  Identities=29%  Similarity=0.705  Sum_probs=36.8

Q ss_pred             CCCcCccccccccCCCe-eeecC-CCC---ccccHhhHHHHHh--cCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDR-LRLLP-KCN---HGFHVRCIDKWLS--SHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~-~~~l~-~C~---H~FH~~Ci~~Wl~--~~~~CP~CR~~~~~  121 (165)
                      ++..|-||+++...... ....| .|.   +..|+.|+..|+.  .+..|..|......
T Consensus        77 ~~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~~  135 (323)
T KOG1609|consen   77 SGPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFIN  135 (323)
T ss_pred             CCCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeeccccccee
Confidence            35789999998765432 23333 243   6779999999995  66789999776554

>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=91.71  E-value=0.17  Score=41.23  Aligned_cols=48  Identities=23%  Similarity=0.640  Sum_probs=34.8

Q ss_pred             cCcccccc-ccCCCeeeecCCCCccccHhhHHHHH-hcCCCCCCCCcccc
Q 042990           73 ECVICLSE-FAAGDRLRLLPKCNHGFHVRCIDKWL-SSHSSCPKCRHCLI  120 (165)
Q Consensus        73 ~C~ICl~~-~~~~~~~~~l~~C~H~FH~~Ci~~Wl-~~~~~CP~CR~~~~  120 (165)
                      .|++|... |-+.+.......|+|..|.+|+++-| .+...||.|-..+-
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLR   51 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILR   51 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhh
Confidence            58899876 33444333333499999999999998 55668999966554

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

Probab=91.25  E-value=0.074  Score=48.36  Aligned_cols=47  Identities=34%  Similarity=0.784  Sum_probs=36.7

Q ss_pred             CcCccccccccCCCeeeecCCCCccccHhhHHHHHhc--CCCCCCCCccccccc
Q 042990           72 TECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS--HSSCPKCRHCLIETC  123 (165)
Q Consensus        72 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~~~~~~  123 (165)
                      ..|.+|++ .   +.....+ |+|.|+.+|+..-+..  ...||.||..+.+..
T Consensus       455 ~~c~ic~~-~---~~~~it~-c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~  503 (674)
T KOG1001|consen  455 HWCHICCD-L---DSFFITR-CGHDFCVECLKKSIQQSENAPCPLCRNVLKEKK  503 (674)
T ss_pred             cccccccc-c---ccceeec-ccchHHHHHHHhccccccCCCCcHHHHHHHHHH
Confidence            78999999 2   3355666 9999999999998833  346999999887643

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

Probab=90.90  E-value=0.86  Score=38.69  Aligned_cols=48  Identities=17%  Similarity=0.306  Sum_probs=40.1

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCC---CCCCCCcc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHS---SCPKCRHC  118 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~---~CP~CR~~  118 (165)
                      +-..|||=.+.-.++..+..+. |||+..++-+.+..+++.   -||+|-..
T Consensus       333 SvF~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~e  383 (394)
T KOG2817|consen  333 SVFICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYCPVE  383 (394)
T ss_pred             ceeecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCCCcc
Confidence            4578999998888888899998 999999999999876544   59999443

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

Probab=90.07  E-value=0.094  Score=47.02  Aligned_cols=39  Identities=31%  Similarity=0.647  Sum_probs=29.7

Q ss_pred             CcCccccccccCCC-eeeecCCCCccccHhhHHHHHhcCCCCC
Q 042990           72 TECVICLSEFAAGD-RLRLLPKCNHGFHVRCIDKWLSSHSSCP  113 (165)
Q Consensus        72 ~~C~ICl~~~~~~~-~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP  113 (165)
                      ..|.||+..|-... .++.+ +|||..++.|+..-  .+.+||
T Consensus        12 l~c~ic~n~f~~~~~~Pvsl-~cghtic~~c~~~l--yn~scp   51 (861)
T KOG3161|consen   12 LLCDICLNLFVVQRLEPVSL-QCGHTICGHCVQLL--YNASCP   51 (861)
T ss_pred             hhchHHHHHHHHHhcCcccc-cccchHHHHHHHhH--hhccCC
Confidence            47999998886544 34455 59999999999885  466777

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

Probab=89.92  E-value=0.085  Score=50.53  Aligned_cols=49  Identities=29%  Similarity=0.604  Sum_probs=38.4

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      ....|.||++.+.+-..+  . .|||.++..|+..|+..+..||.|+...-.
T Consensus      1152 ~~~~c~ic~dil~~~~~I--~-~cgh~~c~~c~~~~l~~~s~~~~~ksi~~d 1200 (1394)
T KOG0298|consen 1152 GHFVCEICLDILRNQGGI--A-GCGHEPCCRCDELWLYASSRCPICKSIKGD 1200 (1394)
T ss_pred             cccchHHHHHHHHhcCCe--e-eechhHhhhHHHHHHHHhccCcchhhhhhh
Confidence            345899999998752222  2 399999999999999999999999844433

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=89.67  E-value=0.17  Score=41.36  Aligned_cols=29  Identities=21%  Similarity=0.633  Sum_probs=22.9

Q ss_pred             CCccccHhhHHHHHhcC-------------CCCCCCCccccc
Q 042990           93 CNHGFHVRCIDKWLSSH-------------SSCPKCRHCLIE  121 (165)
Q Consensus        93 C~H~FH~~Ci~~Wl~~~-------------~~CP~CR~~~~~  121 (165)
                      |..++|.+|+.+|+..+             .+||+||+.+.-
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            77899999999998432             259999987654

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

Probab=89.30  E-value=0.34  Score=35.14  Aligned_cols=52  Identities=19%  Similarity=0.373  Sum_probs=35.9

Q ss_pred             CCCcCccccccccCCC--eeeecCCCCccccHhhHHHHH---hcCCCCCCCCccccccc
Q 042990           70 LDTECVICLSEFAAGD--RLRLLPKCNHGFHVRCIDKWL---SSHSSCPKCRHCLIETC  123 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~--~~~~l~~C~H~FH~~Ci~~Wl---~~~~~CP~CR~~~~~~~  123 (165)
                      .-.+|.||.|.-.+..  ++-.  =||-..+.-|-...|   ..+..||+|++++....
T Consensus        79 ~lYeCnIC~etS~ee~FLKPne--CCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~  135 (140)
T PF05290_consen   79 KLYECNICKETSAEERFLKPNE--CCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS  135 (140)
T ss_pred             CceeccCcccccchhhcCCccc--ccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence            3579999999865533  2222  288888877655544   34778999999988653

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

Probab=89.03  E-value=0.31  Score=44.96  Aligned_cols=52  Identities=29%  Similarity=0.560  Sum_probs=37.8

Q ss_pred             CCCCcCccccccccCCCeeeecC-CCC---ccccHhhHHHHH--hcCCCCCCCCccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLP-KCN---HGFHVRCIDKWL--SSHSSCPKCRHCLIE  121 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~-~C~---H~FH~~Ci~~Wl--~~~~~CP~CR~~~~~  121 (165)
                      +++..|-||+.+=.+++..- -| +|.   ...|++|+.+|+  .+...|-.|+.++.-
T Consensus        10 ~d~~~CRICr~e~~~d~pLf-hPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~F   67 (1175)
T COG5183          10 EDKRSCRICRTEDIRDDPLF-HPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKF   67 (1175)
T ss_pred             ccchhceeecCCCCCCCcCc-ccccccchhHHHHHHHHHHHHhcCCCcceeeecceeee
Confidence            45689999999866555432 23 244   578999999999  445679999887764

>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=88.55  E-value=0.69  Score=33.12  Aligned_cols=27  Identities=11%  Similarity=0.347  Sum_probs=13.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHhhccC
Q 042990            2 VLSVLLCALICSLGLNSIIRCVVRCSS   28 (165)
Q Consensus         2 Il~ill~~ll~~~~l~~i~~~~~r~~~   28 (165)
                      |++|+++++..++++++++.|+.||.+
T Consensus        66 i~~Ii~gv~aGvIg~Illi~y~irR~~   92 (122)
T PF01102_consen   66 IIGIIFGVMAGVIGIILLISYCIRRLR   92 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             eeehhHHHHHHHHHHHHHHHHHHHHHh
Confidence            455555555555555555444444333

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.

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

Probab=87.96  E-value=0.22  Score=29.66  Aligned_cols=29  Identities=31%  Similarity=0.699  Sum_probs=21.7

Q ss_pred             CC-ccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           93 CN-HGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        93 C~-H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      |. |..+..|+...+.....||.|..+++.
T Consensus        18 C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt   47 (50)
T PF03854_consen   18 CSDHYLCLNCLTLMLSRSDRCPICGKPLPT   47 (50)
T ss_dssp             -SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred             ecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence            76 999999999999999999999988763

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

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=87.21  E-value=0.51  Score=36.58  Aligned_cols=41  Identities=41%  Similarity=0.834  Sum_probs=28.9

Q ss_pred             CCCcCcccccc-----ccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCC
Q 042990           70 LDTECVICLSE-----FAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCR  116 (165)
Q Consensus        70 ~~~~C~ICl~~-----~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR  116 (165)
                      -+..|-+|.++     |+. +.+...+.|+.+||+.|+.     +..||-|.
T Consensus       151 kGfiCe~C~~~~~IfPF~~-~~~~~C~~C~~v~H~~C~~-----~~~CpkC~  196 (202)
T PF13901_consen  151 KGFICEICNSDDIIFPFQI-DTTVRCPKCKSVFHKSCFR-----KKSCPKCA  196 (202)
T ss_pred             CCCCCccCCCCCCCCCCCC-CCeeeCCcCccccchhhcC-----CCCCCCcH
Confidence            35678888754     233 2455666799999999965     26799993

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

Probab=87.05  E-value=0.25  Score=42.03  Aligned_cols=38  Identities=32%  Similarity=0.663  Sum_probs=28.5

Q ss_pred             CCCcCccccccc-cCCCeeeecCCCCccccHhhHHHHHhc
Q 042990           70 LDTECVICLSEF-AAGDRLRLLPKCNHGFHVRCIDKWLSS  108 (165)
Q Consensus        70 ~~~~C~ICl~~~-~~~~~~~~l~~C~H~FH~~Ci~~Wl~~  108 (165)
                      ...+|.||..+. ...+...... |+|.|+.+|+.+.+..
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~~-C~H~fC~~C~k~~iev  183 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVLK-CGHRFCKDCVKQHIEV  183 (384)
T ss_pred             ccccCccCccccccHhhhHHHhc-ccchhhhHHhHHHhhh
Confidence            467999999554 4435555554 9999999999998853

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

Probab=86.34  E-value=0.31  Score=40.20  Aligned_cols=41  Identities=32%  Similarity=0.667  Sum_probs=26.5

Q ss_pred             cCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcc
Q 042990           73 ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHC  118 (165)
Q Consensus        73 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~  118 (165)
                      .|--|--.+..  .-|+.+ |.|+||-+|-..  ...+.||.|-..
T Consensus        92 fCd~Cd~PI~I--YGRmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~  132 (389)
T KOG2932|consen   92 FCDRCDFPIAI--YGRMIP-CKHVFCLECARS--DSDKICPLCDDR  132 (389)
T ss_pred             eecccCCccee--eecccc-cchhhhhhhhhc--CccccCcCcccH
Confidence            45556444332  346777 999999999654  345678877543

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

Probab=86.31  E-value=0.5  Score=41.93  Aligned_cols=50  Identities=32%  Similarity=0.761  Sum_probs=40.5

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETCQKI  126 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~~~~  126 (165)
                      +..+.|.+|.+++    ..+..+ |.   |..|...|+..+..||+|+..+.++....
T Consensus       477 ~~~~~~~~~~~~~----~~~~~~-~~---~~~~l~~~~~~~~~~pl~~~~~~~~~~~~  526 (543)
T KOG0802|consen  477 EPNDVCAICYQEM----SARITP-CS---HALCLRKWLYVQEVCPLCHTYMKEDDFLS  526 (543)
T ss_pred             cccCcchHHHHHH----Hhcccc-cc---chhHHHhhhhhccccCCCchhhhcccccC
Confidence            4568999999998    245555 77   99999999999999999999888765543

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

Probab=85.63  E-value=0.29  Score=43.63  Aligned_cols=41  Identities=27%  Similarity=0.757  Sum_probs=25.8

Q ss_pred             CCcCcccccc-----ccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCC
Q 042990           71 DTECVICLSE-----FAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKC  115 (165)
Q Consensus        71 ~~~C~ICl~~-----~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~C  115 (165)
                      ...|.+|...     |+ .+.++....|+++||+.|+.+   +..-||.|
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            4567777322     22 233444445999999999655   44459999

>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls

Probab=85.41  E-value=0.78  Score=32.90  Aligned_cols=25  Identities=12%  Similarity=0.139  Sum_probs=11.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhccCC
Q 042990            5 VLLCALICSLGLNSIIRCVVRCSSL   29 (165)
Q Consensus         5 ill~~ll~~~~l~~i~~~~~r~~~~   29 (165)
                      ++++++++++++++++.|+.+|+++
T Consensus         4 l~~iii~~i~l~~~~~~~~~rRR~r   28 (130)
T PF12273_consen    4 LFAIIIVAILLFLFLFYCHNRRRRR   28 (130)
T ss_pred             eHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            3444444444444444444444433

Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].

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

Probab=85.25  E-value=0.68  Score=38.16  Aligned_cols=43  Identities=21%  Similarity=0.576  Sum_probs=32.6

Q ss_pred             CCcCccccccccCCCeeeecCCC--CccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           71 DTECVICLSEFAAGDRLRLLPKC--NHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C--~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      -.+|+||.+.+...   +.  +|  ||+.+..|=.   +....||.||.++-.
T Consensus        48 lleCPvC~~~l~~P---i~--QC~nGHlaCssC~~---~~~~~CP~Cr~~~g~   92 (299)
T KOG3002|consen   48 LLDCPVCFNPLSPP---IF--QCDNGHLACSSCRT---KVSNKCPTCRLPIGN   92 (299)
T ss_pred             hccCchhhccCccc---ce--ecCCCcEehhhhhh---hhcccCCcccccccc
Confidence            36899999999873   33  26  5899988854   356779999998763

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

Probab=84.78  E-value=0.71  Score=36.03  Aligned_cols=40  Identities=30%  Similarity=0.615  Sum_probs=28.4

Q ss_pred             CccccccccCCCeeeecCCCCc-cccHhhHHHHHhcCCCCCCCCccccc
Q 042990           74 CVICLSEFAAGDRLRLLPKCNH-GFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        74 C~ICl~~~~~~~~~~~l~~C~H-~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      |-.|.+.   +..+..+| |.| .+|..|=..    -..||+|+.....
T Consensus       161 Cr~C~~~---~~~VlllP-CrHl~lC~~C~~~----~~~CPiC~~~~~s  201 (207)
T KOG1100|consen  161 CRKCGER---EATVLLLP-CRHLCLCGICDES----LRICPICRSPKTS  201 (207)
T ss_pred             ceecCcC---CceEEeec-ccceEeccccccc----CccCCCCcChhhc
Confidence            8788765   45588898 997 667778432    4559999876543

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

Probab=83.60  E-value=1  Score=41.23  Aligned_cols=42  Identities=24%  Similarity=0.507  Sum_probs=30.5

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCC
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPK  114 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~  114 (165)
                      ...|.+|...+..  ...-.+.|+|.-|.+|+..|+....-||.
T Consensus       779 ~~~CtVC~~vi~G--~~~~c~~C~H~gH~sh~~sw~~~~s~ca~  820 (839)
T KOG0269|consen  779 SAKCTVCDLVIRG--VDVWCQVCGHGGHDSHLKSWFFKASPCAK  820 (839)
T ss_pred             hcCceeecceeee--eEeecccccccccHHHHHHHHhcCCCCcc
Confidence            3478888776543  12223469999999999999988777765

>smart00249 PHD PHD zinc finger

Probab=83.18  E-value=0.9  Score=25.54  Aligned_cols=31  Identities=23%  Similarity=0.570  Sum_probs=21.2

Q ss_pred             cCccccccccCCCeeeecCCCCccccHhhHHH
Q 042990           73 ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDK  104 (165)
Q Consensus        73 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~  104 (165)
                      .|.+|......+..+ .-..|+..||..|+..
T Consensus         1 ~C~~C~~~~~~~~~i-~C~~C~~~~H~~C~~~   31 (47)
T smart00249        1 YCSVCGKPDDGGELL-QCDGCDRWYHQTCLGP   31 (47)
T ss_pred             CcccCCCcCCCCCEE-ECCCCCchhhhhhCCC
Confidence            377888877444344 3335999999999644

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

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

Probab=81.95  E-value=0.78  Score=35.88  Aligned_cols=44  Identities=27%  Similarity=0.712  Sum_probs=34.6

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCc
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRH  117 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~  117 (165)
                      -..|.+|..-.-.+  + ....|+-.+|..|+..++.....||.|-.
T Consensus       181 lk~Cn~Ch~LvIqg--~-rCg~c~i~~h~~c~qty~q~~~~cphc~d  224 (235)
T KOG4718|consen  181 LKNCNLCHCLVIQG--I-RCGSCNIQYHRGCIQTYLQRRDICPHCGD  224 (235)
T ss_pred             HHHHhHhHHHhhee--e-ccCcccchhhhHHHHHHhcccCcCCchhc
Confidence            36899998875542  3 33348899999999999988889999943

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=81.76  E-value=1.7  Score=35.00  Aligned_cols=53  Identities=21%  Similarity=0.260  Sum_probs=38.9

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETCQ  124 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~~  124 (165)
                      ....|+|-.-+|........+..|||+|-..-+.+.  +..+|++|-+.+-+.+-
T Consensus       110 a~fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~dv  162 (293)
T KOG3113|consen  110 ARFICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDDV  162 (293)
T ss_pred             ceeecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccCe
Confidence            346799988888765544444459999999887774  46789999887775443

>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=80.49  E-value=1.1  Score=26.29  Aligned_cols=42  Identities=29%  Similarity=0.664  Sum_probs=27.5

Q ss_pred             CccccccccCCCeeeecCCCCccccHhhHHHHHh------cCCCCCCCC
Q 042990           74 CVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS------SHSSCPKCR  116 (165)
Q Consensus        74 C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~------~~~~CP~CR  116 (165)
                      |.||...-..++.+.-- .|+..||..|+..=..      ....||.|+
T Consensus         2 C~vC~~~~~~~~~i~C~-~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~   49 (51)
T PF00628_consen    2 CPVCGQSDDDGDMIQCD-SCNRWYHQECVGPPEKAEEIPSGDWYCPNCR   49 (51)
T ss_dssp             BTTTTSSCTTSSEEEBS-TTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred             CcCCCCcCCCCCeEEcC-CCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence            88998854444444444 5999999999765432      134577664

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 ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	165
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		2e-12
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		9e-09
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		6e-08
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		2e-06
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		5e-06
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		2e-05

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 25/45 (55%), Positives = 31/45 (68%)
Query: 72  TECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCR 116
            EC +CL+E   G+  R LP+C HGFH  C+D WL SHS+CP CR
Sbjct: 6   VECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50

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

Iteration: 1
 Score = 56.2 bits (134), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 34/51 (66%), Gaps = 1/51 (1%)
Query: 66  NLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCR 116
           N     T CV+C+ +F +   LR+LP CNH FH +C+DKWL ++ +CP CR
Sbjct: 18  NHQSEQTLCVVCMCDFESRQLLRVLP-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 = 53.5 bits (127), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 25/52 (48%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 69  GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI 120
           G   EC +C  ++A G+ +R LP CNH FH  CI  WL  H SCP CR  L 
Sbjct: 13  GSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLT 63

>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 = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 45  NKGIKQKALKTFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDK 104
           N    ++++   P +  + +    G +  C IC SE+  GD    LP C+H FH  C+  
Sbjct: 14  NPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSI 72
Query: 105 WLSSHSSCPKCR 116
           WL    +CP CR
Sbjct: 73  WLQKSGTCPVCR 84

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 21/44 (47%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 73  ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCR 116
           +C ICLS    G+ +R LP C H FH  C+D+WL ++  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 = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 32/61 (52%), Gaps = 4/61 (6%)
Query: 64  ELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETC 123
           ELNL  L   C +CL +F   D L + P C H FH +C+ KWL     CP C   +++  
Sbjct: 11  ELNLHEL---CAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLA 66
Query: 124 Q 124
           Q
Sbjct: 67  Q 67

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	165
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	3e-27
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	6e-27
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	2e-25
2ect_A	78	Ring finger protein 126; metal binding protein, st	9e-22
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	1e-21
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	5e-21
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	2e-16
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	3e-16
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	2e-13
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	1e-11
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	3e-11
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	4e-10
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	3e-09
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	5e-09
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	2e-08
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	3e-08
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	5e-08
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	1e-07
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	1e-07
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	3e-06
3nw0_A	238	Non-structural maintenance of chromosomes element	4e-06
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	5e-06
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	1e-05
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	4e-05
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	4e-05
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	5e-05
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	1e-04
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	1e-04
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	2e-04

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

 Score = 97.0 bits (242), Expect = 3e-27
 Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 1/84 (1%)

Query: 36  ASNSAAILPNKGIKQKALKTFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNH 95
             + + ++ N    ++++   P +  + +    G +  C IC SE+  GD    LP C+H
Sbjct: 5   HHHHSHMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHH 63

Query: 96  GFHVRCIDKWLSSHSSCPKCRHCL 119
            FH  C+  WL    +CP CR   
Sbjct: 64  YFHKPCVSIWLQKSGTCPVCRCMF 87

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

 Score = 95.0 bits (237), Expect = 6e-27
 Identities = 25/50 (50%), Positives = 33/50 (66%)

Query: 71  DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI 120
             EC +CL+E   G+  R LP+C HGFH  C+D WL SHS+CP CR  ++
Sbjct: 5   GVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV 54

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

 Score = 91.6 bits (228), Expect = 2e-25
 Identities = 25/68 (36%), Positives = 38/68 (55%), Gaps = 2/68 (2%)

Query: 50  QKALKTFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSH 109
             +    P   ++   N     T CV+C+ +F +   LR+LP CNH FH +C+DKWL ++
Sbjct: 3   SGSSGQLPSYRFNPN-NHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKAN 60

Query: 110 SSCPKCRH 117
            +CP CR 
Sbjct: 61  RTCPICRA 68

>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 = 82.5 bits (204), Expect = 9e-22
 Identities = 25/52 (48%), Positives = 30/52 (57%), Gaps = 1/52 (1%)

Query: 68  AGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCL 119
            G   EC +C  ++A G+ +R LP CNH FH  CI  WL  H SCP CR  L
Sbjct: 12  VGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSL 62

>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 = 82.0 bits (203), Expect = 1e-21
 Identities = 21/49 (42%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 69  GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRH 117
             + +C ICLS    G+ +R LP C H FH  C+D+WL ++  CP CR 
Sbjct: 12  DTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRV 59

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

 Score = 80.6 bits (199), Expect = 5e-21
 Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 62  SAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE 121
           S ++    L   C +CL +F   D L + P C H FH +C+ KWL     CP C   +++
Sbjct: 6   SGKVKELNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQ 64

Query: 122 TCQK 125
             Q 
Sbjct: 65  LAQL 68

>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 = 68.1 bits (167), Expect = 2e-16
 Identities = 12/46 (26%), Positives = 18/46 (39%)

Query: 71  DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCR 116
            + C ICL +      +  +  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 = 68.4 bits (167), Expect = 3e-16
 Identities = 14/47 (29%), Positives = 25/47 (53%)

Query: 70  LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCR 116
           +   C+ C +E    D + +  +CNH FH  C+  W+  ++ 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 = 60.5 bits (147), Expect = 2e-13
 Identities = 20/52 (38%), Positives = 26/52 (50%), Gaps = 5/52 (9%)

Query: 71  DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET 122
           + EC IC+   A      +LP C H F  +CIDKW   H +CP CR  +   
Sbjct: 15  EEECCICMDGRA----DLILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGA 61

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

 Score = 56.3 bits (136), Expect = 1e-11
 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 3/51 (5%)

Query: 67  LAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRH 117
           +A +   C ICL +    +    LP C H F   CI +W+  + +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 = 56.4 bits (135), Expect = 3e-11
 Identities = 19/87 (21%), Positives = 29/87 (33%), Gaps = 17/87 (19%)

Query: 44  PNKGIKQKALKTFPVVSYSAELNLAGLDTECVIC--------------LSEFAAGDRLRL 89
              G K+  +K +  V+  A      +   C IC               +   + +    
Sbjct: 13  SGAGKKRFEVKKWNAVALWA---WDIVVDNCAICRNHIMDLCIECQANQASATSEECTVA 69

Query: 90  LPKCNHGFHVRCIDKWLSSHSSCPKCR 116
              CNH FH  CI +WL +   CP   
Sbjct: 70  WGVCNHAFHFHCISRWLKTRQVCPLDN 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 = 53.7 bits (128), Expect = 4e-10
 Identities = 11/41 (26%), Positives = 16/41 (39%)

Query: 76  ICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCR 116
              +   + +       CNH FH  CI +WL +   CP   
Sbjct: 67  ANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 107

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

 Score = 49.9 bits (119), Expect = 3e-09
 Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 3/50 (6%)

Query: 71  DTECVICLSEFA---AGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRH 117
              C IC+  ++      RL +  +C H F  +C+   L + ++CP CR 
Sbjct: 15  TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 64

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

 Score = 49.4 bits (118), Expect = 5e-09
 Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 3/52 (5%)

Query: 69  GLDTECVICLSEF---AAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRH 117
           G    C IC+  +       RL +  +C H F  +C+   L + ++CP CR 
Sbjct: 1   GAMVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 52

>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 = 47.9 bits (114), Expect = 2e-08
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 71  DTECVICLSEF---AAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRH 117
              C IC+  +       RL +  +C H F  +C+   L + ++CP CR 
Sbjct: 10  TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 59

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

 Score = 51.0 bits (121), Expect = 3e-08
 Identities = 13/62 (20%), Positives = 22/62 (35%), Gaps = 15/62 (24%)

Query: 71  DTECVICLSEFAAGDRLRLL----PKCNHGFHVRCIDKWLSS-----------HSSCPKC 115
           +  C IC +    G  + L+     KC    H  C+++W  +              CP C
Sbjct: 308 ELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFC 367

Query: 116 RH 117
           + 
Sbjct: 368 KA 369

>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 = 46.8 bits (111), Expect = 5e-08
 Identities = 13/46 (28%), Positives = 17/46 (36%), Gaps = 5/46 (10%)

Query: 73  ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSH--SSCPKCR 116
            C IC S    G        C    H+ C+ K+  S+    CP C 
Sbjct: 17  ICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCN 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 = 46.4 bits (110), Expect = 1e-07
 Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 4/48 (8%)

Query: 73  ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS-SHSSCPKCRHCL 119
            C IC+ +       RL P C+      CI +WL+   + CP CR  L
Sbjct: 24  RCFICMEKL---RDARLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPL 68

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

 Score = 46.8 bits (110), Expect = 1e-07
 Identities = 14/67 (20%), Positives = 26/67 (38%), Gaps = 19/67 (28%)

Query: 71  DTECVICLSEFAAG--------------DRLRLLPKCNHGFHVRCIDKWLSSHS-----S 111
           + +C+IC+ + A                  +  L KC+H FH+ C+     + +      
Sbjct: 25  EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQ 84

Query: 112 CPKCRHC 118
           CP C+  
Sbjct: 85  CPSCKTI 91

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

 Score = 42.0 bits (99), Expect = 3e-06
 Identities = 13/50 (26%), Positives = 19/50 (38%), Gaps = 3/50 (6%)

Query: 73  ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET 122
            C IC            + +C H F   CI +     + CPKC   + +T
Sbjct: 17  LCSICKGYL---IDATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQT 63

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

 Score = 44.3 bits (104), Expect = 4e-06
 Identities = 13/47 (27%), Positives = 18/47 (38%), Gaps = 5/47 (10%)

Query: 73  ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSS--CPKCRH 117
            C IC S    G        C    H+ C+ K+  S++   CP C  
Sbjct: 182 ICNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCND 225

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

 Score = 41.7 bits (98), Expect = 5e-06
 Identities = 11/47 (23%), Positives = 14/47 (29%), Gaps = 4/47 (8%)

Query: 70  LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCR 116
           +   C IC   F          KC H F   C  +   +   C  C 
Sbjct: 14  IPFRCFICRQAFQNPVVT----KCRHYFCESCALEHFRATPRCYICD 56

>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 = 42.8 bits (100), Expect = 1e-05
 Identities = 13/47 (27%), Positives = 16/47 (34%), Gaps = 5/47 (10%)

Query: 71  DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHS-SCPKCR 116
              C IC          ++ P C H     C+  W  S    CP CR
Sbjct: 332 FQLCKICAENDKDV---KIEP-CGHLMCTSCLTSWQESEGQGCPFCR 374

>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 = 39.8 bits (93), Expect = 4e-05
 Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 3/50 (6%)

Query: 73  ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET 122
            CV+C   F        + +C H F   CI ++L +   CP C   + +T
Sbjct: 17  MCVLCGGYF---IDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKT 63

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

 Score = 40.4 bits (94), Expect = 4e-05
 Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 4/49 (8%)

Query: 71  DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCL 119
           + +C+IC   F       +   C H F   CI++W+     CP CR  +
Sbjct: 64  ELQCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDI 108

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

 Score = 38.7 bits (90), Expect = 5e-05
 Identities = 13/49 (26%), Positives = 15/49 (30%), Gaps = 4/49 (8%)

Query: 71  DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCL 119
             EC ICL        L     C H F   C+         C  CR  +
Sbjct: 15  VPECAICLQTCVHPVSL----PCKHVFCYLCVKGASWLGKRCALCRQEI 59

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

 Score = 38.2 bits (89), Expect = 1e-04
 Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 3/44 (6%)

Query: 74  CVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRH 117
           C IC   F       ++P+C+H +   CI K+LS  + CP C  
Sbjct: 25  CGICFEYFNIA---MIIPQCSHNYCSLCIRKFLSYKTQCPTCCV 65

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

 Score = 39.0 bits (90), Expect = 1e-04
 Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 3/62 (4%)

Query: 71  DTECVICLSEFAAGDRLRLLP---KCNHGFHVRCIDKWLSSHSSCPKCRHCLIETCQKII 127
              C IC+  ++   +   L    +C H F  +C+   L + ++CP CR  +       I
Sbjct: 7   TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPI 66

Query: 128 GC 129
             
Sbjct: 67  YI 68

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

 Score = 37.4 bits (86), Expect = 2e-04
 Identities = 10/48 (20%), Positives = 16/48 (33%), Gaps = 1/48 (2%)

Query: 71  DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS-HSSCPKCRH 117
             EC +C+      D       C +     C  +  +  +  CP CR 
Sbjct: 11  PVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRK 58

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	165
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.8
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.69
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.66
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.63
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.61
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.6
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.6
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.54
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.5
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	99.5
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.49
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.48
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.48
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.44
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.44
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.44
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.42
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.42
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.41
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.39
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.38
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.37
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.36
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.36
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.34
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.31
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.29
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.29
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.29
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.29
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.28
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.28
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.27
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.27
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.25
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.24
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.24
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.2
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.2
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.18
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.16
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.15
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.13
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.12
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.1
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.08
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.07
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.06
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.04
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.04
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.02
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.0
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.0
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	98.99
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	98.95
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	98.91
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	98.89
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	98.86
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	98.83
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	98.82
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.8
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	98.73
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	98.69
2ea5_A	68	Cell growth regulator with ring finger domain prot	98.69
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	98.65
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	98.61
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.49
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.44
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.42
3nw0_A	238	Non-structural maintenance of chromosomes element	98.17
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.04
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	97.05
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	96.06
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	95.8
1we9_A	64	PHD finger family protein; structural genomics, PH	95.23
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	94.81
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	94.16
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	93.84
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	93.56
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	93.08
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	92.96
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	92.58
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	91.95
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	91.59
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	91.24
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	91.1
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	90.92
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	90.92
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	90.17
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	89.62
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	89.51
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	88.51
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	88.26
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	87.96
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	87.73
2yt5_A	66	Metal-response element-binding transcription facto	87.67
1wem_A	76	Death associated transcription factor 1; structura	87.5
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	86.72
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	86.37
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	85.71
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	85.47
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	85.29
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	84.6
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	84.49
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	83.84
1weu_A	91	Inhibitor of growth family, member 4; structural g	83.7
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	83.25
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	83.2
2ks1_B	44	Epidermal growth factor receptor; ERBB1, ERBB2, tr	82.95
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	82.63
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	82.32

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

Probab=99.80  E-value=1.2e-19  Score=122.67  Aligned_cols=84  Identities=27%  Similarity=0.664  Sum_probs=74.1

Q ss_pred             CCccccCCCCCCCHHHhhcCCeEeeccccccCCCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCC
Q 042990           37 SNSAAILPNKGIKQKALKTFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCR  116 (165)
Q Consensus        37 ~~~~~~~~~~~~~~~~~~~lp~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR  116 (165)
                      ..........+++++.++.+|...+.......+.+..|+||++.|..++.++.++ |+|.||..||..|++.+.+||+||
T Consensus         6 ~~~~~~~~~~~~s~~~i~~lp~~~~~~~~~~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~Cr   84 (91)
T 2l0b_A            6 HHHSHMVANPPASKESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCR   84 (91)
T ss_dssp             CCSCCSSCCCCCCHHHHHTSCEEECCTTCSSSSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTTTC
T ss_pred             ccCCCCcCCCCCCHHHHHhCCCeeecccccccCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcCcC
Confidence            3555667788999999999999999876655667789999999999999999998 999999999999999999999999


Q ss_pred             ccccc
Q 042990          117 HCLIE  121 (165)
Q Consensus       117 ~~~~~  121 (165)
                      ..+..
T Consensus        85 ~~~~~   89 (91)
T 2l0b_A           85 CMFPP   89 (91)
T ss_dssp             CBSSC
T ss_pred             ccCCC
Confidence            98764

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

Probab=99.69  E-value=7.9e-18  Score=109.51  Aligned_cols=69  Identities=35%  Similarity=0.834  Sum_probs=57.9

Q ss_pred             HhhcCCeEeeccccccCCCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           52 ALKTFPVVSYSAELNLAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        52 ~~~~lp~~~~~~~~~~~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      .++.+|..++.... ....+..|+||++.|..++.++.++ |+|.||..||..|++.+.+||+||+.+.+.
T Consensus         5 ~i~~lp~~~~~~~~-~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~   73 (75)
T 1x4j_A            5 SSGQLPSYRFNPNN-HQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGPS   73 (75)
T ss_dssp             CCSSCCCEEBCSSS-CSSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCCCCC
T ss_pred             hHhhCCcEEecCcc-ccCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcCCCC
Confidence            35677877776543 2345689999999999988899998 999999999999999999999999988753

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

Probab=99.66  E-value=6.3e-17  Score=98.91  Aligned_cols=52  Identities=48%  Similarity=1.204  Sum_probs=47.0

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI  120 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  120 (165)
                      +++.+|+||++.|..++.+..++.|+|.||..||.+|++.+.+||+||..+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            4578999999999998888888679999999999999999999999998764

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

Probab=99.63  E-value=3.2e-16  Score=101.42  Aligned_cols=53  Identities=36%  Similarity=0.946  Sum_probs=48.2

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      ..+..|+||++.|..+..+..++ |+|.||..||..|++.+.+||+||..+.+.
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~   65 (74)
T 2ep4_A           13 NLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQL   65 (74)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSSC
T ss_pred             CCCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCcccccc
Confidence            45789999999999988888888 999999999999999888999999998764

>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=99.61  E-value=7e-16  Score=98.49  Aligned_cols=53  Identities=40%  Similarity=0.934  Sum_probs=47.8

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      ..+..|+||++.|..++.++.++ |+|.||..||..|++.+.+||+||..+...
T Consensus        12 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   64 (69)
T 2kiz_A           12 DTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQ   64 (69)
T ss_dssp             TCCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBSCSC
T ss_pred             CCCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccccCc
Confidence            45678999999999888888998 999999999999999889999999988754

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

Probab=99.60  E-value=3.5e-16  Score=103.46  Aligned_cols=53  Identities=26%  Similarity=0.693  Sum_probs=43.5

Q ss_pred             CCCcCccccccccC-----------CCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           70 LDTECVICLSEFAA-----------GDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        70 ~~~~C~ICl~~~~~-----------~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      +++.|+||+++|.+           ++.++.++.|+|.||.+||.+|++.+.+||+||+.+...
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            45678888888854           455666656999999999999999999999999998754

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

Probab=99.60  E-value=1e-15  Score=100.02  Aligned_cols=53  Identities=47%  Similarity=1.049  Sum_probs=48.2

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      ..+..|+||++.|..+..+..++ |+|.||..||.+|++.+.+||+||..+...
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            45689999999999888888888 999999999999999889999999998864

>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=99.54  E-value=5.1e-15  Score=90.21  Aligned_cols=50  Identities=28%  Similarity=0.629  Sum_probs=43.2

Q ss_pred             CCCcCccccccccCCC-eeeecCCCCccccHhhHHHHHhcCCCCCCCCcccc
Q 042990           70 LDTECVICLSEFAAGD-RLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI  120 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~-~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  120 (165)
                      .+..|+||++.|.+++ .+..++ |+|.||..||..|++.+.+||+||..+.
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            5689999999996644 566777 9999999999999988899999998764

>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=99.50  E-value=1.6e-14  Score=100.81  Aligned_cols=52  Identities=29%  Similarity=0.728  Sum_probs=42.0

Q ss_pred             CCCcCccccccccCCC---------------eeeecCCCCccccHhhHHHHH-----hcCCCCCCCCcccccc
Q 042990           70 LDTECVICLSEFAAGD---------------RLRLLPKCNHGFHVRCIDKWL-----SSHSSCPKCRHCLIET  122 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~---------------~~~~l~~C~H~FH~~Ci~~Wl-----~~~~~CP~CR~~~~~~  122 (165)
                      .++.|+||++.|..+.               .++.++ |+|.||..||..|+     ..+.+||+||..+...
T Consensus        24 ~~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~   95 (114)
T 1v87_A           24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEK   95 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSC
T ss_pred             CCCcCccCChhhcCcccccccccccccCcccceecCC-CCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCC
Confidence            4679999999996643               333666 99999999999999     3467899999988753

>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=100.57  Aligned_cols=51  Identities=27%  Similarity=0.632  Sum_probs=43.0

Q ss_pred             CCCcCccccccccCC--------------C-eeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAG--------------D-RLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~--------------~-~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      .++.|+||++.|...              + .++.++ |+|.||.+||..|++.+.+||+||+.+.-
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~~  101 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEF  101 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCCE
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecc-cCcEECHHHHHHHHHcCCcCcCCCCccee
Confidence            578999999999754              1 245566 99999999999999999999999998653

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

Probab=99.50  E-value=7.6e-15  Score=93.90  Aligned_cols=53  Identities=25%  Similarity=0.651  Sum_probs=45.2

Q ss_pred             CCCCcCccccccccC----CCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAA----GDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~----~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      +++..|+||++.|.+    ++....++ |||.||..||..|++.+.+||+||..+...
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            457899999999875    24456777 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=1.8e-14  Score=91.47  Aligned_cols=52  Identities=23%  Similarity=0.591  Sum_probs=43.9

Q ss_pred             CCCCcCccccccccCC----CeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           69 GLDTECVICLSEFAAG----DRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~----~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      ..+..|+||++.|.+.    ..+..++ |||.||..||..|++.+..||+||..+..
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            3568999999999753    3446777 99999999999999989999999998753

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

Probab=99.48  E-value=1.2e-14  Score=90.91  Aligned_cols=52  Identities=23%  Similarity=0.591  Sum_probs=44.4

Q ss_pred             CCCcCccccccccCC----CeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           70 LDTECVICLSEFAAG----DRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~----~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      ++..|+||++.+.+.    ..+..++ |||.||..||.+|++.+..||+||..+...
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   57 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHK   57 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEET-TSCEEEHHHHHHHHHHCSBCTTTCCBCTTT
T ss_pred             CCCCCCccChhhhCccccCCCEEeCC-CCCchhHHHHHHHHHcCCCCCCCCccCCcc
Confidence            467899999999752    4456777 999999999999999899999999988764

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

Probab=99.48  E-value=3e-14  Score=94.02  Aligned_cols=53  Identities=28%  Similarity=0.659  Sum_probs=44.3

Q ss_pred             CCCCCcCccccccccCCCeeeecCCCC-----ccccHhhHHHHHhcC--CCCCCCCcccccc
Q 042990           68 AGLDTECVICLSEFAAGDRLRLLPKCN-----HGFHVRCIDKWLSSH--SSCPKCRHCLIET  122 (165)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~~~~l~~C~-----H~FH~~Ci~~Wl~~~--~~CP~CR~~~~~~  122 (165)
                      ...++.|.||+++|++++.+ .+| |+     |.||.+||++|+..+  .+||+||..+...
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            34678999999999877766 577 96     999999999999654  5899999998754

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

Probab=99.44  E-value=4e-14  Score=90.89  Aligned_cols=50  Identities=30%  Similarity=0.512  Sum_probs=43.9

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      ..+..|+||++.+.+   ...++ |||.||..||..|+..+..||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   62 (71)
T 2d8t_A           13 LTVPECAICLQTCVH---PVSLP-CKHVFCYLCVKGASWLGKRCALCRQEIPED   62 (71)
T ss_dssp             SSCCBCSSSSSBCSS---EEEET-TTEEEEHHHHHHCTTCSSBCSSSCCBCCHH
T ss_pred             CCCCCCccCCcccCC---CEEcc-CCCHHHHHHHHHHHHCCCcCcCcCchhCHh
Confidence            356789999999876   56777 999999999999999889999999998764

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

Probab=99.44  E-value=1.1e-13  Score=87.87  Aligned_cols=50  Identities=30%  Similarity=0.780  Sum_probs=43.3

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      .+..|+||++.+.+  ....++ |||.||..|+..|++.+.+||+||..+...
T Consensus         4 ~~~~C~IC~~~~~~--~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~   53 (68)
T 1chc_A            4 VAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVESV   53 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCCE
T ss_pred             CCCCCeeCCccccC--CcEecC-CCCeeHHHHHHHHHhCcCcCcCCChhhHhh
Confidence            56799999999875  246777 999999999999999889999999988643

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

Probab=99.44  E-value=2.5e-14  Score=91.44  Aligned_cols=50  Identities=40%  Similarity=0.918  Sum_probs=43.9

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETC  123 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~  123 (165)
                      ..+..|+||++.+.+    ..++ |+|.||..||..|+..+..||+||..+....
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            456899999999877    5677 9999999999999999999999999887643

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

Probab=99.42  E-value=1.2e-13  Score=88.96  Aligned_cols=50  Identities=26%  Similarity=0.525  Sum_probs=43.0

Q ss_pred             CCCCcCccccccccCCCeeeec-CCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLL-PKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l-~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      .++..|+||++.+.+   ...+ + |||.||..||..|++.+..||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (72)
T 2djb_A           13 TPYILCSICKGYLID---ATTITE-CLHTFCKSCIVRHFYYSNRCPKCNIVVHQT   63 (72)
T ss_dssp             CGGGSCTTTSSCCSS---CEECSS-SCCEECHHHHHHHHHHCSSCTTTCCCCCSS
T ss_pred             CCCCCCCCCChHHHC---cCEECC-CCCHHHHHHHHHHHHcCCcCCCcCcccCcc
Confidence            356789999999987   4444 6 999999999999998899999999988764

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

Probab=99.42  E-value=2.9e-13  Score=89.83  Aligned_cols=52  Identities=31%  Similarity=0.631  Sum_probs=44.6

Q ss_pred             CCCCcCccccccccCCCe-eeecCCCCccccHhhHHHHHhcC---CCCCCCCccccc
Q 042990           69 GLDTECVICLSEFAAGDR-LRLLPKCNHGFHVRCIDKWLSSH---SSCPKCRHCLIE  121 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~-~~~l~~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~~~~  121 (165)
                      .++..|+||++.|.+.+. ++.++ |||.||..||..|++.+   ..||+||..+..
T Consensus        13 ~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   68 (88)
T 2ct2_A           13 REVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKITRI   68 (88)
T ss_dssp             CSCCBCTTTCCBCCTTSSCEEECS-SSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCC
T ss_pred             cCCCCCccCCccccccCCCeEECC-CCChhhHHHHHHHHHcCCCCcCCCCCCCcccc
Confidence            456799999999988664 67787 99999999999999765   789999998765

>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=99.41  E-value=1.8e-14  Score=101.53  Aligned_cols=52  Identities=27%  Similarity=0.589  Sum_probs=1.2

Q ss_pred             CCCcCccccccccCC-------------C-eeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAG-------------D-RLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~-------------~-~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      .++.|+||++.|...             + ..+.+..|+|.||.+||.+|++.+.+||+||.++..
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~~  112 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEF  112 (117)
T ss_dssp             CC----------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCCcCceEcHHHHHHHHHcCCcCCCCCCeeee
Confidence            568999999999752             2 222322499999999999999999999999998654

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

Probab=99.39  E-value=3e-13  Score=87.52  Aligned_cols=52  Identities=21%  Similarity=0.528  Sum_probs=42.3

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcC--CCCCCCCccccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSH--SSCPKCRHCLIETC  123 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~--~~CP~CR~~~~~~~  123 (165)
                      ..+..|+||++.|.+   ...++.|||.||..||..|++.+  ..||+||..+...+
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2yur_A           13 PDELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD   66 (74)
T ss_dssp             CGGGSCSSSCCCCTT---CEECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTT
T ss_pred             CCCCCCcCCChHHhC---CeEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCcc
Confidence            356789999999987   45565599999999999999754  68999999766543

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

Probab=99.38  E-value=3.8e-13  Score=88.36  Aligned_cols=48  Identities=21%  Similarity=0.444  Sum_probs=42.2

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI  120 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  120 (165)
                      ..+..|+||++.|.+   +..++ |||.||..||..|++....||+||..+.
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           13 EIPFRCFICRQAFQN---PVVTK-CRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCSBCSSSCSBCCS---EEECT-TSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCcCCCchhcC---eeEcc-CCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            346789999999977   55677 9999999999999998999999999875

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

Probab=99.37  E-value=5.5e-13  Score=85.64  Aligned_cols=50  Identities=24%  Similarity=0.602  Sum_probs=42.4

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHh---cCCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS---SHSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~---~~~~CP~CR~~~~~~  122 (165)
                      ..+..|+||++.+.+   +..++ |||.||..||..|++   .+..||+||..+...
T Consensus        18 ~~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   70 (73)
T 2ysl_A           18 QEEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLCKTSVRKN   70 (73)
T ss_dssp             CCCCBCTTTCSBCSS---EEECT-TCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCC
T ss_pred             ccCCEeccCCcccCC---eEEcC-CCChhhHHHHHHHHHcCCCCCCCCCCCCcCCcc
Confidence            457899999999986   56677 999999999999996   466899999988753

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

Probab=99.36  E-value=5.9e-13  Score=86.46  Aligned_cols=50  Identities=26%  Similarity=0.640  Sum_probs=42.1

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcC--CCCCCCCcccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSH--SSCPKCRHCLIET  122 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~--~~CP~CR~~~~~~  122 (165)
                      ..++|+||.+.+..++...   .|+|.||.+||.+||+.+  .+||+||..+.-.
T Consensus        14 ~i~~C~IC~~~i~~g~~C~---~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~   65 (74)
T 2ct0_A           14 AVKICNICHSLLIQGQSCE---TCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE   65 (74)
T ss_dssp             SSCBCSSSCCBCSSSEECS---SSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSC
T ss_pred             CCCcCcchhhHcccCCccC---CCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCC
Confidence            4589999999998765443   499999999999999876  7899999887743

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

Probab=99.36  E-value=4.3e-13  Score=84.77  Aligned_cols=50  Identities=22%  Similarity=0.549  Sum_probs=41.8

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHH-hcCCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWL-SSHSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl-~~~~~CP~CR~~~~~~  122 (165)
                      .++..|+||++.+.+   ...++ |||.||..||..|+ +.+..||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   63 (66)
T 2ecy_A           13 EDKYKCEKCHLVLCS---PKQTE-CGHRFCESCMAALLSSSSPKCTACQESIVKD   63 (66)
T ss_dssp             CCCEECTTTCCEESS---CCCCS-SSCCCCHHHHHHHHTTSSCCCTTTCCCCCTT
T ss_pred             CcCCCCCCCChHhcC---eeECC-CCCHHHHHHHHHHHHhCcCCCCCCCcCCChh
Confidence            356789999999987   34466 99999999999999 5677899999988753

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

Probab=99.34  E-value=3.6e-13  Score=97.25  Aligned_cols=48  Identities=31%  Similarity=0.814  Sum_probs=42.5

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      ++..|+||++.|.+   +..++ |||.||..||..|+..+.+||+||..+..
T Consensus        52 ~~~~C~iC~~~~~~---~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           52 NELQCIICSEYFIE---AVTLN-CAHSFCSYCINEWMKRKIECPICRKDIKS   99 (138)
T ss_dssp             HHSBCTTTCSBCSS---EEEET-TSCEEEHHHHHHHTTTCSBCTTTCCBCCC
T ss_pred             ccCCCcccCcccCC---ceECC-CCCCccHHHHHHHHHcCCcCCCCCCcCCC
Confidence            34679999999976   66788 99999999999999999999999998864

>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=99.31  E-value=1.1e-12  Score=89.71  Aligned_cols=49  Identities=31%  Similarity=0.726  Sum_probs=42.2

Q ss_pred             CCCcCccccccccCCCeeee-cCCCCccccHhhHHHHHhcC-CCCCCCCcccccc
Q 042990           70 LDTECVICLSEFAAGDRLRL-LPKCNHGFHVRCIDKWLSSH-SSCPKCRHCLIET  122 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~-l~~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~~~~~  122 (165)
                      ++..|+||++.|.+   ++. ++ |||.||..||..|++.+ ..||+||..+...
T Consensus        21 ~~~~C~IC~~~~~~---p~~~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (100)
T 3lrq_A           21 EVFRCFICMEKLRD---ARLCPH-CSKLCCFSCIRRWLTEQRAQCPHCRAPLQLR   71 (100)
T ss_dssp             HHTBCTTTCSBCSS---EEECTT-TCCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CCCCCccCCccccC---ccccCC-CCChhhHHHHHHHHHHCcCCCCCCCCcCCHH
Confidence            46789999999976   556 76 99999999999999776 7999999998653

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

Probab=99.29  E-value=2.6e-12  Score=83.63  Aligned_cols=49  Identities=24%  Similarity=0.529  Sum_probs=42.4

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc-CCCCCCCCccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS-HSSCPKCRHCLIE  121 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~  121 (165)
                      ..+..|+||++.|.+   +..++ |||.||+.||..|+.. +.+||+||..+..
T Consensus         6 ~~~~~C~IC~~~~~~---Pv~~~-CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~   55 (78)
T 1t1h_A            6 PEYFRCPISLELMKD---PVIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSSSCTTTSCCCSS---EEEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             cccCCCCCccccccC---CEEcC-CCCeecHHHHHHHHHHCcCCCCCCcCCCCh
Confidence            357899999999987   56677 9999999999999976 7889999988764

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

Probab=99.29  E-value=1.4e-12  Score=92.35  Aligned_cols=54  Identities=22%  Similarity=0.544  Sum_probs=45.8

Q ss_pred             CCCcCccccccccCC----CeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccccc
Q 042990           70 LDTECVICLSEFAAG----DRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETCQ  124 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~----~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~~  124 (165)
                      ++..|+||++.|.+.    ..+..++ |||.||..||.+|++.+.+||+||..+.....
T Consensus         6 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l   63 (133)
T 4ap4_A            6 GTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   63 (133)
T ss_dssp             CSCBCTTTCCBHHHHHHTTCCEEEET-TCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCE
T ss_pred             CCCCCcccChhhhCccccccCeEecC-CCChhhHHHHHHHHHhCCCCCCCCCcCccccc
Confidence            567999999999763    4457777 99999999999999999999999998876543

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

Probab=99.29  E-value=2.9e-12  Score=84.12  Aligned_cols=49  Identities=31%  Similarity=0.541  Sum_probs=42.1

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc------CCCCCCCCccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS------HSSCPKCRHCLIE  121 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~------~~~CP~CR~~~~~  121 (165)
                      ..+..|+||++.+.+   ...++ |||.||..||..|+..      ...||+||..+..
T Consensus        17 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecw_A           17 KEEVTCPICLELLKE---PVSAD-CNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPF   71 (85)
T ss_dssp             CTTTSCTTTCSCCSS---CEECT-TSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCT
T ss_pred             ccCCCCcCCChhhCc---ceeCC-CCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCH
Confidence            356799999999977   45677 9999999999999976      6789999998765

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

Probab=99.29  E-value=3e-12  Score=80.03  Aligned_cols=43  Identities=28%  Similarity=0.672  Sum_probs=37.0

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHh---cCCCCCCC
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS---SHSSCPKC  115 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~---~~~~CP~C  115 (165)
                      .++..|+||++.+.+   +..++ |||.||..||..|++   .+..||+|
T Consensus        18 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           18 QEEVICPICLDILQK---PVTID-CGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCBCTTTCSBCSS---CEECT-TSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             ccCCCCCcCCchhCC---eEEeC-CCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            457899999999986   56677 999999999999997   45689998

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

Probab=99.28  E-value=3.1e-12  Score=84.04  Aligned_cols=49  Identities=31%  Similarity=0.605  Sum_probs=42.3

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc------CCCCCCCCccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS------HSSCPKCRHCLIE  121 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~------~~~CP~CR~~~~~  121 (165)
                      ..+..|+||++.+.+   ...++ |||.||..|+..|+..      ...||+||..+..
T Consensus        17 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~   71 (85)
T 2ecv_A           17 KEEVTCPICLELLTQ---PLSLD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISYQP   71 (85)
T ss_dssp             CCCCCCTTTCSCCSS---CBCCS-SSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCS
T ss_pred             cCCCCCCCCCcccCC---ceeCC-CCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCH
Confidence            356899999999977   45677 9999999999999976      7789999998875

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

Probab=99.28  E-value=2.3e-12  Score=81.16  Aligned_cols=52  Identities=21%  Similarity=0.507  Sum_probs=41.2

Q ss_pred             CCCcCccccc-cccCCCee-eecCCCCccccHhhHHHHHh-cCCCCCCCCcccccc
Q 042990           70 LDTECVICLS-EFAAGDRL-RLLPKCNHGFHVRCIDKWLS-SHSSCPKCRHCLIET  122 (165)
Q Consensus        70 ~~~~C~ICl~-~~~~~~~~-~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~~~~~  122 (165)
                      ++..|+||++ .+.+.... ..++ |||.||..||.+|+. ....||+||..+...
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   56 (65)
T 1g25_A            2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKS   56 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSC
T ss_pred             CCCcCCcCCCCccCCCccCeecCC-CCCHhHHHHHHHHHHcCCCcCCCCCCccccc
Confidence            3578999999 77765433 3466 999999999999975 456899999988754

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

Probab=99.27  E-value=8.2e-13  Score=86.01  Aligned_cols=49  Identities=29%  Similarity=0.504  Sum_probs=42.1

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc-------CCCCCCCCccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS-------HSSCPKCRHCLIE  121 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-------~~~CP~CR~~~~~  121 (165)
                      .++..|+||++.|.+   +..++ |||.||..||..|++.       ...||+||..+..
T Consensus        10 ~~~~~C~IC~~~~~~---p~~l~-CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~   65 (79)
T 2egp_A           10 QEEVTCPICLELLTE---PLSLD-CGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSF   65 (79)
T ss_dssp             CCCCEETTTTEECSS---CCCCS-SSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCS
T ss_pred             ccCCCCcCCCcccCC---eeECC-CCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCH
Confidence            457899999999977   45677 9999999999999966       5689999998875

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

Probab=99.27  E-value=2.8e-12  Score=87.23  Aligned_cols=48  Identities=31%  Similarity=0.705  Sum_probs=41.9

Q ss_pred             CCCcCccccccccCCCeeeec-CCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLL-PKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l-~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      ++..|+||++.|.+   ...+ + |||.||..||..|+..+..||+||..+..
T Consensus        21 ~~~~C~IC~~~~~~---p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           21 DLLRCGICFEYFNI---AMIIPQ-CSHNYCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             HHTBCTTTCSBCSS---EEECTT-TCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCCCcccCChhhCC---cCEECC-CCCHhhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            45789999999987   4455 6 99999999999999988999999998875

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

Probab=99.25  E-value=4.2e-12  Score=77.80  Aligned_cols=43  Identities=28%  Similarity=0.880  Sum_probs=36.3

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHH---hcCCCCCCC
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWL---SSHSSCPKC  115 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl---~~~~~CP~C  115 (165)
                      .++..|+||++.+.+   ...++ |||.||..||..|+   +.+..||+|
T Consensus        13 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           13 QVEASCSVCLEYLKE---PVIIE-CGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             CCCCBCSSSCCBCSS---CCCCS-SCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             ccCCCCccCCcccCc---cEeCC-CCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            356899999999987   45677 99999999999995   356789998

>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=99.24  E-value=3.8e-12  Score=87.99  Aligned_cols=49  Identities=29%  Similarity=0.624  Sum_probs=42.7

Q ss_pred             CCCcCccccccccCCCeeeec-CCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLL-PKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l-~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      .+..|+||++.|.+   ...+ + |||.||..||..|+..+..||+||..+...
T Consensus        14 ~~~~C~IC~~~~~~---p~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           14 PHLMCVLCGGYFID---ATTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GGTBCTTTSSBCSS---EEEETT-TCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             CcCCCccCChHHhC---cCEeCC-CCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            56899999999976   4555 7 999999999999999889999999988753

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

Probab=99.24  E-value=3.6e-12  Score=90.27  Aligned_cols=53  Identities=25%  Similarity=0.651  Sum_probs=44.9

Q ss_pred             CCCCcCccccccccC----CCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAA----GDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~----~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      +++..|+||++.|.+    +.....++ |||.||..||.+|++.+.+||+||..+.+.
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            456889999999875    23346676 999999999999999999999999998764

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

Probab=99.20  E-value=1.3e-11  Score=82.71  Aligned_cols=49  Identities=22%  Similarity=0.584  Sum_probs=40.7

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc--CCCCCCCCcccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS--HSSCPKCRHCLI  120 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~--~~~CP~CR~~~~  120 (165)
                      .++..|+||++.|.+   +..++.|||.||..||..|+..  +..||+||..+.
T Consensus        11 ~~~~~C~IC~~~~~~---p~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           11 PDELLCLICKDIMTD---AVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CTTTEETTTTEECSS---CEECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CcCCCCCCCChhhcC---ceECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            456899999999986   4566559999999999999954  368999999874

>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=99.20  E-value=1e-11  Score=87.79  Aligned_cols=48  Identities=25%  Similarity=0.481  Sum_probs=41.3

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc-CCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS-HSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~  121 (165)
                      .+..|+||++.|.+   +..++ |||.||..||..|+.. ...||+||..+..
T Consensus        51 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           51 ETFQCICCQELVFR---PITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHTBCTTTSSBCSS---EEECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             cCCCCCcCChHHcC---cEEee-CCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            45789999999986   56677 9999999999999974 4589999998865

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

Probab=99.18  E-value=3.4e-11  Score=78.87  Aligned_cols=55  Identities=20%  Similarity=0.405  Sum_probs=42.2

Q ss_pred             CCCCcCccccccccCCCe-eeecCCCCccccHhhHHHHHh-cCCCCCCCCcccccccc
Q 042990           69 GLDTECVICLSEFAAGDR-LRLLPKCNHGFHVRCIDKWLS-SHSSCPKCRHCLIETCQ  124 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~-~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~~~~~~~  124 (165)
                      +++..|+||++.+...+. ...++ |||.||..|+..|+. .+..||.||..+.....
T Consensus         9 ~~~~~CpICle~~~~~d~~~~p~~-CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~~   65 (78)
T 1e4u_A            9 EDPVECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPEDPA   65 (78)
T ss_dssp             CCCCBCTTTCCBCCTTTTTCCSST-TSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCSS
T ss_pred             ccCCcCCccCccCccccccccccC-CCCCcCHHHHHHHHhcCCCCCCCCCCccCCCch
Confidence            456799999999864332 22244 999999999999984 46789999999886433

>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=2.1e-11  Score=90.28  Aligned_cols=48  Identities=33%  Similarity=0.663  Sum_probs=40.6

Q ss_pred             CCCcCccccccccCCCeeeec-CCCCccccHhhHHHHHhc-CCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLL-PKCNHGFHVRCIDKWLSS-HSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l-~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~  121 (165)
                      .+..|+||++.|.+   ...+ + |||.||..||..|+.. +..||+||..+..
T Consensus        53 ~~~~C~IC~~~~~~---p~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~  102 (165)
T 2ckl_B           53 SELMCPICLDMLKN---TMTTKE-CLHRFCADCIITALRSGNKECPTCRKKLVS  102 (165)
T ss_dssp             HHHBCTTTSSBCSS---EEEETT-TCCEEEHHHHHHHHHTTCCBCTTTCCBCCS
T ss_pred             CCCCCcccChHhhC---cCEeCC-CCChhHHHHHHHHHHhCcCCCCCCCCcCCC
Confidence            34689999999987   4444 6 9999999999999976 7789999998854

>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=99.15  E-value=2.3e-11  Score=84.12  Aligned_cols=49  Identities=31%  Similarity=0.574  Sum_probs=40.8

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcC---CCCCCCCcccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSH---SSCPKCRHCLIET  122 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~~~~~  122 (165)
                      .+..|+||++.+.+   +..++ |||.||..||..|+..+   ..||+||..+...
T Consensus        20 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   71 (112)
T 1jm7_A           20 KILECPICLELIKE---PVSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKR   71 (112)
T ss_dssp             HHTSCSSSCCCCSS---CCBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTT
T ss_pred             CCCCCcccChhhcC---eEECC-CCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHh
Confidence            35689999999976   45577 99999999999999764   4899999987753

>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=99.13  E-value=2.6e-11  Score=85.08  Aligned_cols=50  Identities=32%  Similarity=0.592  Sum_probs=42.1

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcC-CCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSH-SSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~~~~~  122 (165)
                      .++..|+||++.+.+   ...++ |||.||..||..|++.+ ..||+||..+...
T Consensus        16 ~~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (118)
T 3hct_A           16 ESKYECPICLMALRE---AVQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (118)
T ss_dssp             CGGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCcCChhhcC---eEECC-cCChhhHHHHHHHHhhCCCCCCCCCCCcCHH
Confidence            356799999999987   46677 99999999999999664 4999999988753

>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=99.12  E-value=3.2e-11  Score=84.21  Aligned_cols=49  Identities=33%  Similarity=0.517  Sum_probs=42.2

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc-CCCCCCCCcccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS-HSSCPKCRHCLIET  122 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~~  122 (165)
                      ++..|+||++.+.+   +..++ |||.||..||..|+.. +..||+||..+...
T Consensus        22 ~~~~C~IC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   71 (116)
T 1rmd_A           22 KSISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (116)
T ss_dssp             HHTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCcHhcC---cEEcC-CCCcccHHHHHHHHhHCcCcCCCCCCCCCHh
Confidence            35789999999976   55677 9999999999999976 77899999988764

>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=99.10  E-value=5.2e-11  Score=87.18  Aligned_cols=49  Identities=27%  Similarity=0.514  Sum_probs=41.7

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcC-CCCCCCCcccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSH-SSCPKCRHCLIET  122 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~~~~~  122 (165)
                      .+..|+||++.|.+   +..++ |||.||..||..|+..+ ..||+||..+...
T Consensus        77 ~~~~C~IC~~~~~~---pv~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVYQ---PVTTE-CFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCSS---EEECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhhcC---CEEcC-CCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            34689999999987   56677 99999999999999765 4899999988754

>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=99.08  E-value=5.2e-11  Score=75.02  Aligned_cols=48  Identities=23%  Similarity=0.407  Sum_probs=40.7

Q ss_pred             CCCcCccccccccCCCeeeec--CCCCcc-ccHhhHHHHHhcCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLL--PKCNHG-FHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l--~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      ++.+|.||++...+   ...+  | |||. |+..|+..|.+.+..||+||..+..
T Consensus         7 ~~~~C~IC~~~~~~---~~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~   57 (64)
T 2vje_A            7 AIEPCVICQGRPKN---GCIVHGK-TGHLMACFTCAKKLKKRNKPCPVCRQPIQM   57 (64)
T ss_dssp             GGSCCTTTSSSCSC---EEEEETT-EEEEEECHHHHHHHHHTTCCCTTTCCCCCE
T ss_pred             CcCCCCcCCCCCCC---EEEECCC-CCChhhHHHHHHHHHHcCCcCCCcCcchhc
Confidence            46789999998766   3444  8 9999 8999999999888899999998753

>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=99.07  E-value=2.2e-11  Score=84.95  Aligned_cols=48  Identities=27%  Similarity=0.644  Sum_probs=41.4

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc-CCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS-HSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~  121 (165)
                      ++..|+||++.|.+   +..++ |||.||..||..|+.. +..||+||..+..
T Consensus        14 ~~~~C~iC~~~~~~---p~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           14 SECQCGICMEILVE---PVTLP-CNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             HHHBCTTTCSBCSS---CEECT-TSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCccCCcccCc---eeEcC-CCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            35789999999976   56677 9999999999999965 6789999998874

>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=99.06  E-value=1.3e-10  Score=96.68  Aligned_cols=50  Identities=26%  Similarity=0.606  Sum_probs=43.5

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHh-cCCCCCCCCccccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS-SHSSCPKCRHCLIETC  123 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~~~~~~  123 (165)
                      ....|+||++.+.+   +..++ |||.||..|+..|+. .+..||+||..+....
T Consensus       331 ~~~~C~ICle~~~~---pv~lp-CGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~~  381 (389)
T 2y1n_A          331 TFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE  381 (389)
T ss_dssp             SSSBCTTTSSSBCC---EEEET-TCCEECHHHHHHHHHHTCSBCTTTCCBCCEEE
T ss_pred             CCCCCCccCcCCCC---eEEeC-CCChhhHHHHHHHHhcCCCCCCCCCCccCCce
Confidence            45799999999866   67788 999999999999997 6889999999988643

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

Probab=99.04  E-value=2.1e-10  Score=76.15  Aligned_cols=48  Identities=17%  Similarity=0.063  Sum_probs=43.5

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      .+..|+||++-|.+   +..++ |||.|++.||..|+..+.+||+||..+..
T Consensus        13 ~~~~CpI~~~~m~d---PV~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   60 (85)
T 2kr4_A           13 DEFRDPLMDTLMTD---PVRLP-SGTVMDRSIILRHLLNSPTDPFNRQMLTE   60 (85)
T ss_dssp             TTTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             hheECcccCchhcC---CeECC-CCCEECHHHHHHHHhcCCCCCCCcCCCCh
Confidence            56899999999998   77888 99999999999999888899999988764

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

Probab=99.04  E-value=7.1e-11  Score=72.34  Aligned_cols=47  Identities=26%  Similarity=0.469  Sum_probs=39.8

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      .++..|+||++.|.+   ++.++ |||.||..|+..|   ...||+||..+...
T Consensus         4 ~~~~~C~IC~~~~~~---p~~l~-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~   50 (56)
T 1bor_A            4 FQFLRCQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLG   50 (56)
T ss_dssp             CCCSSCSSSCSSCBC---CSCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCC
T ss_pred             ccCCCceEeCCccCC---eEEcC-CCCcccHHHHccC---CCCCCcCCcEeecC
Confidence            456789999999987   57788 9999999999884   67899999987753

>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=99.02  E-value=7.6e-11  Score=85.47  Aligned_cols=49  Identities=24%  Similarity=0.421  Sum_probs=41.4

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcC-CCCCCCCccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSH-SSCPKCRHCLIE  121 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~-~~CP~CR~~~~~  121 (165)
                      +.+..|+||++.+.+   +..++ |||.||..||..|++.+ ..||+||.++..
T Consensus        29 ~~~~~C~IC~~~~~~---pv~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~   78 (141)
T 3knv_A           29 EAKYLCSACRNVLRR---PFQAQ-CGHRYCSFCLASILSSGPQNCAACVHEGIY   78 (141)
T ss_dssp             CGGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHGGGSCEECHHHHHTTCC
T ss_pred             CcCcCCCCCChhhcC---cEECC-CCCccCHHHHHHHHhcCCCCCCCCCCcccc
Confidence            467899999999987   45676 99999999999999755 489999998653

>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=99.00  E-value=1.5e-10  Score=72.68  Aligned_cols=48  Identities=19%  Similarity=0.397  Sum_probs=40.2

Q ss_pred             CCCcCccccccccCCCeeeec--CCCCcc-ccHhhHHHHHhcCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLL--PKCNHG-FHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l--~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      .+..|.||++...+   ...+  | |||. |+..|+..|.+.+..||+||..+..
T Consensus         6 ~~~~C~IC~~~~~~---~~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~~   56 (63)
T 2vje_B            6 LLKPCSLCEKRPRD---GNIIHGR-TGHLVTCFHCARRLKKAGASCPICKKEIQL   56 (63)
T ss_dssp             GGSBCTTTSSSBSC---EEEEETT-EEEEEECHHHHHHHHHTTCBCTTTCCBCCE
T ss_pred             cCCCCcccCCcCCC---eEEEecC-CCCHhHHHHHHHHHHHhCCcCCCcCchhhc
Confidence            46789999998765   3344  7 9998 9999999999888899999998853

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B

Probab=99.00  E-value=2.6e-10  Score=78.00  Aligned_cols=48  Identities=17%  Similarity=0.058  Sum_probs=43.4

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      .+..|+||++-|.+   +..++ |||.|++.||..|+..+.+||+||..+..
T Consensus        28 ~~~~CpI~~~~m~d---PV~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   75 (100)
T 2kre_A           28 DEFRDPLMDTLMTD---PVRLP-SGTIMDRSIILRHLLNSPTDPFNRQTLTE   75 (100)
T ss_dssp             TTTBCTTTCSBCSS---EEEET-TTEEEEHHHHHHHTTSCSBCSSSCCBCCT
T ss_pred             HhhCCcCccCcccC---CeECC-CCCEEchHHHHHHHHcCCCCCCCCCCCCh
Confidence            56899999999998   77888 99999999999999888899999988764

>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=98.99  E-value=3.8e-10  Score=76.91  Aligned_cols=48  Identities=19%  Similarity=0.064  Sum_probs=43.2

Q ss_pred             CCCcCccccccccCCCeeeecCCCC-ccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCN-HGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~-H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      .+..|+||++.|.+   +..++ || |.|++.||..|+..+.+||+||..+..
T Consensus        21 ~~~~CpI~~~~m~d---PV~~~-cG~htf~r~cI~~~l~~~~~cP~~~~~l~~   69 (98)
T 1wgm_A           21 DEFLDPIMSTLMCD---PVVLP-SSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             TTTBCTTTCSBCSS---EEECT-TTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             HhcCCcCccccccC---CeECC-CCCeEECHHHHHHHHHhCCCCCCCCCCCCh
Confidence            56899999999998   67787 99 999999999999888899999988764

>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=98.95  E-value=1.9e-10  Score=80.49  Aligned_cols=45  Identities=22%  Similarity=0.496  Sum_probs=39.4

Q ss_pred             CCCcCccccccccCCCeeeec-CCCCccccHhhHHHHHhcCCCCCCCCcccc
Q 042990           70 LDTECVICLSEFAAGDRLRLL-PKCNHGFHVRCIDKWLSSHSSCPKCRHCLI  120 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l-~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  120 (165)
                      .+..|+||++.|.+   +..+ + |||.||..||..|+.  ..||+||..+.
T Consensus        21 ~~~~C~IC~~~~~~---pv~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~   66 (117)
T 1jm7_B           21 KLLRCSRCTNILRE---PVCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAW   66 (117)
T ss_dssp             HTTSCSSSCSCCSS---CBCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCS
T ss_pred             hCCCCCCCChHhhC---ccEeCC-CCCHHHHHHHHHHhc--CCCcCCCCcCc
Confidence            46799999999977   5566 6 999999999999987  78999999874

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

Probab=98.91  E-value=3.7e-10  Score=92.27  Aligned_cols=54  Identities=24%  Similarity=0.597  Sum_probs=40.6

Q ss_pred             CCCCcCccccccccCCC-eeee---cCCCCccccHhhHHHHHhcC-----------CCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGD-RLRL---LPKCNHGFHVRCIDKWLSSH-----------SSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~-~~~~---l~~C~H~FH~~Ci~~Wl~~~-----------~~CP~CR~~~~~~  122 (165)
                      +...+|+||++.+.++. .+..   .++|+|.||..|+.+||++.           ..||+||.++.-.
T Consensus       306 e~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~s  374 (381)
T 3k1l_B          306 NEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTS  374 (381)
T ss_dssp             CSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGG
T ss_pred             cCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCcc
Confidence            45679999999998733 2211   23599999999999999652           2599999987644

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

Probab=98.89  E-value=3.7e-10  Score=72.92  Aligned_cols=45  Identities=24%  Similarity=0.617  Sum_probs=38.9

Q ss_pred             CCCcCccccccccCCCeeeecCCCCcc-ccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHG-FHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      ++..|+||++.+.+   +..++ |||. |+..|+..|    ..||+||..+...
T Consensus        23 ~~~~C~iC~~~~~~---~~~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~   68 (74)
T 4ic3_A           23 EEKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEAV----DKCPMCYTVITFK   68 (74)
T ss_dssp             HHTBCTTTSSSBCC---EEEET-TCCBCCCHHHHTTC----SBCTTTCCBCSEE
T ss_pred             cCCCCCCCCCCCCC---EEEcC-CCChhHHHHhhhcC----ccCCCcCcCccCc
Confidence            45789999999876   67788 9999 999999998    8899999988653

>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=98.86  E-value=1.2e-09  Score=80.99  Aligned_cols=50  Identities=32%  Similarity=0.588  Sum_probs=42.2

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc-CCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS-HSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~~  122 (165)
                      .++..|+||++.+.+   +..++ |||.|+..||..|++. +..||+||..+...
T Consensus        16 ~~~~~C~IC~~~~~~---pv~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~   66 (170)
T 3hcs_A           16 ESKYECPICLMALRE---AVQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLEN   66 (170)
T ss_dssp             CGGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCCCCCCCChhhcC---cEECC-CCCHHHHHHHHHHHHhCCCCCCCCccCcchh
Confidence            356899999999987   46677 9999999999999965 45999999988753

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

Probab=98.83  E-value=2.4e-09  Score=66.58  Aligned_cols=48  Identities=23%  Similarity=0.585  Sum_probs=36.9

Q ss_pred             CCCCcCccccccccCCCeeeecCCCC--c---cccHhhHHHHHh--cCCCCCCCCcccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCN--H---GFHVRCIDKWLS--SHSSCPKCRHCLI  120 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~--H---~FH~~Ci~~Wl~--~~~~CP~CR~~~~  120 (165)
                      +++..|.||+++..+  .. .+| |.  +   .||..|+.+|+.  ++.+||+|+..+.
T Consensus         4 ~~~~~CrIC~~~~~~--~l-~~P-C~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~   58 (60)
T 1vyx_A            4 EDVPVCWICNEELGN--ER-FRA-CGCTGELENVHRSCLSTWLTISRNTACQICGVVYN   58 (60)
T ss_dssp             CSCCEETTTTEECSC--CC-CCS-CCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCC
T ss_pred             CCCCEeEEeecCCCC--ce-ecC-cCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeee
Confidence            356789999998432  33 466 65  4   999999999995  3678999998764

>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=98.82  E-value=3.3e-09  Score=71.54  Aligned_cols=46  Identities=24%  Similarity=0.476  Sum_probs=38.4

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcC------CCCCC--CCcc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSH------SSCPK--CRHC  118 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~------~~CP~--CR~~  118 (165)
                      .+..|+||++.|.+   +..++.|||.|++.||..|+..+      .+||+  |+..
T Consensus         6 ~~~~CPI~~~~~~d---PV~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~   59 (94)
T 2yu4_A            6 SGFTCPITKEEMKK---PVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHT   59 (94)
T ss_dssp             SCCBCTTTCSBCSS---EEEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCC
T ss_pred             cEeECcCcCchhcC---CEEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCccc
Confidence            46789999999987   56663499999999999999653      58999  9865

>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=98.80  E-value=3.9e-09  Score=83.15  Aligned_cols=48  Identities=15%  Similarity=0.081  Sum_probs=41.8

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc-CCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS-HSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~  121 (165)
                      .+..|+||++.|.+   +..++ |||.|++.||..|+.. +.+||+||.++..
T Consensus       207 ~~~~c~i~~~~~~d---Pv~~~-~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~  255 (281)
T 2c2l_A          207 DYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQ  255 (281)
T ss_dssp             STTBCTTTCSBCSS---EEECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             cccCCcCcCCHhcC---CeECC-CCCEECHHHHHHHHHHCCCCCcCCCCCCch
Confidence            56789999999988   77888 9999999999999965 5569999998864

>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=98.73  E-value=5.3e-09  Score=70.28  Aligned_cols=51  Identities=25%  Similarity=0.632  Sum_probs=41.2

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc--------CCCCCC--CCcc--ccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS--------HSSCPK--CRHC--LIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~--------~~~CP~--CR~~--~~~  121 (165)
                      ....|+||++.+...+.....+ |||.|+.+|+..|+..        ...||.  |+..  +.+
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~-CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~~~~~~   66 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQGHLQE   66 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSCCEECH
T ss_pred             CCcCCcccCcccccccceEcCC-CCCcccHHHHHHHHHHHhhcCCcccccCccccCCCCCccCH
Confidence            4578999999998776666666 9999999999999853        236999  9988  544

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

Probab=98.69  E-value=7e-09  Score=66.93  Aligned_cols=44  Identities=25%  Similarity=0.634  Sum_probs=36.8

Q ss_pred             CCCcCccccccccCCCeeeecCCCCcc-ccHhhHHHHHhcCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHG-FHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      ++..|+||++.+.+   +..++ |||. |+..|+..    ...||+||..+..
T Consensus        24 ~~~~C~IC~~~~~~---~~~~p-CgH~~~C~~C~~~----~~~CP~Cr~~i~~   68 (75)
T 2ecg_A           24 EEKLCKICMDRNIA---IVFVP-CGHLVTCKQCAEA----VDKCPMCYTVITF   68 (75)
T ss_dssp             HHHSCSSSCSSCCC---BCCSS-SCCCCBCHHHHHH----CSBCTTTCCBCCC
T ss_pred             CCCCCCcCCCCCCC---EEEec-CCCHHHHHHHhhC----CCCCccCCceecC
Confidence            35689999999876   66788 9999 99999964    4789999998865

>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=2e-08  Score=63.85  Aligned_cols=46  Identities=30%  Similarity=0.754  Sum_probs=38.7

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCcc-ccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHG-FHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      .++..|.||++...+   +..+| |||. |+..|+..    ...||+||..+...
T Consensus        13 ~~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~----~~~CP~CR~~i~~~   59 (68)
T 2ea5_A           13 ENSKDCVVCQNGTVN---WVLLP-CRHTCLCDGCVKY----FQQCPMCRQFVQES   59 (68)
T ss_dssp             CCSSCCSSSSSSCCC---CEETT-TTBCCSCTTHHHH----CSSCTTTCCCCCCE
T ss_pred             CCCCCCCCcCcCCCC---EEEEC-CCChhhhHHHHhc----CCCCCCCCcchhce
Confidence            356789999998766   77888 9999 99999884    57899999988764

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

Probab=98.65  E-value=1.7e-08  Score=75.87  Aligned_cols=49  Identities=14%  Similarity=0.059  Sum_probs=42.0

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc-CCCCCCCCccccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS-HSSCPKCRHCLIE  121 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~  121 (165)
                      ..+..|+||++.|.+   +..++ |||.|++.||..|+.. +.+||+|+..+..
T Consensus       104 p~~f~CPI~~elm~D---PV~~~-~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~  153 (179)
T 2f42_A          104 PDYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFDPVTRSPLTQ  153 (179)
T ss_dssp             CGGGBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCG
T ss_pred             cHhhcccCccccCCC---CeECC-CCCEECHHHHHHHHHhCCCCCCCCcCCCCh
Confidence            356789999999998   67777 9999999999999965 4579999988754

>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=98.61  E-value=8.5e-09  Score=67.41  Aligned_cols=45  Identities=27%  Similarity=0.602  Sum_probs=38.4

Q ss_pred             CCCcCccccccccCCCeeeecCCCCcc-ccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHG-FHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      ++..|.||++.+.+   +..+| |||. |+..|+..|    ..||+||..+...
T Consensus        17 ~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~   62 (79)
T 2yho_A           17 EAMLCMVCCEEEIN---STFCP-CGHTVCCESCAAQL----QSCPVCRSRVEHV   62 (79)
T ss_dssp             HHTBCTTTSSSBCC---EEEET-TCBCCBCHHHHTTC----SBCTTTCCBCCEE
T ss_pred             CCCEeEEeCcccCc---EEEEC-CCCHHHHHHHHHhc----CcCCCCCchhhCe
Confidence            45689999998776   67888 9999 999999887    3899999988764

>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=98.49  E-value=7.7e-08  Score=59.83  Aligned_cols=48  Identities=13%  Similarity=0.081  Sum_probs=41.0

Q ss_pred             CCcCccccccccCCCeeeec-CCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           71 DTECVICLSEFAAGDRLRLL-PKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l-~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      ...|+||++.|.+   +..+ + +||.|.+.||.+|++++.+||+.+..+...
T Consensus         3 ~~~CpIs~~~m~d---PV~~~~-sG~~yer~~I~~~l~~~~~cP~t~~~L~~~   51 (61)
T 2bay_A            3 HMLCAISGKVPRR---PVLSPK-SRTIFEKSLLEQYVKDTGNDPITNEPLSIE   51 (61)
T ss_dssp             -CCCTTTCSCCSS---EEEETT-TTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             eEEecCCCCCCCC---CEEeCC-CCcEEcHHHHHHHHHhCCCCcCCcCCCChh
Confidence            4689999999987   5566 5 999999999999998777899999988754

>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=98.44  E-value=4.5e-08  Score=80.47  Aligned_cols=44  Identities=23%  Similarity=0.675  Sum_probs=38.7

Q ss_pred             CCCcCccccccccCCCeeeecCCCCcc-ccHhhHHHHHhcCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHG-FHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~-FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      .+..|+||++.+.+   +..+| |||. ||..|+..|    ..||+||..+..
T Consensus       294 ~~~~C~IC~~~~~~---~v~lp-CgH~~fC~~C~~~~----~~CP~CR~~i~~  338 (345)
T 3t6p_A          294 EERTCKVCMDKEVS---VVFIP-CGHLVVCQECAPSL----RKCPICRGIIKG  338 (345)
T ss_dssp             TTCBCTTTSSSBCC---EEEET-TCCEEECTTTGGGC----SBCTTTCCBCCE
T ss_pred             CCCCCCccCCcCCc---eEEcC-CCChhHhHHHHhcC----CcCCCCCCCccC
Confidence            56799999999877   67788 9999 999999988    789999998764

>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=98.42  E-value=1.1e-07  Score=75.10  Aligned_cols=49  Identities=27%  Similarity=0.568  Sum_probs=39.2

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcC--CCCCC--CCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSH--SSCPK--CRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~--~~CP~--CR~~~~~  121 (165)
                      .+..|+||++.|.+  .++... |||.|++.||..|+..+  ..||+  ||..+..
T Consensus       180 ~el~CPIcl~~f~D--PVts~~-CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~  232 (267)
T 3htk_C          180 IELTCPITCKPYEA--PLISRK-CNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSM  232 (267)
T ss_dssp             CCSBCTTTSSBCSS--EEEESS-SCCEEEHHHHHHHSTTCSCEECSGGGCSCEECG
T ss_pred             eeeECcCccCcccC--CeeeCC-CCCcccHHHHHHHHHhCCCCCCCcccccCcCch
Confidence            44679999999977  233345 99999999999999653  47999  9987654

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

Probab=98.17  E-value=1.4e-06  Score=68.15  Aligned_cols=50  Identities=26%  Similarity=0.621  Sum_probs=40.4

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcC--CCCCCCCcccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSH--SSCPKCRHCLIET  122 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~--~~CP~CR~~~~~~  122 (165)
                      ....|.||.+-...+.   ..+.|+|.||..|+..|++.+  ..||.|+..+.-.
T Consensus       179 ~i~~C~iC~~iv~~g~---~C~~C~~~~H~~C~~~~~~~~~~~~CP~C~~~W~~~  230 (238)
T 3nw0_A          179 AVKICNICHSLLIQGQ---SCETCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE  230 (238)
T ss_dssp             TCCBCTTTCSBCSSCE---ECSSSCCEECHHHHHHHTTTCSSCBCTTTCCBCCSC
T ss_pred             CCCcCcchhhHHhCCc---ccCccChHHHHHHHHHHHHhCCCCCCCCCCCCCCCC
Confidence            4678999999988753   333499999999999999764  4899999987654

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

Probab=98.04  E-value=3.5e-06  Score=56.95  Aligned_cols=49  Identities=24%  Similarity=0.447  Sum_probs=39.3

Q ss_pred             cCccccccccCCCeeeecCCCCccccHhhHHHHH-hcCCCCCCCCcccccccc
Q 042990           73 ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWL-SSHSSCPKCRHCLIETCQ  124 (165)
Q Consensus        73 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl-~~~~~CP~CR~~~~~~~~  124 (165)
                      -|.+|--.+..  ..|..| |+|+|+-+|+..|. ++.++||.|+..+...+.
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            47777766654  578888 99999999999998 457899999998875544

>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=96.06  E-value=0.0079  Score=39.20  Aligned_cols=35  Identities=23%  Similarity=0.465  Sum_probs=24.8

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHH
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKW  105 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~W  105 (165)
                      ..|+.|.||- .+..++....- .|+-+||..|+.+-
T Consensus        13 ~~D~~C~VC~-~~t~~~l~pCR-vC~RvfH~~CL~r~   47 (89)
T 1wil_A           13 VNDEMCDVCE-VWTAESLFPCR-VCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTTC-CCCSSCCSSCS-SSSSCCCHHHHHHH
T ss_pred             CCCcccCccc-cccccceeccc-cccccccHhhcccc
Confidence            4789999995 34443333233 39999999999996

>2lri_C Autoimmune regulator; Zn binding protein domain, apeced, transcription; NMR {Homo sapiens}

Probab=95.80  E-value=0.0076  Score=37.57  Aligned_cols=47  Identities=23%  Similarity=0.419  Sum_probs=33.8

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc----CCCCCCCCccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS----HSSCPKCRHCL  119 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~~  119 (165)
                      ..+..|.||.+.   ++ +.....|...||..|++..+..    .-.||.|+...
T Consensus        10 ~~~~~C~vC~~~---~~-ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C           10 APGARCGVCGDG---TD-VLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             CTTCCCTTTSCC---TT-CEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCCcCCCCCC---Ce-EEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            356789999853   33 4444469999999999887743    34799996543

>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=95.23  E-value=0.0034  Score=38.65  Aligned_cols=49  Identities=24%  Similarity=0.546  Sum_probs=35.4

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHh-----cCCCCCCCCc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS-----SHSSCPKCRH  117 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-----~~~~CP~CR~  117 (165)
                      +++..|++|...+.++...+..-.|...||..|+..-..     ....||.|+.
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            356779999999876555555556999999999865421     3457999965

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

Probab=94.81  E-value=0.022  Score=37.74  Aligned_cols=34  Identities=15%  Similarity=0.358  Sum_probs=25.8

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhHHHH
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKW  105 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~W  105 (165)
                      +..|.||++.+.......-+. |+|.|+..|+..+
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            568999998754333333476 9999999999984

>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=94.16  E-value=0.023  Score=42.40  Aligned_cols=49  Identities=22%  Similarity=0.436  Sum_probs=35.9

Q ss_pred             CcCccccccccCCCe---eeecCCCCccccHhhHHHH------Hh-----cCCCCCCCCcccc
Q 042990           72 TECVICLSEFAAGDR---LRLLPKCNHGFHVRCIDKW------LS-----SHSSCPKCRHCLI  120 (165)
Q Consensus        72 ~~C~ICl~~~~~~~~---~~~l~~C~H~FH~~Ci~~W------l~-----~~~~CP~CR~~~~  120 (165)
                      ..|+||...|.+++.   .+....|...||..|+.--      +.     ....||.|+..-.
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            469999999988762   4555569999999997431      11     2678999987644

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=93.84  E-value=0.014  Score=37.00  Aligned_cols=51  Identities=20%  Similarity=0.353  Sum_probs=35.5

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHh----cCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS----SHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~----~~~~CP~CR~~~~~  121 (165)
                      +...|.+|..... ++..+..-.|...||..|+..-..    ....||.|+..+..
T Consensus        17 ~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~k   71 (75)
T 2k16_A           17 QIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKK   71 (75)
T ss_dssp             EEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHCS
T ss_pred             CCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchhh
Confidence            3457999988764 333444445999999999876542    24569999776543

>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=93.56  E-value=0.057  Score=33.38  Aligned_cols=36  Identities=25%  Similarity=0.419  Sum_probs=27.1

Q ss_pred             CCCCcCccccccccCCCeeeecC-CCCccccHhhHHH
Q 042990           69 GLDTECVICLSEFAAGDRLRLLP-KCNHGFHVRCIDK  104 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~-~C~H~FH~~Ci~~  104 (165)
                      +....|.+|...+.+++..+..- .|...||..|+.-
T Consensus         6 ~~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvgl   42 (65)
T 2vpb_A            6 DPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTGM   42 (65)
T ss_dssp             ---CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHTC
T ss_pred             CCcCcCccCCCccCCCCCeEecccCccccCchhccCC
Confidence            35678999999998776666665 6999999999753

>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=93.08  E-value=0.038  Score=32.48  Aligned_cols=44  Identities=16%  Similarity=0.285  Sum_probs=31.2

Q ss_pred             cCccccccccCCCeeeecC-CCCccccHhhHHHHH----hcCCCCCCCC
Q 042990           73 ECVICLSEFAAGDRLRLLP-KCNHGFHVRCIDKWL----SSHSSCPKCR  116 (165)
Q Consensus        73 ~C~ICl~~~~~~~~~~~l~-~C~H~FH~~Ci~~Wl----~~~~~CP~CR  116 (165)
                      .|.+|...+.+++..+..- .|...||..|+.--.    ..+..||.|+
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            4779999987666555554 599999999976422    2566799885

>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=92.96  E-value=0.099  Score=33.35  Aligned_cols=48  Identities=19%  Similarity=0.470  Sum_probs=33.3

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhHHHHHh-----cCCCCCCCCccc
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS-----SHSSCPKCRHCL  119 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-----~~~~CP~CR~~~  119 (165)
                      ...| ||...+.++...+....|...||..|+.---.     ....||.|+...
T Consensus        12 ~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   64 (79)
T 1wep_A           12 PVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             ccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCccccc
Confidence            4556 99998864444444446999999999864221     355799998754

>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=92.58  E-value=0.044  Score=37.23  Aligned_cols=47  Identities=23%  Similarity=0.581  Sum_probs=32.2

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHh----cCCCCCCCC
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS----SHSSCPKCR  116 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~----~~~~CP~CR  116 (165)
                      .+++.|.||.+.-+..+.+.- ..|+..||..|+...+.    ....||.|+
T Consensus         5 ~~~~~C~~C~~~g~~~~ll~C-~~C~~~~H~~Cl~~~~~~~~~~~W~C~~C~   55 (111)
T 2ysm_A            5 SSGANCAVCDSPGDLLDQFFC-TTCGQHYHGMCLDIAVTPLKRAGWQCPECK   55 (111)
T ss_dssp             CCCSCBTTTCCCCCTTTSEEC-SSSCCEECTTTTTCCCCTTTSTTCCCTTTC
T ss_pred             CCCCCCcCCCCCCCCcCCeEC-CCCCCCcChHHhCCccccccccCccCCcCC
Confidence            467899999887433333433 45999999999988763    233566664

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=91.95  E-value=0.095  Score=31.81  Aligned_cols=45  Identities=27%  Similarity=0.746  Sum_probs=32.0

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHh----cCCCCCCCCc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS----SHSSCPKCRH  117 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~----~~~~CP~CR~  117 (165)
                      ..+..|.+|.+.   ++ +.....|...||..|+..-+.    ..-.||.|+.
T Consensus         9 ~~~~~C~vC~~~---g~-ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~   57 (61)
T 2l5u_A            9 DHQDYCEVCQQG---GE-IILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEK   57 (61)
T ss_dssp             CCCSSCTTTSCC---SS-EEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGG
T ss_pred             CCCCCCccCCCC---Cc-EEECCCCChhhhhhccCCCCCCCCCCceECccccc
Confidence            457889999873   33 444445999999999987442    2446999965

>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=91.59  E-value=0.053  Score=40.08  Aligned_cols=46  Identities=28%  Similarity=0.571  Sum_probs=33.4

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc----CCCCCCCCccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS----HSSCPKCRHCL  119 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~~  119 (165)
                      +++.|.+|.+.   ++ +.....|...||..|+..-+..    ...||.|+..-
T Consensus         3 ~~~~C~~C~~~---g~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   52 (184)
T 3o36_A            3 NEDWCAVCQNG---GE-LLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLS   52 (184)
T ss_dssp             SCSSCTTTCCC---SS-CEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCccccCCCC---Ce-eeecCCCCcccCccccCCCCCCCCCCCEECccccCcc
Confidence            56889999854   33 4455569999999998766532    44699997643

>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=91.24  E-value=0.057  Score=40.71  Aligned_cols=47  Identities=30%  Similarity=0.497  Sum_probs=34.0

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc----CCCCCCCCccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS----HSSCPKCRHCL  119 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~~  119 (165)
                      .+++.|.+|.+.   + .+.....|...||..|+..-+..    ...||.|+..-
T Consensus         5 ~~~~~C~~C~~~---g-~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A            5 PNEDWCAVCQNG---G-DLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             SSCSSBTTTCCC---E-EEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCCCCCCCCC---C-ceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            467889999854   2 35555569999999999776532    34699997643

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=91.10  E-value=0.28  Score=35.01  Aligned_cols=47  Identities=28%  Similarity=0.593  Sum_probs=34.2

Q ss_pred             CCCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHh-----------cCCCCCCCCcc
Q 042990           68 AGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS-----------SHSSCPKCRHC  118 (165)
Q Consensus        68 ~~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-----------~~~~CP~CR~~  118 (165)
                      .+.++.|.+|.+.   ++ +.....|...||..|+.+-+.           ....||.|+..
T Consensus        60 Dg~~d~C~vC~~G---G~-LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~~  117 (142)
T 2lbm_A           60 DGMDEQCRWCAEG---GN-LICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPE  117 (142)
T ss_dssp             TSCBCSCSSSCCC---SS-EEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCCC
T ss_pred             CCCCCeecccCCC---Cc-EEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccCc
Confidence            3567899999875   33 344445999999999997652           24469999754

>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=90.92  E-value=0.068  Score=32.47  Aligned_cols=48  Identities=23%  Similarity=0.594  Sum_probs=32.5

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHh----cCCCCCCCCcccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS----SHSSCPKCRHCLI  120 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~----~~~~CP~CR~~~~  120 (165)
                      .++..|.+|.+.   ++ +.....|...||..|+..-+.    ..-.||.|+....
T Consensus         7 ~~~~~C~vC~~~---g~-ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~   58 (61)
T 1mm2_A            7 HHMEFCRVCKDG---GE-LLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPAL   58 (61)
T ss_dssp             SSCSSCTTTCCC---SS-CBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTCC
T ss_pred             CCCCcCCCCCCC---CC-EEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCchh
Confidence            356789999863   33 334445999999999885432    2346999976543

>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=90.92  E-value=0.15  Score=34.41  Aligned_cols=49  Identities=24%  Similarity=0.372  Sum_probs=35.0

Q ss_pred             CCcCccccccccCCCeeeecC-CCCccccHhhHHHHH----------hcCCCCCCCCccc
Q 042990           71 DTECVICLSEFAAGDRLRLLP-KCNHGFHVRCIDKWL----------SSHSSCPKCRHCL  119 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~-~C~H~FH~~Ci~~Wl----------~~~~~CP~CR~~~  119 (165)
                      ...|.+|...|.++...+..- .|...||..|+.-=-          .....||.|+..-
T Consensus         3 ~~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~   62 (105)
T 2xb1_A            3 VYPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTK   62 (105)
T ss_dssp             CCBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTT
T ss_pred             cCCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcC
Confidence            467999999997665555543 599999999985321          1455799997643

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=90.17  E-value=0.15  Score=29.49  Aligned_cols=44  Identities=27%  Similarity=0.688  Sum_probs=29.1

Q ss_pred             cCccccccccCCCeeeecCCCCccccHhhHHHHHh----cCCCCCCCCc
Q 042990           73 ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS----SHSSCPKCRH  117 (165)
Q Consensus        73 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~----~~~~CP~CR~  117 (165)
                      .|.||...-..++.+ ....|...||..|+..=+.    ..-.||.|+.
T Consensus         2 ~C~vC~~~~~~~~ll-~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDDKLI-LCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSCCE-ECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCCCEE-ECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            488888764443334 4445999999999965332    2335999864

>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=89.62  E-value=0.059  Score=39.35  Aligned_cols=48  Identities=21%  Similarity=0.484  Sum_probs=34.1

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHH-----hcCCCCCCCCcc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWL-----SSHSSCPKCRHC  118 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl-----~~~~~CP~CR~~  118 (165)
                      ....| +|...+.++...+....|...||..|+..--     .....||.|+..
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            45678 9999876555455555699999999985321     235579999753

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=89.51  E-value=0.039  Score=36.20  Aligned_cols=50  Identities=20%  Similarity=0.439  Sum_probs=34.1

Q ss_pred             CCCCcCccccccc-cCCCeeeecCCCCccccHhhHHHHH--hcCCCCCCCCcc
Q 042990           69 GLDTECVICLSEF-AAGDRLRLLPKCNHGFHVRCIDKWL--SSHSSCPKCRHC  118 (165)
Q Consensus        69 ~~~~~C~ICl~~~-~~~~~~~~l~~C~H~FH~~Ci~~Wl--~~~~~CP~CR~~  118 (165)
                      +++..|.||.+.- .+.+.+.....|.-.||..|+..-.  .....||.|...
T Consensus        23 ~~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~   75 (88)
T 2l43_A           23 DEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQS   75 (88)
T ss_dssp             CCCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHH
T ss_pred             CCCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCc
Confidence            4678999999764 2333455555699999999987532  234468888654

>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=88.51  E-value=0.67  Score=32.47  Aligned_cols=47  Identities=26%  Similarity=0.527  Sum_probs=33.5

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHH------h-----cCCCCCCCCccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWL------S-----SHSSCPKCRHCL  119 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl------~-----~~~~CP~CR~~~  119 (165)
                      ..++.|.+|.+.    ..+.....|...||..||.+-+      +     ..-.|++|+..-
T Consensus        55 g~~~~C~vC~dG----G~LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~~p  112 (129)
T 3ql9_A           55 GMDEQCRWCAEG----GNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPEP  112 (129)
T ss_dssp             SCBSSCTTTCCC----SEEEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCCGG
T ss_pred             CCCCcCeecCCC----CeeEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCCHH
Confidence            467889999875    3344545699999999999752      1     234799996543

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=88.26  E-value=0.044  Score=33.14  Aligned_cols=48  Identities=25%  Similarity=0.719  Sum_probs=33.1

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHh----cCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS----SHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~----~~~~CP~CR~~~~~  121 (165)
                      ++..|.+|.+.   ++.+ ....|...||..|+..=+.    ..-.||.|+.....
T Consensus         4 ~~~~C~vC~~~---g~ll-~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~~   55 (60)
T 2puy_A            4 HEDFCSVCRKS---GQLL-MCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQMLK   55 (60)
T ss_dssp             CCSSCTTTCCC---SSCE-ECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHHHH
T ss_pred             CCCCCcCCCCC---CcEE-EcCCCCcCEECCcCCCCcCCCCCCceEChhccChhhc
Confidence            57889999874   3334 4445999999999885432    23469999665543

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=87.96  E-value=0.89  Score=30.72  Aligned_cols=47  Identities=19%  Similarity=0.424  Sum_probs=31.1

Q ss_pred             CCCcCccccccc-----cCCCeeeecCCCCccccHhhHHH------HH-hcCCCCCCCC
Q 042990           70 LDTECVICLSEF-----AAGDRLRLLPKCNHGFHVRCIDK------WL-SSHSSCPKCR  116 (165)
Q Consensus        70 ~~~~C~ICl~~~-----~~~~~~~~l~~C~H~FH~~Ci~~------Wl-~~~~~CP~CR  116 (165)
                      ....|.+|+..-     ..++.+..-..|+..||..|+..      .+ ...-.||-|+
T Consensus         4 p~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~~~~~~~~~~~~~~W~C~~C~   62 (112)
T 3v43_A            4 PIPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLKFSPELTVRVKALRWQCIECK   62 (112)
T ss_dssp             CCSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHTCCHHHHHHHHTSCCCCTTTC
T ss_pred             cCccccccCCchhhCcCCCchhceEhhhcCCCCCCchhcCCHHHHHHhhccccccccCC
Confidence            467899998763     12334445556999999999953      22 3345677775

>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=87.73  E-value=0.095  Score=34.28  Aligned_cols=51  Identities=22%  Similarity=0.526  Sum_probs=35.4

Q ss_pred             CCCcCccccccccC-CCeeeecCCCCccccHhhHHHHHh--------cCCCCCCCCcccc
Q 042990           70 LDTECVICLSEFAA-GDRLRLLPKCNHGFHVRCIDKWLS--------SHSSCPKCRHCLI  120 (165)
Q Consensus        70 ~~~~C~ICl~~~~~-~~~~~~l~~C~H~FH~~Ci~~Wl~--------~~~~CP~CR~~~~  120 (165)
                      .+..|.+|...-.. +..+...-.|...||..|+..=+.        ....|+.|+....
T Consensus        15 ~~~~C~vC~~~~~~~~~~ll~CD~C~~~yH~~Cl~Ppl~~~~~~~p~g~W~C~~C~~~~~   74 (88)
T 1wev_A           15 MGLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMK   74 (88)
T ss_dssp             HCCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHC
T ss_pred             CCCcCCCCCCCCCCCCCceEECCCCCCeEcCccCCCcccccccCCCCCCeeCccccchhh
Confidence            35789999987442 234555556999999999886442        2446999976554

>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=87.67  E-value=0.35  Score=29.41  Aligned_cols=49  Identities=27%  Similarity=0.685  Sum_probs=33.6

Q ss_pred             CCCCcCcccccccc-CCCeeeecCCCCccccHhhHHHHH-------hcCCCCCCCCc
Q 042990           69 GLDTECVICLSEFA-AGDRLRLLPKCNHGFHVRCIDKWL-------SSHSSCPKCRH  117 (165)
Q Consensus        69 ~~~~~C~ICl~~~~-~~~~~~~l~~C~H~FH~~Ci~~Wl-------~~~~~CP~CR~  117 (165)
                      .++..|.||..... ++..+.....|...||..|+..=+       .....|+.|+.
T Consensus         4 ~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~   60 (66)
T 2yt5_A            4 GSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVF   60 (66)
T ss_dssp             CCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcC
Confidence            46789999998753 233444555699999999987532       23446888854

>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=87.50  E-value=0.18  Score=31.81  Aligned_cols=46  Identities=22%  Similarity=0.433  Sum_probs=31.6

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhHHHHH---------hcCCCCCCCCcc
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWL---------SSHSSCPKCRHC  118 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl---------~~~~~CP~CR~~  118 (165)
                      ...| ||...+..+..+.-- .|...||..|+..-.         .....||.|+..
T Consensus        16 ~~~C-~C~~~~~~~~MI~Cd-~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~   70 (76)
T 1wem_A           16 ALYC-ICRQPHNNRFMICCD-RCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             CCCS-TTCCCCCSSCEEECS-SSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             CCEE-ECCCccCCCCEEEeC-CCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCc
Confidence            3567 899887644444444 599999999985321         246789999653

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=86.72  E-value=0.1  Score=32.14  Aligned_cols=46  Identities=26%  Similarity=0.656  Sum_probs=31.8

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHh----cCCCCCCCCcc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS----SHSSCPKCRHC  118 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~----~~~~CP~CR~~  118 (165)
                      .+++.|.||.+.   ++ +.....|...||..|+..-+.    ..-.||.|...
T Consensus         6 ~~~~~C~vC~~~---g~-ll~CD~C~~~fH~~Cl~ppl~~~P~g~W~C~~C~~~   55 (66)
T 1xwh_A            6 KNEDECAVCRDG---GE-LICCDGCPRAFHLACLSPPLREIPSGTWRCSSCLQA   55 (66)
T ss_dssp             SCCCSBSSSSCC---SS-CEECSSCCCEECTTTSSSCCSSCCSSCCCCHHHHHT
T ss_pred             CCCCCCccCCCC---CC-EEEcCCCChhhcccccCCCcCcCCCCCeECccccCc
Confidence            467899999874   33 344445999999999885432    24469999643

>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=86.37  E-value=0.14  Score=31.85  Aligned_cols=46  Identities=24%  Similarity=0.519  Sum_probs=30.0

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHH---hcCCCCCCCCc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWL---SSHSSCPKCRH  117 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl---~~~~~CP~CR~  117 (165)
                      +...| ||...+..+..+ ....|...||..|+.---   .....||.|+.
T Consensus        18 ~~~~C-iC~~~~~~~~MI-qCd~C~~WfH~~Cvgi~~~~~~~~~~C~~C~~   66 (68)
T 3o70_A           18 GLVTC-FCMKPFAGRPMI-ECNECHTWIHLSCAKIRKSNVPEVFVCQKCRD   66 (68)
T ss_dssp             TCCCS-TTCCCCTTCCEE-ECTTTCCEEETTTTTCCTTSCCSSCCCHHHHT
T ss_pred             CceEe-ECCCcCCCCCEE-ECCCCCccccccccCcCcccCCCcEECCCCCC
Confidence            44668 998877633344 444599999999986422   12446888854

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=85.71  E-value=0.079  Score=31.54  Aligned_cols=44  Identities=30%  Similarity=0.797  Sum_probs=29.6

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHh----cCCCCCCCC
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS----SHSSCPKCR  116 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~----~~~~CP~CR  116 (165)
                      .++..|.+|.+.   ++ +.....|...||..|+..=+.    ..-.||.|+
T Consensus         7 ~~~~~C~vC~~~---g~-ll~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~   54 (56)
T 2yql_A            7 GHEDFCSVCRKS---GQ-LLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQ   54 (56)
T ss_dssp             SSCCSCSSSCCS---SC-CEECSSSSCEECSSSSSSCCCSCCCSSCCCHHHH
T ss_pred             CCCCCCccCCCC---Ce-EEEcCCCCcceECccCCCCcCCCCCCceEChhhh
Confidence            457889999875   33 334445999999999875332    233577774

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=85.47  E-value=0.55  Score=30.70  Aligned_cols=46  Identities=30%  Similarity=0.603  Sum_probs=32.6

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc----CCCCCCCCcc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS----HSSCPKCRHC  118 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~  118 (165)
                      .+++.|.+|.+.   ++ +.....|.-.||..|+..=+..    ...||.|+..
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---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   72 (88)
T ss_dssp             SSSSCCSSSCSS---SC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCC
T ss_pred             CCCCcCcCcCCC---CC-EEECCCCCCceecccCCCCCCCCcCCCcCCccccCC
Confidence            467899999875   33 3444459999999999764422    3469999754

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=85.29  E-value=0.31  Score=32.38  Aligned_cols=44  Identities=25%  Similarity=0.492  Sum_probs=30.5

Q ss_pred             CcCccccccccCCCeeeecCCCCccccHhhHHHHHh---cCCCCCCCCc
Q 042990           72 TECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS---SHSSCPKCRH  117 (165)
Q Consensus        72 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~---~~~~CP~CR~  117 (165)
                      ..| ||......+..+.- ..|...||..|+..=..   ....||.|+.
T Consensus        29 vrC-iC~~~~~~~~mi~C-d~C~~w~H~~C~~~~~~~~p~~w~C~~C~~   75 (98)
T 2lv9_A           29 TRC-ICGFTHDDGYMICC-DKCSVWQHIDCMGIDRQHIPDTYLCERCQP   75 (98)
T ss_dssp             CCC-TTSCCSCSSCEEEB-TTTCBEEETTTTTCCTTSCCSSBCCTTTSS
T ss_pred             EEe-ECCCccCCCcEEEc-CCCCCcCcCcCCCCCccCCCCCEECCCCcC
Confidence            457 89877666555544 45999999999865321   2347999974

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=84.60  E-value=0.29  Score=33.23  Aligned_cols=45  Identities=29%  Similarity=0.658  Sum_probs=30.5

Q ss_pred             cCccccccccCCCeeeecCCCCccccHhhHHHHHhc----CCCCCCCCc
Q 042990           73 ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS----HSSCPKCRH  117 (165)
Q Consensus        73 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~  117 (165)
                      .|.+|.+.-.+++.+.....|...||..|+..-+..    .-.||.|+.
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            688888753333445555569999999998754422    346999864

>1weo_A Cellulose synthase, catalytic subunit (IRX3); structure genomics, ring-finger, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: g.44.1.1

Probab=84.49  E-value=2.3  Score=27.77  Aligned_cols=51  Identities=20%  Similarity=0.416  Sum_probs=37.9

Q ss_pred             CCCcCcccccccc---CCCeeeecCCCCccccHhhHHHHH-hcCCCCCCCCcccc
Q 042990           70 LDTECVICLSEFA---AGDRLRLLPKCNHGFHVRCIDKWL-SSHSSCPKCRHCLI  120 (165)
Q Consensus        70 ~~~~C~ICl~~~~---~~~~~~~l~~C~H~FH~~Ci~~Wl-~~~~~CP~CR~~~~  120 (165)
                      ....|.||-+++.   +++.-.....|+--.++.|..-=. ..+..||.|++.+.
T Consensus        15 ~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCktrYk   69 (93)
T 1weo_A           15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYK   69 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCC
T ss_pred             CCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhccCccccccCCccc
Confidence            3468999999964   344444444588889999988766 45778999998886

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=83.84  E-value=2.3  Score=27.33  Aligned_cols=39  Identities=15%  Similarity=0.268  Sum_probs=29.6

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS  108 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~  108 (165)
                      ....|.+|.+.+++..-+..-..=+|.|+..|-...+++
T Consensus        14 a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~   52 (93)
T 2cs3_A           14 GPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   52 (93)
T ss_dssp             CSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHh
Confidence            457899999999986655332234599999999998854

>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=83.70  E-value=0.63  Score=30.61  Aligned_cols=46  Identities=24%  Similarity=0.526  Sum_probs=28.7

Q ss_pred             CCCcCccccccccCCCeeeecCC--CC-ccccHhhHHHHH--hcCCCCCCCCcc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPK--CN-HGFHVRCIDKWL--SSHSSCPKCRHC  118 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~--C~-H~FH~~Ci~~Wl--~~~~~CP~CR~~  118 (165)
                      +..-| ||..... ++ .+..-.  |. ..||..|+..=-  ..+..||.|+..
T Consensus        35 e~~yC-iC~~~~~-g~-MI~CD~~dC~~~WfH~~CVgl~~~p~g~W~Cp~C~~~   85 (91)
T 1weu_A           35 EPTYC-LCHQVSY-GE-MIGCDNPDCSIEWFHFACVGLTTKPRGKWFCPRCSQE   85 (91)
T ss_dssp             CCBCS-TTCCBCC-SC-CCCCSCSSCSCCCCCSTTTTCSSCCCSSCCCTTTCCC
T ss_pred             CCcEE-ECCCCCC-CC-EeEecCCCCCCCCEecccCCcCcCCCCCEECcCccCc
Confidence            44567 9988753 33 333334  55 689999987211  124579999754

>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=83.25  E-value=0.85  Score=28.44  Aligned_cols=46  Identities=24%  Similarity=0.526  Sum_probs=28.7

Q ss_pred             CCCcCccccccccCCCeeeecCC--CC-ccccHhhHHHHH--hcCCCCCCCCcc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPK--CN-HGFHVRCIDKWL--SSHSSCPKCRHC  118 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~--C~-H~FH~~Ci~~Wl--~~~~~CP~CR~~  118 (165)
                      +..-| ||..... ++ .+..-.  |. ..||..|+..=-  ..+..||.|+..
T Consensus        15 ~~~~C-~C~~~~~-g~-MI~CD~~~C~~~wfH~~Cvgl~~~p~g~w~Cp~C~~~   65 (71)
T 1wen_A           15 EPTYC-LCHQVSY-GE-MIGCDNPDCSIEWFHFACVGLTTKPRGKWFCPRCSQE   65 (71)
T ss_dssp             SCCCS-TTCCCSC-SS-EECCSCSSCSCCCEETTTTTCSSCCSSCCCCTTTSSC
T ss_pred             CCCEE-ECCCCCC-CC-EeEeeCCCCCCccEecccCCcCcCCCCCEECCCCCcc
Confidence            44668 8988643 33 334444  55 699999997211  124469999654

>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=83.20  E-value=0.96  Score=30.68  Aligned_cols=45  Identities=20%  Similarity=0.473  Sum_probs=29.1

Q ss_pred             CcCcccccccc------CCCeeeecCCCCccccHhhHHHH------H-hcCCCCCCCC
Q 042990           72 TECVICLSEFA------AGDRLRLLPKCNHGFHVRCIDKW------L-SSHSSCPKCR  116 (165)
Q Consensus        72 ~~C~ICl~~~~------~~~~~~~l~~C~H~FH~~Ci~~W------l-~~~~~CP~CR  116 (165)
                      +.|.+|+..-.      +++.......|+..||..|+..+      + ...-.||.|+
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            57999987642      12344444469999999998754      2 2344677664

>2ks1_B Epidermal growth factor receptor; ERBB1, ERBB2, transmembrane, heterodimer, complex, tyrosine receptor, bicelles, transferase; NMR {Homo sapiens}

Probab=82.95  E-value=2.6  Score=23.78  Aligned_cols=23  Identities=13%  Similarity=-0.067  Sum_probs=9.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhc
Q 042990            4 SVLLCALICSLGLNSIIRCVVRC   26 (165)
Q Consensus         4 ~ill~~ll~~~~l~~i~~~~~r~   26 (165)
                      +++..++++++.+..++++++|+
T Consensus        16 gVVgGv~~~~ii~~~~~~~~RRr   38 (44)
T 2ks1_B           16 GMVGALLLLLVVALGIGLFMRRR   38 (44)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             ehhHHHHHHHHHHHHHHHHhhhh
Confidence            34443444444444444444443

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=82.63  E-value=1.5  Score=27.29  Aligned_cols=49  Identities=20%  Similarity=0.447  Sum_probs=33.1

Q ss_pred             CCCCcCccccccc-cCCCeeeecCCCCccccHhhHHHHH--hcCCCCCCCCc
Q 042990           69 GLDTECVICLSEF-AAGDRLRLLPKCNHGFHVRCIDKWL--SSHSSCPKCRH  117 (165)
Q Consensus        69 ~~~~~C~ICl~~~-~~~~~~~~l~~C~H~FH~~Ci~~Wl--~~~~~CP~CR~  117 (165)
                      .++..|.||.+.- .+++.......|.-.||..|+..-.  ...-.||.|+.
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            4678999998764 2334455555699999999987432  22445887754

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=82.32  E-value=0.35  Score=35.94  Aligned_cols=44  Identities=30%  Similarity=0.625  Sum_probs=30.7

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhHHHHHh----cCCCCCCCCcc
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS----SHSSCPKCRHC  118 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~----~~~~CP~CR~~  118 (165)
                      ++.|.+|.+.   ++.+ ....|...||..|+..=+.    ....||.|+..
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---GDLV-MCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVL   49 (189)
T ss_dssp             CCCBTTTCCC---SSCC-CCTTTCCBCCSTTSTTCCSSCCCTTCCTTTTSCS
T ss_pred             CCcCccCCCC---Ccee-ECCCCCchhccccCCCCcccCCCCCCCCcCccCC
Confidence            5689999865   3333 3445999999999865332    23469999765

---

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	165
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	7e-17
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	1e-10
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	1e-08
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	5e-08
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	7e-08
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-06
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	1e-05
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	2e-05
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	2e-05
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	7e-04
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	0.001
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	0.002

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 68.4 bits (167), Expect = 7e-17
 Identities = 25/50 (50%), Positives = 33/50 (66%)

Query: 71  DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI 120
             EC +CL+E   G+  R LP+C HGFH  C+D WL SHS+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 = 52.3 bits (125), Expect = 1e-10
 Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 3/60 (5%)

Query: 67  LAGLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETCQKI 126
           +A +   C ICL + +          C H F   CI +W+  + +CP C+  +      I
Sbjct: 1   MATVAERCPICLEDPSNYSMA---LPCLHAFCYVCITRWIRQNPTCPLCKVPVESVVHTI 57

>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 = 46.6 bits (110), Expect = 1e-08
 Identities = 10/46 (21%), Positives = 16/46 (34%), Gaps = 1/46 (2%)

Query: 73  ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS-SHSSCPKCRH 117
           EC +C+      D       C +     C  +  +  +  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 = 46.3 bits (109), Expect = 5e-08
 Identities = 14/60 (23%), Positives = 18/60 (30%), Gaps = 14/60 (23%)

Query: 71  DTECVICLSEFAA--------------GDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCR 116
              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 = 45.2 bits (106), Expect = 7e-08
 Identities = 13/51 (25%), Positives = 19/51 (37%), Gaps = 2/51 (3%)

Query: 71  DTECVICLSEFAAGDRLRLLP-KCNHGFHVRCIDKWLS-SHSSCPKCRHCL 119
           D  C  C +       L+L+   C H     C+D        +CP+C   L
Sbjct: 3   DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPL 53

>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 = 42.3 bits (99), Expect = 1e-06
 Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 5/55 (9%)

Query: 74  CVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSS-CPKCRHCLIETCQKII 127
           C IC         +++ P C H     C+  W  S    CP CR  +  T   ++
Sbjct: 26  CKICAEND---KDVKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIVV 76

>d1v87a_ g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 114

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Deltex protein 2 RING-H2 domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.4 bits (93), Expect = 1e-05
 Identities = 11/49 (22%), Positives = 19/49 (38%), Gaps = 5/49 (10%)

Query: 73  ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS-----HSSCPKCR 116
              +  S+      +  L KC+H FH+ C+     +        CP C+
Sbjct: 41  YSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCK 89

>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 = 38.7 bits (89), Expect = 2e-05
 Identities = 10/48 (20%), Positives = 14/48 (29%), Gaps = 3/48 (6%)

Query: 74  CVICLSEFAAGDRLRLLPK-CNHGFHVRCIDKWLSSH--SSCPKCRHC 118
           C IC  E                  H  C+  WL+    ++C  C   
Sbjct: 9   CWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVV 56

>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 = 37.9 bits (88), Expect = 2e-05
 Identities = 12/45 (26%), Positives = 17/45 (37%), Gaps = 7/45 (15%)

Query: 73  ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRH 117
            C  C +E       +LLP C H     C++        CP C+ 
Sbjct: 8   RCQQCQAEA---KCPKLLP-CLHTLCSGCLEAS---GMQCPICQA 45

>d1wima_ g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA0161) {Human (Homo sapiens) [TaxId: 9606]} Length = 94

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: UbcM4-interacting protein 4 (KIAA0161)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.1 bits (80), Expect = 7e-04
 Identities = 10/54 (18%), Positives = 18/54 (33%), Gaps = 9/54 (16%)

Query: 71  DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHS--------SCPKCR 116
            + C +CL E+       +   C   F   C+ +++            SCP   
Sbjct: 5   SSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAA 57

>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 = 34.7 bits (79), Expect = 0.001
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 7/50 (14%)

Query: 73  ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHS---SCPKCRHCL 119
           EC ICL       +  +  KC+H F   C+ K L+       CP C++ +
Sbjct: 23  ECPICLELI----KEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDI 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 = 33.6 bits (76), Expect = 0.002
 Identities = 10/47 (21%), Positives = 14/47 (29%), Gaps = 5/47 (10%)

Query: 73  ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCL 119
            C  C +          L  C H F   C+   + +   CP C    
Sbjct: 24  RCSRCTNIL---REPVCLGGCEHIFCSNCVSDCIGTG--CPVCYTPA 65

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	165
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.77
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.59
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.55
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.54
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.51
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.5
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.48
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.38
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.32
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.29
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.28
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.24
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.08
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.08
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.05
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	98.84
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	98.67
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	95.18
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	94.58
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	94.4
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	94.39
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	93.7
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	92.15
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	92.08
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	90.4
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	86.58
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	86.12
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	85.37
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	84.55
d2co8a2	36	Nedd9 interacting protein with calponin homology,	84.28
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	83.99
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	82.87
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	82.71
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	82.57
d1dvpa2	72	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	82.51
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	81.51
d1vfya_	67	vps27p protein {Baker's yeast (Saccharomyces cerev	80.26

>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=9.3e-20  Score=110.94  Aligned_cols=52  Identities=48%  Similarity=1.204  Sum_probs=47.3

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLI  120 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~  120 (165)
                      +++.+|+||+++|..++.++.++.|+|.||..||.+|++++.+||+||++++
T Consensus         3 ed~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           3 DDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CCSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            3567899999999999988887669999999999999999999999999875

>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=99.59  E-value=4.5e-16  Score=98.21  Aligned_cols=49  Identities=31%  Similarity=0.796  Sum_probs=42.6

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      ..++|+||++.+.+  .++.++ |||.||..||.+|++.+.+||+||+.+..
T Consensus         4 ~~d~C~IC~~~~~~--~~~~~~-C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~   52 (68)
T d1chca_           4 VAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCccCCcCccC--CcEEeC-CCCcCcHHHHHHHHHhCCcCCCCCcchHh
Confidence            45789999999965  356677 99999999999999999999999998754

>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=99.55  E-value=6.6e-16  Score=92.49  Aligned_cols=48  Identities=23%  Similarity=0.492  Sum_probs=40.2

Q ss_pred             cCccccccccCCCee-eecCCCCccccHhhHHHHHhc-CCCCCCCCccccc
Q 042990           73 ECVICLSEFAAGDRL-RLLPKCNHGFHVRCIDKWLSS-HSSCPKCRHCLIE  121 (165)
Q Consensus        73 ~C~ICl~~~~~~~~~-~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~  121 (165)
                      +|+||+++|+.++.. ..++ |||.||.+|+.+|++. +..||+||.++.+
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            799999999876554 4455 9999999999999975 5579999998864

>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=1.8e-15  Score=100.09  Aligned_cols=51  Identities=27%  Similarity=0.593  Sum_probs=42.7

Q ss_pred             CCCcCccccccccCCC---------------eeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGD---------------RLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~---------------~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      .++.|+||++.+.+..               .+..++ |||.||.+||.+||+.+.+||+||+.+.-
T Consensus        20 ~~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   85 (88)
T d3dplr1          20 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEF   85 (88)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCCE
T ss_pred             CCCcCEEccchhhCccccccccccccccccCCeEEcc-ccCcccHHHHHHHHHHCCcCCCCCCcccc
Confidence            4678999999986532               245566 99999999999999999999999998764

>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=99.51  E-value=1.1e-14  Score=100.29  Aligned_cols=51  Identities=29%  Similarity=0.712  Sum_probs=40.2

Q ss_pred             CCCcCccccccccCC---------------CeeeecCCCCccccHhhHHHHHhcC-----CCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAG---------------DRLRLLPKCNHGFHVRCIDKWLSSH-----SSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~---------------~~~~~l~~C~H~FH~~Ci~~Wl~~~-----~~CP~CR~~~~~  121 (165)
                      .++.|+||+++|...               ..+..++ |+|+||..||..|++.+     .+||+||+.+..
T Consensus        24 ~~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~-CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~   94 (114)
T d1v87a_          24 PEEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGE   94 (114)
T ss_dssp             CSCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSS
T ss_pred             ccccccchhheecccccccccccccccccccceEECC-CCChhhHHHHHHHHHhcCcCCCCccccccchhcc
Confidence            467899999998542               2345666 99999999999999643     479999988754

>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=99.50  E-value=1.5e-14  Score=93.72  Aligned_cols=51  Identities=25%  Similarity=0.593  Sum_probs=43.1

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHh-cCCCCCCCCcccccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS-SHSSCPKCRHCLIETCQ  124 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~~~~~~~  124 (165)
                      ....|+||++.+.+   ++.++ |||.||..||..|+. ++..||+||..+.....
T Consensus        22 ~~~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~   73 (79)
T d1fbva4          22 TFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEP   73 (79)
T ss_dssp             CTTBCTTTSSSBCC---EECSS-SCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCC
T ss_pred             CCCCCccCCCcCCC---eEEeC-CCCeeeHHHHHHHHHHCcCcCCCCCcCccCCce
Confidence            34579999999876   77888 999999999999996 45789999999986543

>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=99.48  E-value=1.3e-14  Score=90.64  Aligned_cols=53  Identities=23%  Similarity=0.491  Sum_probs=41.1

Q ss_pred             CCCcCccccccccCC-C-eeeecCCCCccccHhhHHHHHhc-CCCCCCCCccccccc
Q 042990           70 LDTECVICLSEFAAG-D-RLRLLPKCNHGFHVRCIDKWLSS-HSSCPKCRHCLIETC  123 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~-~-~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~~~  123 (165)
                      ++..|+||++.+..+ + ....++ |||.||..||..|+++ +..||+||..+....
T Consensus         2 dd~~CpIC~~~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~~CP~CR~~i~~~~   57 (65)
T d1g25a_           2 DDQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKSN   57 (65)
T ss_dssp             CTTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCC
T ss_pred             CCCCCCcCCceeecCCceEEEeCc-cChHhhHHHHHHHhCcCcCCCCCCCcCccccc
Confidence            468999999986432 3 334556 9999999999999954 567999999886543

>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=99.38  E-value=8.7e-14  Score=84.25  Aligned_cols=47  Identities=17%  Similarity=0.165  Sum_probs=41.3

Q ss_pred             cCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCcccccc
Q 042990           73 ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIET  122 (165)
Q Consensus        73 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~  122 (165)
                      .|+||++.+++   ...++.|||.||++||.+|++++.+||+||.++...
T Consensus         2 ~C~Ic~~~~~~---Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~   48 (56)
T d2baya1           2 LCAISGKVPRR---PVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   48 (56)
T ss_dssp             CCTTTCSCCSS---EEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             CCccCCchHHh---cCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHH
Confidence            59999999987   555555999999999999999888999999988764

>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=99.32  E-value=5.8e-13  Score=87.35  Aligned_cols=48  Identities=33%  Similarity=0.539  Sum_probs=41.4

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhHHHHHh-cCCCCCCCCcccccc
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS-SHSSCPKCRHCLIET  122 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~~~~~  122 (165)
                      ...|+||++.+.+   +..++ |||.|++.||.+|++ ++..||+||.++.+.
T Consensus        23 ~l~C~IC~~~~~~---pv~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~   71 (86)
T d1rmda2          23 SISCQICEHILAD---PVETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPT   71 (86)
T ss_dssp             HTBCTTTCSBCSS---EEECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGG
T ss_pred             CcCCccCCcchhc---ceecC-CCChhhHHHHHHHHhhCCCcCcccCCCCChh
Confidence            3579999999987   67887 999999999999996 456899999988654

>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=99.29  E-value=3e-13  Score=81.84  Aligned_cols=46  Identities=26%  Similarity=0.532  Sum_probs=39.3

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccccc
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIETC  123 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~~~  123 (165)
                      ..+|+||++.|.+   ++.++ |||.||..||.+|   +..||+||..+....
T Consensus         6 ~l~C~IC~~~~~~---p~~lp-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~   51 (56)
T d1bora_           6 FLRCQQCQAEAKC---PKLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGA   51 (56)
T ss_dssp             CSSCSSSCSSCBC---CSCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCS
T ss_pred             CCCCcccCcccCC---CEEec-CCCHHhHHHHHcC---CCcCcCCCCcccCCC
Confidence            4689999999987   57788 9999999999876   678999999987643

>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=99.28  E-value=9e-13  Score=80.68  Aligned_cols=52  Identities=19%  Similarity=0.358  Sum_probs=38.3

Q ss_pred             CCCCcCccccccccCCCeee-ecCCCCccccHhhHHHHHh--cCCCCCCCCcccc
Q 042990           69 GLDTECVICLSEFAAGDRLR-LLPKCNHGFHVRCIDKWLS--SHSSCPKCRHCLI  120 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~-~l~~C~H~FH~~Ci~~Wl~--~~~~CP~CR~~~~  120 (165)
                      ++...|.||++++++..... ....|+|.||..||..|++  ++.+||+||+.+.
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            45678999999987643211 1112569999999999994  4668999998764

>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=99.24  E-value=1.9e-12  Score=87.40  Aligned_cols=48  Identities=31%  Similarity=0.587  Sum_probs=40.0

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcC---CCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSH---SSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~---~~CP~CR~~~~~  121 (165)
                      ....|+||++.|.+   +..++ |||.||..||..|++.+   ..||+||..+..
T Consensus        20 ~~l~CpIC~~~~~~---pv~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   70 (103)
T d1jm7a_          20 KILECPICLELIKE---PVSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK   70 (103)
T ss_dssp             HHTSCSSSCCCCSS---CCBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCT
T ss_pred             cCcCCCccCchhCC---eEEcC-CCCchhhHHHHHHHHHCCCCCcCcCCCCcCCh
Confidence            34689999999976   56677 99999999999999554   379999998754

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.08  E-value=5.6e-11  Score=76.46  Aligned_cols=48  Identities=15%  Similarity=0.075  Sum_probs=41.8

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHh-cCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLS-SHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~~~~  121 (165)
                      ++..|+||++-|.+   +..++ |||.|++.||..|+. .+..||.||..+..
T Consensus         6 ~~l~CpIc~~l~~d---Pv~~~-cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~   54 (80)
T d2c2la2           6 DYLCGKISFELMRE---PCITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQ   54 (80)
T ss_dssp             STTBCTTTCSBCSS---EEECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             ccccCcCcCchhhh---hcccC-CcCeecHHHHHHHHhcCCccCCCccccccc
Confidence            56889999999988   66787 999999999999995 46689999988764

>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=99.08  E-value=1.3e-11  Score=82.30  Aligned_cols=47  Identities=21%  Similarity=0.448  Sum_probs=37.4

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      ....|+||++.|.+   +..+..|||.||..||.+|+.  ..||.||..+..
T Consensus        21 ~~l~C~IC~~~~~~---pv~~~~CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~   67 (97)
T d1jm7b_          21 KLLRCSRCTNILRE---PVCLGGCEHIFCSNCVSDCIG--TGCPVCYTPAWI   67 (97)
T ss_dssp             HTTSCSSSCSCCSS---CBCCCSSSCCBCTTTGGGGTT--TBCSSSCCBCSC
T ss_pred             hcCCCccCCchhhc---CceeCCCCCchhHHHHHHHHh--ccccccCCcCch
Confidence            35689999999977   344323999999999999984  359999987654

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.05  E-value=8.7e-11  Score=75.16  Aligned_cols=48  Identities=25%  Similarity=0.551  Sum_probs=41.7

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc-CCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS-HSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~-~~~CP~CR~~~~~  121 (165)
                      ++..|+||++.|.+   ++.++ |||.|++.||..|++. +..||.|+..+..
T Consensus         7 ~~l~CpIc~~~m~d---PV~~~-cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~   55 (78)
T d1t1ha_           7 EYFRCPISLELMKD---PVIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSSCTTTSCCCSS---EEEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             ccCCCcCcCchhhC---ceEcc-CCCcchHHHHHHHHHHCCCCCCcccccCCc
Confidence            57899999999988   66787 9999999999999965 5679999987754

>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=98.84  E-value=1.5e-09  Score=72.26  Aligned_cols=49  Identities=18%  Similarity=0.059  Sum_probs=42.4

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~  121 (165)
                      ++..|+||++-|.+   +.+++.|+|.|.+.||.+|++.+..||+||.++..
T Consensus        21 ~~f~CPI~~~lm~d---PV~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~   69 (98)
T d1wgma_          21 DEFLDPIMSTLMCD---PVVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTM   69 (98)
T ss_dssp             TTTBCTTTCSBCSS---EEECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCT
T ss_pred             HHhCCcCchhHHHH---HHhcccccchhhHHHHHHHHHhcCCcccccccccc
Confidence            57899999999998   67787344689999999999999999999998764

>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=2.7e-09  Score=70.17  Aligned_cols=46  Identities=22%  Similarity=0.585  Sum_probs=37.3

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcC----C----CCCCCC
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSH----S----SCPKCR  116 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~----~----~CP~CR  116 (165)
                      ...+|+||++++...+.+..++ |+|.||.+|+..|++.+    .    .||.|+
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~   57 (94)
T d1wima_           4 GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAA   57 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTT
T ss_pred             CCCcCccCCCcccCCceEEECC-CCCEeCCcCHHHHHHHHHhcCCccccCCcCCC
Confidence            4579999999998777777776 99999999999999431    1    499854

>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=95.18  E-value=0.0081  Score=37.37  Aligned_cols=35  Identities=23%  Similarity=0.493  Sum_probs=26.7

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHH
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKW  105 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~W  105 (165)
                      .+|+.|.|| +.+...+..-.- -|+.+||..|+.+-
T Consensus        13 ~~D~mC~vC-~v~t~~~l~pCR-vCtRv~H~~CL~r~   47 (89)
T d1wila_          13 VNDEMCDVC-EVWTAESLFPCR-VCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCSCCCTTT-CCCCSSCCSSCS-SSSSCCCHHHHHHH
T ss_pred             CcCcccccc-Ccccccceecce-eecchhhHHHHHHh
Confidence            478999999 777665543222 39999999999996

>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=94.58  E-value=0.0083  Score=33.70  Aligned_cols=44  Identities=30%  Similarity=0.694  Sum_probs=31.0

Q ss_pred             cCccccccccCCCeeeecCCCCccccHhhHHHHHhc----CCCCCCCCc
Q 042990           73 ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS----HSSCPKCRH  117 (165)
Q Consensus        73 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~  117 (165)
                      .|.||...-..+. ......|...||..|+..-+..    ...||.||.
T Consensus         2 ~C~vC~~~~~~~~-~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGEDDK-LILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCSC-CEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCCCC-EEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            4888977654443 4445569999999999886532    335999974

>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=94.40  E-value=0.012  Score=34.67  Aligned_cols=48  Identities=23%  Similarity=0.499  Sum_probs=36.0

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHH---H--hcCCCCCCCCc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKW---L--SSHSSCPKCRH  117 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~W---l--~~~~~CP~CR~  117 (165)
                      .+..|.+|...+.+++..+....|+..||..|+..=   .  ..+..||.|+.
T Consensus         5 ~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~   57 (64)
T d1we9a_           5 SSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             SCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcC
Confidence            567899999988777665666679999999998632   1  12457999964

>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=94.39  E-value=0.054  Score=33.06  Aligned_cols=47  Identities=19%  Similarity=0.487  Sum_probs=33.0

Q ss_pred             CcCccccccccCCCeeeecCCCCccccHhhHHH--H-Hh--cCCCCCCCCccc
Q 042990           72 TECVICLSEFAAGDRLRLLPKCNHGFHVRCIDK--W-LS--SHSSCPKCRHCL  119 (165)
Q Consensus        72 ~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~--W-l~--~~~~CP~CR~~~  119 (165)
                      .-| ||...+..+...+....|.-.||..|+..  . ..  .+..||.|+...
T Consensus        13 v~C-iC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~   64 (79)
T d1wepa_          13 VYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             eEe-ECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCc
Confidence            345 99988776655556667999999999852  2 22  246899997644

>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=93.70  E-value=0.0081  Score=35.15  Aligned_cols=48  Identities=23%  Similarity=0.593  Sum_probs=33.1

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc----CCCCCCCCcccc
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS----HSSCPKCRHCLI  120 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~~~  120 (165)
                      +.++.|.+|.+.   ++ +.....|...||..|+...+..    ...||.|+..-.
T Consensus         7 ~~~~~C~~C~~~---g~-lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~~   58 (61)
T d1mm2a_           7 HHMEFCRVCKDG---GE-LLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPAL   58 (61)
T ss_dssp             SSCSSCTTTCCC---SS-CBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTCC
T ss_pred             CCcCCCcCCCCC---Ce-EEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCccc
Confidence            456789999853   33 4444469999999998765532    446999976543

>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=92.15  E-value=0.018  Score=35.99  Aligned_cols=50  Identities=22%  Similarity=0.514  Sum_probs=33.1

Q ss_pred             CCcCccccccccC-CCeeeecCCCCccccHhhHHHHH-----h---cCCCCCCCCcccc
Q 042990           71 DTECVICLSEFAA-GDRLRLLPKCNHGFHVRCIDKWL-----S---SHSSCPKCRHCLI  120 (165)
Q Consensus        71 ~~~C~ICl~~~~~-~~~~~~l~~C~H~FH~~Ci~~Wl-----~---~~~~CP~CR~~~~  120 (165)
                      ...|.||...... ...++....|+..||..|+...+     .   ....||.|.....
T Consensus        16 ~~~C~iC~~~~~~~~~~~v~Cd~C~~~~H~~C~~p~~~~~~~~~~~~~W~C~~C~~~~~   74 (88)
T d1weva_          16 GLACVVCRQMTVASGNQLVECQECHNLYHQDCHKPQVTDKEVNDPRLVWYCARCTRQMK   74 (88)
T ss_dssp             CCSCSSSCCCCCCTTCCEEECSSSCCEEETTTSSSCCCHHHHHCTTCCCCCHHHHHHHC
T ss_pred             cCCccCCCCccCCCCCeEEEcCCCCCccccccCCCcccccccccCCCeEECcccCchHh
Confidence            4569999876543 23455555699999999976432     1   1457999965433

>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=92.08  E-value=0.044  Score=32.73  Aligned_cols=45  Identities=31%  Similarity=0.614  Sum_probs=30.1

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc----CCCCCCCCccc
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS----HSSCPKCRHCL  119 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~----~~~CP~CR~~~  119 (165)
                      ...|.+|.+.   ++ +.....|...||..|+...+..    ...||.|+..-
T Consensus         7 c~~C~~C~~~---~~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~   55 (70)
T d1fp0a1           7 ATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   55 (70)
T ss_dssp             SSCCSSSCSS---SC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCC
T ss_pred             CCCCCCCCCc---CE-EEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcC
Confidence            3456677543   44 4444469999999999977632    34699996544

>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=90.40  E-value=0.1  Score=31.19  Aligned_cols=46  Identities=24%  Similarity=0.527  Sum_probs=30.5

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhHH------HHH---hcCCCCCCCCcc
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCID------KWL---SSHSSCPKCRHC  118 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~------~Wl---~~~~~CP~CR~~  118 (165)
                      ...| ||......+.. +....|.-.||..|+.      ...   .....||.|+..
T Consensus        16 ~~~C-iC~~~~~~~~m-i~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~   70 (76)
T d1wema_          16 ALYC-ICRQPHNNRFM-ICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTIL   70 (76)
T ss_dssp             CCCS-TTCCCCCSSCE-EECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHH
T ss_pred             cCEE-ECCCccCCCeE-EEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCc
Confidence            3458 89887655444 4444699999999982      111   235789999543

>d1g47a1 g.39.1.3 (A:1-35) Pinch (particularly interesting new Cys-His) protein {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: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.58  E-value=0.2  Score=25.46  Aligned_cols=30  Identities=20%  Similarity=0.491  Sum_probs=25.0

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhh
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRC  101 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~C  101 (165)
                      ....|.-|.+.|++.+++...  =|.++|.+|
T Consensus         6 ~~~~C~RC~~gF~p~EkiVNS--nGEl~H~qC   35 (35)
T d1g47a1           6 ASATCERCKGGFAPAEKIVNS--NGELYHEQC   35 (35)
T ss_dssp             CCCBCSSSCCBCCSTTTCEEE--TTEEECTTT
T ss_pred             HHHHHHHHccCCCchHHhhcC--CCccccccC
Confidence            357899999999998888775  588899877

>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=86.12  E-value=0.12  Score=30.89  Aligned_cols=45  Identities=27%  Similarity=0.555  Sum_probs=25.7

Q ss_pred             CcCccccccccCCCeeee-cCCCC-ccccHhhHHHHH--hcCCCCCCCCcc
Q 042990           72 TECVICLSEFAAGDRLRL-LPKCN-HGFHVRCIDKWL--SSHSSCPKCRHC  118 (165)
Q Consensus        72 ~~C~ICl~~~~~~~~~~~-l~~C~-H~FH~~Ci~~Wl--~~~~~CP~CR~~  118 (165)
                      .-| ||.+.... +.+.. ...|. ..||..|+..=-  .....||.|+..
T Consensus        17 ~~C-iC~~~~~~-~~i~c~~~~C~~~wfH~~Cvgl~~~p~~~w~C~~C~~~   65 (71)
T d1wesa_          17 TYC-LCNQVSYG-EMIGCDNEQCPIEWFHFSCVSLTYKPKGKWYCPKCRGD   65 (71)
T ss_dssp             CCS-TTCCCCCS-SEECCSCTTCSCCCEETTTTTCSSCCSSCCCCTTTSSC
T ss_pred             CEE-EeCCCCCC-CEEEEECCCCCCcCccCccCCCCcCCCCcEECcCCccc
Confidence            456 99876433 33323 12354 579999985210  124469999753

>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=85.37  E-value=0.37  Score=28.92  Aligned_cols=48  Identities=21%  Similarity=0.473  Sum_probs=31.1

Q ss_pred             CCcCccccccccCCCeeeec-CCCCccccHhhHHH----HH-----hcCCCCCCCCccc
Q 042990           71 DTECVICLSEFAAGDRLRLL-PKCNHGFHVRCIDK----WL-----SSHSSCPKCRHCL  119 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l-~~C~H~FH~~Ci~~----Wl-----~~~~~CP~CR~~~  119 (165)
                      ...| ||.+....+..+-.- ..|...||..|+.-    +-     .....||.|+..-
T Consensus        16 ~~~C-~C~~~~~~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~   73 (78)
T d1wewa_          16 KVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTS   73 (78)
T ss_dssp             CCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCC
T ss_pred             ccEe-ECCCccCCCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcC
Confidence            3568 899887765544332 25999999999842    10     1136799996543

>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=84.55  E-value=0.094  Score=26.99  Aligned_cols=28  Identities=21%  Similarity=0.576  Sum_probs=21.8

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhH
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCI  102 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci  102 (165)
                      -+.|.+|.+.+.+    +.+...|..||-.|+
T Consensus         8 lEkC~~C~~~I~d----riLrA~Gk~yHP~CF   35 (35)
T d2dloa1           8 LEKCATCSQPILD----RILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCBCTTTCCBCCS----CCEEETTEEECTTTC
T ss_pred             HHHHHHhchHHHH----HHHHHhCCCCCCCCC
Confidence            4689999999877    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=84.28  E-value=0.29  Score=25.32  Aligned_cols=31  Identities=29%  Similarity=0.544  Sum_probs=22.2

Q ss_pred             CCCCcCccccccccCCCeeeecCCCCccccHhhH
Q 042990           69 GLDTECVICLSEFAAGDRLRLLPKCNHGFHVRCI  102 (165)
Q Consensus        69 ~~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci  102 (165)
                      +..+.|.+|-...-.-+.+.   .=|+.||+.|+
T Consensus         6 g~~~~C~~C~K~VY~~Erl~---a~g~~yHk~CF   36 (36)
T d2co8a2           6 GAGDLCALCGEHLYVLERLC---VNGHFFHRSCF   36 (36)
T ss_dssp             CSSCBCSSSCCBCCTTTBCC---BTTBCCBTTTC
T ss_pred             CCCCcccccCCEEeeeeEEE---ecCcEeccccC
Confidence            35689999988866644332   26799999984

>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=83.99  E-value=0.21  Score=24.94  Aligned_cols=28  Identities=18%  Similarity=0.507  Sum_probs=23.9

Q ss_pred             cCccccccccCCCeeeecCCCCccccHhhH
Q 042990           73 ECVICLSEFAAGDRLRLLPKCNHGFHVRCI  102 (165)
Q Consensus        73 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci  102 (165)
                      .|+-|...+...|.++.-  =+++||-.|+
T Consensus         4 ~Ca~C~~~I~~~e~VmRA--~~~VyHl~CF   31 (31)
T d1rutx3           4 ACSACGQSIPASELVMRA--QGNVYHLKCF   31 (31)
T ss_dssp             ECTTTCCEECTTSEEEEE--TTEEECGGGC
T ss_pred             ccccccCcCChhHhheec--ccceeeeccC
Confidence            699999999999888774  5799999984

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.87  E-value=0.86  Score=27.05  Aligned_cols=39  Identities=15%  Similarity=0.268  Sum_probs=29.0

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhc
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSS  108 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~  108 (165)
                      ....|.+|.+.+++..-+..-.-=+|.|+..|-...+++
T Consensus         7 ~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~   45 (80)
T d2cs3a1           7 GPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKA   45 (80)
T ss_dssp             CSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHH
T ss_pred             CceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHh
Confidence            347899999999986554322223599999999998854

>d1y02a2 g.50.1.1 (A:20-70) Rififylin (FYVE-RING finger protein Sakura) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Rififylin (FYVE-RING finger protein Sakura)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.71  E-value=0.058  Score=30.30  Aligned_cols=43  Identities=23%  Similarity=0.509  Sum_probs=27.4

Q ss_pred             cCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCC
Q 042990           73 ECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKC  115 (165)
Q Consensus        73 ~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~C  115 (165)
                      .|.+|...|.....-..-..||.+|+..|....-+..+.|..|
T Consensus         2 ~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~RvC~~C   44 (51)
T d1y02a2           2 SCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLC   44 (51)
T ss_dssp             CCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHH
T ss_pred             CccccCCcccCCccCcccccCCcccCccccCCCCCCCeECHhH
Confidence            5888999887644333444699999999966543334456555

>d1z60a1 g.49.1.2 (A:328-386) TFIIH p44 subunit cysteine-rich domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Cysteine-rich domain
superfamily: Cysteine-rich domain
family: TFIIH p44 subunit cysteine-rich domain
domain: TFIIH p44 subunit cysteine-rich domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.57  E-value=0.36  Score=27.68  Aligned_cols=45  Identities=27%  Similarity=0.460  Sum_probs=32.3

Q ss_pred             CCCcCccccccccCCCeeeecCCCCccccHhhHHHHHhcCCCCCCC
Q 042990           70 LDTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKWLSSHSSCPKC  115 (165)
Q Consensus        70 ~~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~Wl~~~~~CP~C  115 (165)
                      ....|--|+.++.+. .+...+.|++.|+.+|=.---..-.+||.|
T Consensus        14 ~~~~C~gC~~~l~~~-~~y~C~~C~~~FC~dCD~fiHe~lh~CpgC   58 (59)
T d1z60a1          14 GERFCYGCQGELKDQ-HVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             SCCEETTTTEECTTS-EEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CCCCccCCCCcCCCC-ceEECcCCCCccccccchhhhhhhcCCCCC
Confidence            357899999988653 445566799999999943322455579987

>d1dvpa2 g.50.1.1 (A:149-220) Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: Hrs
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=82.51  E-value=0.41  Score=28.43  Aligned_cols=34  Identities=26%  Similarity=0.497  Sum_probs=25.4

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhHHH
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDK  104 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~  104 (165)
                      ++.|.+|..+|..-..-.....||++|+..|...
T Consensus        13 ~~~C~~C~~~F~~~~rrhhCr~CG~~~C~~C~~~   46 (72)
T d1dvpa2          13 GRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTAK   46 (72)
T ss_dssp             CSBCTTTCCBCCSSSCCEECTTTCCEECSTTSCE
T ss_pred             CCccccCCCcccCccccccccccCCeeChhhhCC
Confidence            4679999999976544444446999999999543

>d1weoa_ g.44.1.1 (A:) Cellulose synthase A catalytic subunit 7, IRX3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Cellulose synthase A catalytic subunit 7, IRX3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=81.51  E-value=1.5  Score=26.94  Aligned_cols=52  Identities=19%  Similarity=0.408  Sum_probs=38.1

Q ss_pred             CCCcCcccccccc---CCCeeeecCCCCccccHhhHHHHHh-cCCCCCCCCccccc
Q 042990           70 LDTECVICLSEFA---AGDRLRLLPKCNHGFHVRCIDKWLS-SHSSCPKCRHCLIE  121 (165)
Q Consensus        70 ~~~~C~ICl~~~~---~~~~~~~l~~C~H~FH~~Ci~~Wl~-~~~~CP~CR~~~~~  121 (165)
                      +...|-||-+.+.   +++..+....|+--.++.|..-=.+ .++.||.|++.+..
T Consensus        15 ~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Ykr   70 (93)
T d1weoa_          15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKR   70 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCC
T ss_pred             ccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhhh
Confidence            4568999999975   3444444556888889999876553 47789999888753

>d1vfya_ g.50.1.1 (A:) vps27p protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: FYVE, a phosphatidylinositol-3-phosphate binding domain
domain: vps27p protein
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=80.26  E-value=0.69  Score=26.93  Aligned_cols=35  Identities=20%  Similarity=0.370  Sum_probs=25.0

Q ss_pred             CCcCccccccccCCCeeeecCCCCccccHhhHHHH
Q 042990           71 DTECVICLSEFAAGDRLRLLPKCNHGFHVRCIDKW  105 (165)
Q Consensus        71 ~~~C~ICl~~~~~~~~~~~l~~C~H~FH~~Ci~~W  105 (165)
                      ++.|.+|..+|..-..---...||.+|+..|...+
T Consensus         5 ~~~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~   39 (67)
T d1vfya_           5 SDACMICSKKFSLLNRKHHCRSCGGVFCQEHSSNS   39 (67)
T ss_dssp             CSBCTTTCCBCBTTBCCEECTTTCCEECGGGSCEE
T ss_pred             CcccccCCCcccCcccccccccCCCEecccccCCc
Confidence            46799999999764333334469999999995443