Citrus Sinensis ID: 038049

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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-
Protein Sequence
SADLNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMVALPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPSLDEIVTA
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHcccccccccHHHHHcccEEEccccccccccccccccccccccccccEEEcccccccccccccHHHHHcccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHcccccHHHHHHccEEEEEccccccccccccEEEEEcccccccEEEEcccccccccHHHHHHHHHccccccHHHHccccccccccccccccc
Coil and Loop (DISEMBL)
SADLNIMVIVAAMLCALVCALGLHSMLQCVFQCTQralteprqWVVSRRLNsglkrkemvalptvtyansgsspssasagCAICLldfidgdeirllpkcnhrfHVACIDKWllshsscptcrqrlkpsdampsldeivta
Flexible Loop (DISEMBL)
SADLNIMVIVAAMLCALVCALGLHSMLQCVFQCTQralteprqwvvsrrlnsglkrkemVALPTVTYansgsspssASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCrqrlkpsdampsldeivta
Low Complexity Region (SEG)
SADLNIMVIvaamlcalvcalglHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMVALPTVTYANsgsspssasagCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPSLDEIVTA
Disordered region (IsUnstruct)
***LNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMVALPTVTY***********AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPT********************
Disordered Region (DISOPRED)
**DLNIMVIVAAMLCALVCALGLHSMLQCVFQC*************************MVALPTVTYANS******ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRL***************
Disordered Region (DISEMBL)
SADLNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMVALPTVTYA**********AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPSLDEIVTA
Disordered Region (DISPRO)
SADLNIMVIVAAMLCALVCALGLHSMLQCVFQCT******************GLKRKEMVALPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRL***************
Transmembrane Helix (TMHMM)
ooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
ooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
SADLNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMVALPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPSLDEIVTA
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	141	2.2.26 [Sep-21-2011]
Q9FLC6	176	RING-H2 finger protein AT	yes	no	0.971	0.778	0.423	3e-29
Q9SG96	181	RING-H2 finger protein AT	no	no	0.858	0.668	0.481	5e-26
Q6NQG7	219	RING-H2 finger protein AT	no	no	0.858	0.552	0.447	3e-25
O22755	185	RING-H2 finger protein AT	no	no	0.865	0.659	0.451	8e-25
P0C034	251	RING-H2 finger protein AT	no	no	0.843	0.474	0.414	2e-24
Q6NML0	225	E3 ubiquitin-protein liga	no	no	0.843	0.528	0.398	2e-24
Q9LM69	197	RING-H2 finger protein AT	no	no	0.843	0.604	0.480	3e-24
Q9LS99	220	RING-H2 finger protein AT	no	no	0.843	0.540	0.387	2e-23
Q8LC69	185	RING-H2 finger protein AT	no	no	0.858	0.654	0.435	9e-23
Q94BY6	226	RING-H2 finger protein AT	no	no	0.843	0.526	0.382	2e-22

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

 Score =  127 bits (318), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 61/144 (42%), Positives = 94/144 (65%), Gaps = 7/144 (4%)

Query: 1   SADLNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMV 60
           S D ++++I+AA+LCAL+CALG++S+L+CV +CT+R          +  +  G+K++ + 
Sbjct: 36  SMDTHMVIILAALLCALICALGINSVLRCVLRCTRRFTPNEDPVDTNANVAKGIKKRALK 95

Query: 61  ALPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCP 120
            +P  +Y+      ++    C ICL DF++G+ +R+LPKCNH FHV CID WLLSHSSCP
Sbjct: 96  VIPVDSYSPELKMKATE---CLICLGDFVEGETVRVLPKCNHGFHVKCIDTWLLSHSSCP 152

Query: 121 TCRQRL----KPSDAMPSLDEIVT 140
           TCRQ L     P++     D++ T
Sbjct: 153 TCRQSLLEHQTPANGSRRGDDVAT 176

Arabidopsis thaliana (taxid: 3702)

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

 Score =  116 bits (290), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 64/133 (48%), Positives = 85/133 (63%), Gaps = 12/133 (9%)

Query: 3   DLNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRLN---------SG 53
           D N+++I+AA+LCAL+CAL L+S L+CV + T+R  T   Q   +   N         +G
Sbjct: 30  DTNMVIILAALLCALICALSLNSALRCVLRITRR-FTSDDQVSNASNANANLGRLAAATG 88

Query: 54  LKRKEMVALPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWL 113
           LK++ +  +P   Y  SG     A+  C ICL DF DG+++R+LPKCNH FHV CID WL
Sbjct: 89  LKKQALKQIPVGLYG-SGIIDMKATE-CLICLGDFEDGEKVRVLPKCNHGFHVRCIDTWL 146

Query: 114 LSHSSCPTCRQRL 126
           LS SSCPTCRQ L
Sbjct: 147 LSRSSCPTCRQSL 159

Arabidopsis thaliana (taxid: 3702)

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

 Score =  113 bits (283), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 55/123 (44%), Positives = 83/123 (67%), Gaps = 2/123 (1%)

Query: 3   DLNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRL-NSGLKRKEMVA 61
           D N++++++ +LCALVC+LGL+S+++C  +C+    +E        RL N+G+KRK + +
Sbjct: 53  DANVVMVLSVLLCALVCSLGLNSIIRCALRCSNLVPSEAGGDNYPVRLTNTGVKRKALKS 112

Query: 62  LPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPT 121
             TV+Y+   + P      CAICL +F+  + ++LLP C+H FHV CIDKWL SHSSCPT
Sbjct: 113 FQTVSYSTELNLPG-LDTECAICLSEFVAEERVKLLPTCHHGFHVRCIDKWLSSHSSCPT 171

Query: 122 CRQ 124
           CR 
Sbjct: 172 CRH 174

Arabidopsis thaliana (taxid: 3702)

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

 Score =  112 bits (279), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 60/133 (45%), Positives = 86/133 (64%), Gaps = 11/133 (8%)

Query: 1   SADLNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMV 60
           +A+ +++VI++A+LCAL+C  GL ++++C +    R  T       S   N GLK+K + 
Sbjct: 23  AAESDMVVILSALLCALICVAGLAAVVRCAWL---RRFTAGGD---SPSPNKGLKKKALQ 76

Query: 61  ALPTVTYANSGSSPSSA-----SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS 115
           +LP  T+  + S+  +A     S  CAICL DF DG+EIR+LP C H FHV CIDKWL+S
Sbjct: 77  SLPRSTFTAAESTSGAAAEEGDSTECAICLTDFADGEEIRVLPLCGHSFHVECIDKWLVS 136

Query: 116 HSSCPTCRQRLKP 128
            SSCP+CR+ L P
Sbjct: 137 RSSCPSCRRILTP 149

Arabidopsis thaliana (taxid: 3702)

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

 Score =  110 bits (276), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 51/123 (41%), Positives = 79/123 (64%), Gaps = 4/123 (3%)

Query: 5   NIMVIVAAMLCALVCALGLHSMLQCVFQCTQR-ALTEPRQWVVSRR--LNSGLKRKEMVA 61
           N+M++++ ++C ++C LGLH +++C  + + R  ++EP   + S R   N G+K+K +  
Sbjct: 57  NVMMLLSILICGIICCLGLHYIIRCALRRSTRFMISEPVPSLSSTRGSSNKGIKKKALRM 116

Query: 62  LPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPT 121
            P V+Y+   + P      C ICL DF+ G+++RLLPKCNH FHV CIDKWL  H +CP 
Sbjct: 117 FPVVSYSPEMNLPG-LDEECVICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQQHLTCPK 175

Query: 122 CRQ 124
           CR 
Sbjct: 176 CRN 178

Arabidopsis thaliana (taxid: 3702)

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

 Score =  110 bits (276), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 49/123 (39%), Positives = 77/123 (62%), Gaps = 4/123 (3%)

Query: 5   NIMVIVAAMLCALVCALGLHSMLQCVFQCTQR-ALTEP--RQWVVSRRLNSGLKRKEMVA 61
           N++++++ ++C ++C LGLH +++C F+ + R  ++EP           N G+K+K +  
Sbjct: 57  NVLMLLSVLICGIICCLGLHYIIRCAFRRSSRFMISEPISSLSTPRSSSNKGIKKKALRM 116

Query: 62  LPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPT 121
            P V+Y+   + P      C ICL DF+ G+++RLLPKCNH FHV CIDKWL  H +CP 
Sbjct: 117 FPVVSYSREMNLPGIGEE-CVICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQHHLTCPK 175

Query: 122 CRQ 124
           CR 
Sbjct: 176 CRH 178

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

 Score =  110 bits (275), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 63/131 (48%), Positives = 87/131 (66%), Gaps = 12/131 (9%)

Query: 5   NIMVIVAAMLCALVCALGLHSMLQCVF--------QCTQRALTEPRQWVVSRRLNSGLKR 56
           +++VI+AA+LCAL+C LGL ++ +CV+        +    + T+  Q  V+   N GLK+
Sbjct: 29  DLVVILAALLCALICVLGLIAVSRCVWLRRLAAGNRTVSGSQTQSPQPPVAAA-NKGLKK 87

Query: 57  KEMVALPTVTYANSGSSPSSAS-AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS 115
           K + +LP +T+  S  SP S   A CAICL +F  GDE+R+LP+C H FHVACID WL S
Sbjct: 88  KVLQSLPKLTF--SPESPESEKFAECAICLAEFSAGDELRVLPQCGHGFHVACIDTWLGS 145

Query: 116 HSSCPTCRQRL 126
           HSSCP+CRQ L
Sbjct: 146 HSSCPSCRQIL 156

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  107 bits (267), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 48/124 (38%), Positives = 79/124 (63%), Gaps = 5/124 (4%)

Query: 5   NIMVIVAAMLCALVCALGLHSMLQCVF-QCTQRALTEPRQWVVSRR---LNSGLKRKEMV 60
           N++++++ +LC ++C+LGLH +++C F +     +++P     + R   +N G+K+K + 
Sbjct: 51  NVLMLLSILLCGIICSLGLHYIIRCAFIRSRSFMISDPISIPSTPRDSSVNKGIKKKALK 110

Query: 61  ALPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCP 120
            LP V Y+   + P      C ICL DF+ G+++R+LPKCNH FH+ CIDKWL  H +CP
Sbjct: 111 MLPVVNYSPEINLPGVGEE-CVICLSDFVAGEQLRVLPKCNHGFHLRCIDKWLTQHMTCP 169

Query: 121 TCRQ 124
            CR 
Sbjct: 170 KCRH 173

Arabidopsis thaliana (taxid: 3702)

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

 Score =  105 bits (262), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 54/124 (43%), Positives = 80/124 (64%), Gaps = 3/124 (2%)

Query: 5   NIMVIVAAMLCALVCALGLHSMLQCVF--QCTQRALTEPRQWVVSRRLNSGLKRKEMVAL 62
           ++++I+A +LCAL C +GL ++ +C +  +   R  ++          N GLK+K + +L
Sbjct: 27  DLVLILAVLLCALTCIIGLIAVSRCAWLRRIASRNRSDQTHPPPVAAANKGLKKKVLRSL 86

Query: 63  PTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTC 122
           P +TY+   S P+     CAICL +F  GDE+R+LP+C H FHV+CID WL SHSSCP+C
Sbjct: 87  PKLTYS-PDSPPAEKLVECAICLTEFAAGDELRVLPQCGHGFHVSCIDTWLGSHSSCPSC 145

Query: 123 RQRL 126
           RQ L
Sbjct: 146 RQIL 149

Arabidopsis thaliana (taxid: 3702)

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

 Score =  104 bits (259), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 47/123 (38%), Positives = 77/123 (62%), Gaps = 4/123 (3%)

Query: 5   NIMVIVAAMLCALVCALGLHSMLQCVFQCTQR-ALTEPRQWVVS--RRLNSGLKRKEMVA 61
           N++++++ ++C ++C LGLH +++C F+ T    ++EP   + +     N G+ +K +  
Sbjct: 58  NVLMLLSVLICGIICCLGLHYIIRCAFRRTSSFMISEPIAGLSTPCGSSNKGINKKALRM 117

Query: 62  LPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPT 121
            P V+Y+   + P      C ICL DF+ G++IR+LPKC+H FHV CIDKWL  H +CP 
Sbjct: 118 FPVVSYSPEMNLPGLGEE-CVICLSDFVSGEQIRMLPKCHHGFHVRCIDKWLQQHLTCPK 176

Query: 122 CRQ 124
           CR 
Sbjct: 177 CRH 179

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	141
224138564	138	predicted protein [Populus trichocarpa]	0.971	0.992	0.776	2e-57
224074133	166	predicted protein [Populus trichocarpa]	0.964	0.819	0.748	4e-53
356558238	169	PREDICTED: RING-H2 finger protein ATL73-	0.971	0.810	0.673	1e-49
147818109	163	hypothetical protein VITISV_025310 [Viti	0.964	0.834	0.702	9e-47
359472767	163	PREDICTED: RING-H2 finger protein ATL73	0.964	0.834	0.695	2e-46
255585451	178	ring finger protein, putative [Ricinus c	0.978	0.775	0.673	7e-46
357449215	196	RING-H2 finger protein ATL2A [Medicago t	0.957	0.688	0.620	1e-44
356528138	168	PREDICTED: RING-H2 finger protein ATL73-	0.978	0.821	0.643	2e-44
242093856	162	hypothetical protein SORBIDRAFT_10g02665	0.929	0.808	0.610	9e-42
297725163	181	Os06g0666500 [Oryza sativa Japonica Grou	0.879	0.685	0.622	1e-40

>gi|224138564|ref|XP_002326634.1| predicted protein [Populus trichocarpa] gi|222833956|gb|EEE72433.1| predicted protein [Populus trichocarpa]

 Score =  226 bits (576), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 108/139 (77%), Positives = 125/139 (89%), Gaps = 2/139 (1%)

Query: 3   DLNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMVAL 62
           D N+MVIVAAM+CALVCALGL+SMLQCVFQCT+RA+TEP +W+ SRR NSGLK+KEMVAL
Sbjct: 2   DFNVMVIVAAMICALVCALGLNSMLQCVFQCTRRAVTEPAEWISSRRRNSGLKKKEMVAL 61

Query: 63  PTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTC 122
           PT TYA+ G SPSSAS GCAICL DF DGD+IR+LPKCNHRFH  CIDKWLLSHSSCPTC
Sbjct: 62  PTSTYAHQG-SPSSAS-GCAICLADFTDGDKIRVLPKCNHRFHADCIDKWLLSHSSCPTC 119

Query: 123 RQRLKPSDAMPSLDEIVTA 141
           R RLK ++++PSL++IVTA
Sbjct: 120 RHRLKSNESVPSLEQIVTA 138

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224074133|ref|XP_002304266.1| predicted protein [Populus trichocarpa] gi|222841698|gb|EEE79245.1| predicted protein [Populus trichocarpa]

 Score =  212 bits (539), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 104/139 (74%), Positives = 117/139 (84%), Gaps = 3/139 (2%)

Query: 3   DLNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMVAL 62
           D N+MVIVAAMLCA VCALGL+SMLQCVFQCTQR +TE   W+ SRR NSGLK++EMV L
Sbjct: 29  DFNVMVIVAAMLCAFVCALGLNSMLQCVFQCTQRTVTETAGWISSRRQNSGLKKREMVGL 88

Query: 63  PTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTC 122
           PT TYA+ G SPSS S GCAICL DF DGD+IR+LPKCNH FHV CIDKWLLSHSSCPTC
Sbjct: 89  PTSTYAHQG-SPSSTS-GCAICLADFTDGDKIRVLPKCNHEFHVDCIDKWLLSHSSCPTC 146

Query: 123 RQRLKPSD-AMPSLDEIVT 140
           R RLK  D ++PSL++IVT
Sbjct: 147 RHRLKSIDESVPSLEQIVT 165

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356558238|ref|XP_003547414.1| PREDICTED: RING-H2 finger protein ATL73-like [Glycine max]

 Score =  201 bits (510), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 93/138 (67%), Positives = 113/138 (81%), Gaps = 1/138 (0%)

Query: 4   LNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMVALP 63
           +N+MV++A ++CA +CALGL++MLQCVFQC  R LTEP QW+ SRRLNSGLK++EMVALP
Sbjct: 32  INLMVVLAVIVCAFLCALGLNTMLQCVFQCANRVLTEPLQWIASRRLNSGLKKREMVALP 91

Query: 64  TVTYANSGSSPSSASAG-CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTC 122
           T TY +S +SPSS S   CAICL +F DGD IR LP CNHRFHV CIDKWLLSHSSCPTC
Sbjct: 92  TSTYTHSCASPSSPSNNICAICLTEFSDGDRIRFLPNCNHRFHVDCIDKWLLSHSSCPTC 151

Query: 123 RQRLKPSDAMPSLDEIVT 140
           R  LKP+D++ SL  +V+
Sbjct: 152 RNLLKPTDSVHSLHTVVS 169

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147818109|emb|CAN67111.1| hypothetical protein VITISV_025310 [Vitis vinifera]

 Score =  191 bits (485), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 97/138 (70%), Positives = 117/138 (84%), Gaps = 2/138 (1%)

Query: 3   DLNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMVAL 62
           D N++VIVAAM+C LVCALGL+S LQCV +CT+ ALTEP QW  SRRLNSGLK+K+MVAL
Sbjct: 27  DFNLVVIVAAMVCFLVCALGLNSTLQCVVRCTRLALTEPVQWAASRRLNSGLKKKDMVAL 86

Query: 63  PTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTC 122
           PT TY+NSGS   S S+GC ICL DF DG++IR+LPKCNH FHV CIDKWLLSHSSCPTC
Sbjct: 87  PTSTYSNSGSP--SRSSGCVICLADFSDGEKIRVLPKCNHWFHVLCIDKWLLSHSSCPTC 144

Query: 123 RQRLKPSDAMPSLDEIVT 140
           R +LK +D++PSL+ ++T
Sbjct: 145 RNQLKSNDSLPSLETLIT 162

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359472767|ref|XP_002275910.2| PREDICTED: RING-H2 finger protein ATL73 [Vitis vinifera]

 Score =  190 bits (482), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 96/138 (69%), Positives = 117/138 (84%), Gaps = 2/138 (1%)

Query: 3   DLNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMVAL 62
           D N++VIVAAM+C LVCALGL+S LQCV +CT+ ALTEP QW  SRRLNSGLK+K+MVAL
Sbjct: 27  DFNLVVIVAAMVCFLVCALGLNSTLQCVVRCTRLALTEPVQWAASRRLNSGLKKKDMVAL 86

Query: 63  PTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTC 122
           PT TY+NSGS   S S+GC ICL DF DG++IR+LPKCNH FHV CIDKWLL+HSSCPTC
Sbjct: 87  PTSTYSNSGS--PSRSSGCVICLADFSDGEKIRVLPKCNHWFHVLCIDKWLLAHSSCPTC 144

Query: 123 RQRLKPSDAMPSLDEIVT 140
           R +LK +D++PSL+ ++T
Sbjct: 145 RNQLKSNDSLPSLETLIT 162

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255585451|ref|XP_002533419.1| ring finger protein, putative [Ricinus communis] gi|223526732|gb|EEF28962.1| ring finger protein, putative [Ricinus communis]

 Score =  188 bits (477), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 97/144 (67%), Positives = 115/144 (79%), Gaps = 6/144 (4%)

Query: 3   DLNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMVAL 62
           + N+MVIV AMLCALVCALGL+SMLQC  QCT R +T P +WV SRR NSGLK+KEMVAL
Sbjct: 33  NFNVMVIVGAMLCALVCALGLNSMLQCAIQCTHRVITGPVEWVASRRQNSGLKKKEMVAL 92

Query: 63  PTVTYAN------SGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH 116
           PT TY N      + +S S++++ CAICL DF DG++IR+LP+CNHRFHV CIDKWLLSH
Sbjct: 93  PTSTYVNSTSSPSASASSSASASSCAICLADFSDGEKIRVLPQCNHRFHVGCIDKWLLSH 152

Query: 117 SSCPTCRQRLKPSDAMPSLDEIVT 140
            SCPTCR+RLK SD+  SLD IVT
Sbjct: 153 PSCPTCRRRLKCSDSRTSLDHIVT 176

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357449215|ref|XP_003594884.1| RING-H2 finger protein ATL2A [Medicago truncatula] gi|355483932|gb|AES65135.1| RING-H2 finger protein ATL2A [Medicago truncatula]

 Score =  184 bits (467), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 85/137 (62%), Positives = 109/137 (79%), Gaps = 2/137 (1%)

Query: 4   LNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMVALP 63
           LN MV+VAA++CAL+CALGL++MLQCVFQC  R LTEP QW+ +RR NSGLK+KEMVALP
Sbjct: 62  LNSMVLVAAIVCALLCALGLNTMLQCVFQCANRVLTEPLQWIATRRRNSGLKKKEMVALP 121

Query: 64  TVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCR 123
           T  Y  +  SP S  + CAICL +F DGD ++LLPKCNHRFHV CID+WLL+HS CPTCR
Sbjct: 122 TSIY--NTHSPPSLDSNCAICLAEFCDGDNMKLLPKCNHRFHVVCIDEWLLAHSFCPTCR 179

Query: 124 QRLKPSDAMPSLDEIVT 140
           + +K +D++  L  +++
Sbjct: 180 KMIKSNDSVHCLSIVIS 196

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356528138|ref|XP_003532662.1| PREDICTED: RING-H2 finger protein ATL73-like [Glycine max]

 Score =  183 bits (464), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 92/143 (64%), Positives = 108/143 (75%), Gaps = 5/143 (3%)

Query: 2   ADLNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMVA 61
              + +V+VAA+LCA VCALGL++MLQCVFQC  R LTEPRQW+ SRRLNSGLK+KEMVA
Sbjct: 25  GGFDWIVLVAAILCAFVCALGLNTMLQCVFQCACRVLTEPRQWIASRRLNSGLKKKEMVA 84

Query: 62  LPTVTYANS-----GSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH 116
           LPT TY  +      SS S  S+ C ICL +F DGD IR LPKCNH FHV CIDKWLLSH
Sbjct: 85  LPTSTYTTTHSAAASSSSSPNSSSCVICLAEFSDGDPIRFLPKCNHYFHVVCIDKWLLSH 144

Query: 117 SSCPTCRQRLKPSDAMPSLDEIV 139
           SSCPTCR  LK +D++ SL  ++
Sbjct: 145 SSCPTCRHLLKSNDSLHSLHIVI 167

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242093856|ref|XP_002437418.1| hypothetical protein SORBIDRAFT_10g026650 [Sorghum bicolor] gi|241915641|gb|EER88785.1| hypothetical protein SORBIDRAFT_10g026650 [Sorghum bicolor]

 Score =  174 bits (441), Expect = 9e-42,   Method: Compositional matrix adjust.
 Identities = 83/136 (61%), Positives = 103/136 (75%), Gaps = 5/136 (3%)

Query: 3   DLNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMVAL 62
           D +++VI+AAMLCALVCALGL+SMLQCV +CT+RA+++P  WV  RR N+GLKR+E+VAL
Sbjct: 26  DYDVVVILAAMLCALVCALGLNSMLQCVVRCTRRAVSDPAAWVAHRRANAGLKREEVVAL 85

Query: 63  PTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTC 122
           P  TY       S A AGCAICL DF DG+ IR+LP C HRFHV CID+WL+SH SCPTC
Sbjct: 86  PVATYV-----ASPAPAGCAICLSDFADGERIRVLPVCGHRFHVVCIDRWLVSHCSCPTC 140

Query: 123 RQRLKPSDAMPSLDEI 138
           R+RL    A+   D +
Sbjct: 141 RRRLSSDSAVGGHDRL 156

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297725163|ref|NP_001174945.1| Os06g0666500 [Oryza sativa Japonica Group] gi|52076527|dbj|BAD45404.1| RING zinc finger protein-like [Oryza sativa Japonica Group] gi|125556398|gb|EAZ02004.1| hypothetical protein OsI_24035 [Oryza sativa Indica Group] gi|255677304|dbj|BAH93673.1| Os06g0666500 [Oryza sativa Japonica Group]

 Score =  171 bits (432), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 79/127 (62%), Positives = 100/127 (78%), Gaps = 3/127 (2%)

Query: 3   DLNIMVIVAAMLCALVCALGLHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMVAL 62
           D +++VI+AAMLCALVCALGL+SMLQCV +CT+RA+ +P  WV  RR  +GLKR+++VAL
Sbjct: 36  DYDVVVILAAMLCALVCALGLNSMLQCVVRCTRRAVADPVGWVEHRRAGAGLKREDVVAL 95

Query: 63  PTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTC 122
           P  TY    +SP+ + AGCAICL DF DG+ +RLLP C HRFHV CID+WLL+H SCPTC
Sbjct: 96  PVATYV---ASPAPSVAGCAICLSDFADGERVRLLPACGHRFHVVCIDRWLLAHCSCPTC 152

Query: 123 RQRLKPS 129
           R+R  P 
Sbjct: 153 RRRPSPE 159

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

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	141
TAIR|locus:2153554	176	DAF "DEFECTIVE IN ANTHER DEHIS	0.957	0.767	0.376	4.3e-22
TAIR|locus:2181032	159	DAFL2 "DAF-Like gene 2" [Arabi	0.851	0.754	0.362	1.2e-19
TAIR|locus:2103162	181	DAFL1 "DAF-Like gene 1" [Arabi	0.943	0.734	0.380	5.1e-19
TAIR|locus:2028406	225	AT1G49210 [Arabidopsis thalian	0.723	0.453	0.415	5.1e-19
TAIR|locus:2028436	219	AT1G49230 [Arabidopsis thalian	0.872	0.561	0.368	5.1e-19
TAIR|locus:2053863	185	RHA3A "RING-H2 finger A3A" [Ar	0.553	0.421	0.530	1.1e-18
TAIR|locus:2028506	251	AT1G49220 [Arabidopsis thalian	0.858	0.482	0.368	1.4e-18
TAIR|locus:2825708	197	AT1G20823 [Arabidopsis thalian	0.531	0.380	0.539	2.8e-18
TAIR|locus:2011686	185	ATL8 [Arabidopsis thaliana (ta	0.531	0.405	0.539	3.6e-18
TAIR|locus:2830088	220	AT3G18773 [Arabidopsis thalian	0.723	0.463	0.383	2.5e-17

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

 Score = 257 (95.5 bits), Expect = 4.3e-22, P = 4.3e-22
 Identities = 55/146 (37%), Positives = 81/146 (55%)

Query:     1 SADLNIMVIXXXXXXXXXXXXXXHSMLQCVFQCTQRALTEPRQWVVSRRLN--SGLKRKE 58
             S D ++++I              +S+L+CV +CT+R  T P +  V    N   G+K++ 
Sbjct:    36 SMDTHMVIILAALLCALICALGINSVLRCVLRCTRR-FT-PNEDPVDTNANVAKGIKKRA 93

Query:    59 MVALPTVTYANXXXXXXXXXXXCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSS 118
             +  +P  +Y+            C ICL DF++G+ +R+LPKCNH FHV CID WLLSHSS
Sbjct:    94 LKVIPVDSYSPELKMKATE---CLICLGDFVEGETVRVLPKCNHGFHVKCIDTWLLSHSS 150

Query:   119 CPTCRQRL----KPSDAMPSLDEIVT 140
             CPTCRQ L     P++     D++ T
Sbjct:   151 CPTCRQSLLEHQTPANGSRRGDDVAT 176

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

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

 Score = 234 (87.4 bits), Expect = 1.2e-19, P = 1.2e-19
 Identities = 45/124 (36%), Positives = 66/124 (53%)

Query:     3 DLNIMVIXXXXXXXXXXXXXXHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMVAL 62
             D N+++I              +S+L+C  +C     +      V+ R  +GLK++E+   
Sbjct:    31 DANMVIILAALLCALILALGLNSILRCAMRCGFGLSSSAAAGTVADR--AGLKKRELKKF 88

Query:    63 PTVTYANXXXXXXXXXXXCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTC 122
             P   Y +           CAICL +F DG+ +R+LP CNH FH++CID WL+SHSSCP C
Sbjct:    89 PVAEYGSGEVKIAATE--CAICLGEFADGERVRVLPPCNHSFHMSCIDTWLVSHSSCPNC 146

Query:   123 RQRL 126
             R  L
Sbjct:   147 RHSL 150

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

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

 Score = 228 (85.3 bits), Expect = 5.1e-19, P = 5.1e-19
 Identities = 56/147 (38%), Positives = 78/147 (53%)

Query:     3 DLNIMVIXXXXXXXXXXXXXXHSMLQCVFQCTQRALTEPRQWVVSR------RLNS--GL 54
             D N+++I              +S L+CV + T+R  ++ +    S       RL +  GL
Sbjct:    30 DTNMVIILAALLCALICALSLNSALRCVLRITRRFTSDDQVSNASNANANLGRLAAATGL 89

Query:    55 KRKEMVALPTVTYANXXXXXXXXXXXCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL 114
             K++ +  +P   Y +           C ICL DF DG+++R+LPKCNH FHV CID WLL
Sbjct:    90 KKQALKQIPVGLYGSGIIDMKATE--CLICLGDFEDGEKVRVLPKCNHGFHVRCIDTWLL 147

Query:   115 SHSSCPTCRQRL---KPSD-AMPSLDE 137
             S SSCPTCRQ L   +PS  A+   DE
Sbjct:   148 SRSSCPTCRQSLLLEQPSPMAVSRRDE 174

GO:0005634 "nucleus" evidence=ISM

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

GO:0010413 "glucuronoxylan metabolic process" evidence=RCA

GO:0045492 "xylan biosynthetic process" evidence=RCA

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

 Score = 228 (85.3 bits), Expect = 5.1e-19, P = 5.1e-19
 Identities = 44/106 (41%), Positives = 63/106 (59%)

Query:    24 HSMLQCVFQCTQR-ALTEPRQWVVSRRL--NSGLKRKEMVALPTVTYANXXXXXXXXXXX 80
             H +++C F+ + R  ++EP   + + R   N G+K+K +   P V+Y+            
Sbjct:    76 HYIIRCAFRRSSRFMISEPISSLSTPRSSSNKGIKKKALRMFPVVSYSREMNLPGIGEE- 134

Query:    81 CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRL 126
             C ICL DF+ G+++RLLPKCNH FHV CIDKWL  H +CP CR  L
Sbjct:   135 CVICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQHHLTCPKCRHCL 180

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

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

GO:0016567 "protein ubiquitination" evidence=IDA

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

 Score = 228 (85.3 bits), Expect = 5.1e-19, P = 5.1e-19
 Identities = 46/125 (36%), Positives = 69/125 (55%)

Query:     3 DLNIMVIXXXXXXXXXXXXXXHSMLQCVFQCTQRALTEPRQWVVSRRL-NSGLKRKEMVA 61
             D N++++              +S+++C  +C+    +E        RL N+G+KRK + +
Sbjct:    53 DANVVMVLSVLLCALVCSLGLNSIIRCALRCSNLVPSEAGGDNYPVRLTNTGVKRKALKS 112

Query:    62 LPTVTYANXXXXXXXXXXXCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPT 121
               TV+Y+            CAICL +F+  + ++LLP C+H FHV CIDKWL SHSSCPT
Sbjct:   113 FQTVSYSTELNLPGLDTE-CAICLSEFVAEERVKLLPTCHHGFHVRCIDKWLSSHSSCPT 171

Query:   122 CRQRL 126
             CR  L
Sbjct:   172 CRHCL 176

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

TAIR|locus:2053863 RHA3A "RING-H2 finger A3A" [Arabidopsis thaliana (taxid:3702)]

 Score = 225 (84.3 bits), Expect = 1.1e-18, P = 1.1e-18
 Identities = 44/83 (53%), Positives = 52/83 (62%)

Query:    51 NSGLKRKEMVALP--TVTYANXXXXXXXX---XXXCAICLLDFIDGDEIRLLPKCNHRFH 105
             N GLK+K + +LP  T T A               CAICL DF DG+EIR+LP C H FH
Sbjct:    67 NKGLKKKALQSLPRSTFTAAESTSGAAAEEGDSTECAICLTDFADGEEIRVLPLCGHSFH 126

Query:   106 VACIDKWLLSHSSCPTCRQRLKP 128
             V CIDKWL+S SSCP+CR+ L P
Sbjct:   127 VECIDKWLVSRSSCPSCRRILTP 149

GO:0005634 "nucleus" evidence=ISM

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

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

 Score = 224 (83.9 bits), Expect = 1.4e-18, P = 1.4e-18
 Identities = 46/125 (36%), Positives = 67/125 (53%)

Query:     5 NIMVIXXXXXXXXXXXXXXHSMLQCVFQCTQR-ALTEPRQWVVSRR--LNSGLKRKEMVA 61
             N+M++              H +++C  + + R  ++EP   + S R   N G+K+K +  
Sbjct:    57 NVMMLLSILICGIICCLGLHYIIRCALRRSTRFMISEPVPSLSSTRGSSNKGIKKKALRM 116

Query:    62 LPTVTYANXXXXXXXXXXXCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPT 121
              P V+Y+            C ICL DF+ G+++RLLPKCNH FHV CIDKWL  H +CP 
Sbjct:   117 FPVVSYSPEMNLPGLDEE-CVICLSDFVSGEQLRLLPKCNHGFHVRCIDKWLQQHLTCPK 175

Query:   122 CRQRL 126
             CR  L
Sbjct:   176 CRNCL 180

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

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

 Score = 221 (82.9 bits), Expect = 2.8e-18, P = 2.8e-18
 Identities = 41/76 (53%), Positives = 52/76 (68%)

Query:    51 NSGLKRKEMVALPTVTYANXXXXXXXXXXXCAICLLDFIDGDEIRLLPKCNHRFHVACID 110
             N GLK+K + +LP +T++            CAICL +F  GDE+R+LP+C H FHVACID
Sbjct:    82 NKGLKKKVLQSLPKLTFSPESPESEKFAE-CAICLAEFSAGDELRVLPQCGHGFHVACID 140

Query:   111 KWLLSHSSCPTCRQRL 126
              WL SHSSCP+CRQ L
Sbjct:   141 TWLGSHSSCPSCRQIL 156

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

GO:0009507 "chloroplast" evidence=ISM

GO:0010200 "response to chitin" evidence=IEP

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

 Score = 220 (82.5 bits), Expect = 3.6e-18, P = 3.6e-18
 Identities = 41/76 (53%), Positives = 52/76 (68%)

Query:    51 NSGLKRKEMVALPTVTYANXXXXXXXXXXXCAICLLDFIDGDEIRLLPKCNHRFHVACID 110
             N GLK+K + +LP +TY+            CAICL +F  GDE+R+LP+C H FHV+CID
Sbjct:    75 NKGLKKKVLRSLPKLTYSPDSPPAEKLVE-CAICLTEFAAGDELRVLPQCGHGFHVSCID 133

Query:   111 KWLLSHSSCPTCRQRL 126
              WL SHSSCP+CRQ L
Sbjct:   134 TWLGSHSSCPSCRQIL 149

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:2830088 AT3G18773 [Arabidopsis thaliana (taxid:3702)]

 Score = 212 (79.7 bits), Expect = 2.5e-17, P = 2.5e-17
 Identities = 41/107 (38%), Positives = 61/107 (57%)

Query:    24 HSMLQCVF-QCTQRALTEPRQWVVSRR---LNSGLKRKEMVALPTVTYANXXXXXXXXXX 79
             H +++C F +     +++P     + R   +N G+K+K +  LP V Y+           
Sbjct:    70 HYIIRCAFIRSRSFMISDPISIPSTPRDSSVNKGIKKKALKMLPVVNYSPEINLPGVGEE 129

Query:    80 XCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRL 126
              C ICL DF+ G+++R+LPKCNH FH+ CIDKWL  H +CP CR  L
Sbjct:   130 -CVICLSDFVAGEQLRVLPKCNHGFHLRCIDKWLTQHMTCPKCRHCL 175

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	141
COG5540	374	COG5540, COG5540, RING-finger-containing ubiquitin	2e-16
pfam13639	46	pfam13639, zf-RING_2, Ring finger domain	2e-13
cd00162	45	cd00162, RING, RING-finger (Really Interesting New	2e-09
pfam12678	73	pfam12678, zf-rbx1, RING-H2 zinc finger	8e-09
PHA02929	238	PHA02929, PHA02929, N1R/p28-like protein; Provisio	2e-06
COG5219	1525	COG5219, COG5219, Uncharacterized conserved protei	5e-06
COG5243	491	COG5243, HRD1, HRD ubiquitin ligase complex, ER me	2e-05
smart00184	40	smart00184, RING, Ring finger	3e-05
COG5194	88	COG5194, APC11, Component of SCF ubiquitin ligase	5e-05
pfam13923	45	pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RI	6e-05
pfam12861	85	pfam12861, zf-Apc11, Anaphase-promoting complex su	3e-04
pfam11793	70	pfam11793, FANCL_C, FANCL C-terminal domain	0.001
TIGR00599	397	TIGR00599, rad18, DNA repair protein rad18	0.004

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

 Score = 73.5 bits (180), Expect = 2e-16
 Identities = 28/49 (57%), Positives = 36/49 (73%), Gaps = 2/49 (4%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS-SCPTCRQRLKP 128
           CAIC+ +FI  D +R+LP C+HRFHV C+DKWLL +S  CP CR  + P
Sbjct: 326 CAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373

Length = 374

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

 Score = 60.1 bits (146), Expect = 2e-13
 Identities = 23/45 (51%), Positives = 30/45 (66%), Gaps = 1/45 (2%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQR 125
           C ICL +F  G+E+ +LP C H FH  C+DKWL S ++CP CR  
Sbjct: 3   CPICLDEFEPGEEVVVLP-CGHVFHKECLDKWLRSSNTCPLCRAP 46

Length = 46

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

 Score = 49.8 bits (119), Expect = 2e-09
 Identities = 21/47 (44%), Positives = 27/47 (57%), Gaps = 4/47 (8%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRL 126
           C ICL +F    E  +L  C H F  +CIDKWL S  ++CP CR  +
Sbjct: 2   CPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45

Length = 45

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

 Score = 49.0 bits (117), Expect = 8e-09
 Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 9/52 (17%)

Query: 81  CAICLLDFID--------GDEIRL-LPKCNHRFHVACIDKWLLSHSSCPTCR 123
           CAIC   F          GD+  +   +C H FH+ CI +WL + ++CP CR
Sbjct: 22  CAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 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|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional

 Score = 44.8 bits (106), Expect = 2e-06
 Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 6/48 (12%)

Query: 81  CAICLLDFIDGDEIR-----LLPKCNHRFHVACIDKWLLSHSSCPTCR 123
           CAIC+    D  EI+     +L  CNH F + CID W    ++CP CR
Sbjct: 177 CAICMEKVYD-KEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCR 223

Length = 238

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

 Score = 44.7 bits (105), Expect = 5e-06
 Identities = 22/52 (42%), Positives = 28/52 (53%), Gaps = 13/52 (25%)

Query: 81   CAIC--LLDFIDGDEIRLLPK-----CNHRFHVACIDKWLLS--HSSCPTCR 123
            CAIC  +LD +D    R LP      C ++FH  C+ KW  S   S+CP CR
Sbjct: 1472 CAICYSVLDMVD----RSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCR 1519

Length = 1525

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

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 27/110 (24%), Positives = 40/110 (36%), Gaps = 21/110 (19%)

Query: 23  LHSMLQCVFQCTQRALTEPRQWVVSRRLNSGLKRKEMVALPTVTYANSGSSPSSASAGCA 82
           +  M  C +   +R     R    ++ LN+          PT T     +S  +    C 
Sbjct: 244 IRQMYTCFYALFRRIREHARFRRATKDLNA--------MYPTATEEQLTNSDRT----CT 291

Query: 83  ICLLDFIDGDEIRL------LPK---CNHRFHVACIDKWLLSHSSCPTCR 123
           IC+ +    D   L       PK   C H  H+ C+  WL    +CP CR
Sbjct: 292 ICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICR 341

Length = 491

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

 Score = 38.6 bits (90), Expect = 3e-05
 Identities = 18/43 (41%), Positives = 26/43 (60%), Gaps = 4/43 (9%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS-SCPTC 122
           C ICL +++   +  +LP C H F  +CI KWL S + +CP C
Sbjct: 1   CPICLEEYLK--DPVILP-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|227521 COG5194, APC11, Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]

 Score = 39.4 bits (92), Expect = 5e-05
 Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 12/56 (21%)

Query: 81  CAICLLDFID-----------GDEIRLL-PKCNHRFHVACIDKWLLSHSSCPTCRQ 124
           CAIC    +            GDE  ++   CNH FH  CI +WL +   CP  RQ
Sbjct: 23  CAICRNHIMGTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQ 78

Length = 88

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

 Score = 37.9 bits (88), Expect = 6e-05
 Identities = 17/44 (38%), Positives = 20/44 (45%), Gaps = 3/44 (6%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQ 124
           C ICL    D     +L  C H F   CI ++L   S CP CR 
Sbjct: 5   CPICLDLLRD---PVVLTPCGHVFCRECILRYLKKKSKCPICRT 45

Length = 45

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

 Score = 37.1 bits (86), Expect = 3e-04
 Identities = 23/59 (38%), Positives = 28/59 (47%), Gaps = 12/59 (20%)

Query: 81  CAICLLDF--------IDGDEIRL-LPKCNHRFHVACIDKWLLSHSS---CPTCRQRLK 127
           C IC + F          GD+  L   KC H FH+ CI KWL + +S   CP CRQ   
Sbjct: 24  CGICRVSFDGTCPQCKFPGDDCPLVWGKCKHNFHMHCILKWLATETSKGLCPMCRQTFV 82

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

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

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 15/66 (22%)

Query: 81  CAICLLDFIDGDEIRLL----PKCNHRFHVACIDKWLLSHSS-----------CPTCRQR 125
           C IC    +DG EI  +    PKC   FH+AC+ +WL +              CP C+ +
Sbjct: 5   CGICYAYRLDGGEIPDISCDNPKCGLPFHIACLYEWLRTLRDSRQSFNVSFGTCPYCKAK 64

Query: 126 LKPSDA 131
           +    +
Sbjct: 65  ISVKFS 70

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

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

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 4/43 (9%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCR 123
           C IC  DF D   + +L  C+H F   CI + L +   CP CR
Sbjct: 29  CHICK-DFFD---VPVLTSCSHTFCSLCIRRCLSNQPKCPLCR 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	141
KOG4628	348	consensus Predicted E3 ubiquitin ligase [Posttrans	99.88
PF13639	44	zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C	99.78
PHA02929	238	N1R/p28-like protein; Provisional	99.66
PF12678	73	zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766	99.61
COG5243	491	HRD1 HRD ubiquitin ligase complex, ER membrane com	99.58
COG5540	374	RING-finger-containing ubiquitin ligase [Posttrans	99.58
KOG0317	293	consensus Predicted E3 ubiquitin ligase, integral	99.54
PLN03208	193	E3 ubiquitin-protein ligase RMA2; Provisional	99.43
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	99.4
PF13923	39	zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger);	99.38
cd00162	45	RING RING-finger (Really Interesting New Gene) dom	99.38
KOG0823	230	consensus Predicted E3 ubiquitin ligase [Posttrans	99.3
PF12861	85	zf-Apc11: Anaphase-promoting complex subunit 11 RI	99.29
KOG0320	187	consensus Predicted E3 ubiquitin ligase [Posttrans	99.29
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	99.27
PHA02926	242	zinc finger-like protein; Provisional	99.26
PF14634	44	zf-RING_5: zinc-RING finger domain	99.25
PF15227	42	zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB:	99.23
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	99.2
PF00097	41	zf-C3HC4: Zinc finger, C3HC4 type (RING finger); I	99.2
smart00184	39	RING Ring finger. E3 ubiquitin-protein ligase acti	99.13
TIGR00599	397	rad18 DNA repair protein rad18. This family is bas	99.07
KOG0828	636	consensus Predicted E3 ubiquitin ligase [Posttrans	99.02
COG5194	88	APC11 Component of SCF ubiquitin ligase and anapha	99.0
KOG1734	328	consensus Predicted RING-containing E3 ubiquitin l	98.99
COG5574	271	PEX10 RING-finger-containing E3 ubiquitin ligase [	98.98
KOG1493	84	consensus Anaphase-promoting complex (APC), subuni	98.88
KOG0287	442	consensus Postreplication repair protein RAD18 [Re	98.86
smart00744	49	RINGv The RING-variant domain is a C4HC3 zinc-fing	98.82
KOG2164	513	consensus Predicted E3 ubiquitin ligase [Posttrans	98.8
PF11793	70	FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.	98.79
PF13445	43	zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.	98.76
PF04564	73	U-box: U-box domain; InterPro: IPR003613 Quality c	98.74
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.74
TIGR00570	309	cdk7 CDK-activating kinase assembly factor MAT1. A	98.73
KOG2930	114	consensus SCF ubiquitin ligase, Rbx1 component [Po	98.73
COG5432	391	RAD18 RING-finger-containing E3 ubiquitin ligase [	98.69
COG5219	1525	Uncharacterized conserved protein, contains RING Z	98.56
KOG4265	349	consensus Predicted E3 ubiquitin ligase [Posttrans	98.55
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	98.54
KOG2177	386	consensus Predicted E3 ubiquitin ligase [Posttrans	98.54
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	98.53
KOG4172	62	consensus Predicted E3 ubiquitin ligase [Posttrans	98.43
KOG0311	381	consensus Predicted E3 ubiquitin ligase [Posttrans	98.4
KOG1645	463	consensus RING-finger-containing E3 ubiquitin liga	98.24
KOG1039	344	consensus Predicted E3 ubiquitin ligase [Posttrans	98.21
KOG0825	1134	consensus PHD Zn-finger protein [General function	98.18
KOG0978	698	consensus E3 ubiquitin ligase involved in syntaxin	98.16
KOG4445	368	consensus Uncharacterized conserved protein, conta	98.11
KOG0297	391	consensus TNF receptor-associated factor [Signal t	98.06
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	98.03
KOG3970	299	consensus Predicted E3 ubiquitin ligase [Posttrans	98.02
KOG1941	518	consensus Acetylcholine receptor-associated protei	97.98
KOG4159	398	consensus Predicted E3 ubiquitin ligase [Posttrans	97.91
KOG1785	563	consensus Tyrosine kinase negative regulator CBL [	97.89
PF14570	48	zf-RING_4: RING/Ubox like zinc-binding domain; PDB	97.89
PF11789	57	zf-Nse: Zinc-finger of the MIZ type in Nse subunit	97.88
PHA02862	156	5L protein; Provisional	97.85
PF05883	134	Baculo_RING: Baculovirus U-box/Ring-like domain; I	97.8
KOG0826	357	consensus Predicted E3 ubiquitin ligase involved i	97.78
PHA02825	162	LAP/PHD finger-like protein; Provisional	97.77
KOG2660	331	consensus Locus-specific chromosome binding protei	97.58
KOG2879	298	consensus Predicted E3 ubiquitin ligase [Posttrans	97.54
KOG0801	205	consensus Predicted E3 ubiquitin ligase [Posttrans	97.53
KOG1428	3738	consensus Inhibitor of type V adenylyl cyclases/Ne	97.51
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.41
KOG1952	950	consensus Transcription factor NF-X1, contains NFX	97.39
KOG1571	355	consensus Predicted E3 ubiquitin ligase [Posttrans	97.37
COG5152	259	Uncharacterized conserved protein, contains RING a	97.35
KOG3039	303	consensus Uncharacterized conserved protein [Funct	97.3
PF12906	47	RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.	97.2
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	97.19
KOG1814	445	consensus Predicted E3 ubiquitin ligase [Posttrans	97.19
COG5236	493	Uncharacterized conserved protein, contains RING Z	97.17
PHA03096	284	p28-like protein; Provisional	97.09
PF08746	43	zf-RING-like: RING-like domain; InterPro: IPR01485	97.07
KOG4692	489	consensus Predicted E3 ubiquitin ligase [Posttrans	97.02
KOG4739	233	consensus Uncharacterized protein involved in syna	96.95
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	96.94
KOG3268	234	consensus Predicted E3 ubiquitin ligase [Posttrans	96.89
PF14447	55	Prok-RING_4: Prokaryotic RING finger family 4	96.84
KOG4275	350	consensus Predicted E3 ubiquitin ligase [Posttrans	96.75
KOG1813	313	consensus Predicted E3 ubiquitin ligase [Posttrans	96.71
PF04641	260	Rtf2: Rtf2 RING-finger	96.68
KOG0827	465	consensus Predicted E3 ubiquitin ligase [Posttrans	96.63
COG5222	427	Uncharacterized conserved protein, contains RING Z	96.52
KOG2034	911	consensus Vacuolar sorting protein PEP3/VPS18 [Int	96.5
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.48
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	96.36
KOG0309	1081	consensus Conserved WD40 repeat-containing protein	96.27
KOG1001	674	consensus Helicase-like transcription factor HLTF/	96.08
PF10272	358	Tmpp129: Putative transmembrane protein precursor;	95.96
KOG1940	276	consensus Zn-finger protein [General function pred	95.9
KOG4185	296	consensus Predicted E3 ubiquitin ligase [Posttrans	95.83
PF07800	162	DUF1644: Protein of unknown function (DUF1644); In	95.83
KOG2817	394	consensus Predicted E3 ubiquitin ligase [Posttrans	95.67
PF03854	50	zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc	94.72
KOG3002	299	consensus Zn finger protein [General function pred	94.71
KOG2932	389	consensus E3 ubiquitin ligase involved in ubiquiti	94.62
KOG1100	207	consensus Predicted E3 ubiquitin ligase [Posttrans	94.57
COG5183	1175	SSM4 Protein involved in mRNA turnover and stabili	94.55
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	94.49
KOG0298	1394	consensus DEAD box-containing helicase-like transc	94.47
KOG1609	323	consensus Protein involved in mRNA turnover and st	93.55
KOG3800	300	consensus Predicted E3 ubiquitin ligase containing	93.54
COG5220	314	TFB3 Cdk activating kinase (CAK)/RNA polymerase II	93.38
KOG3053	293	consensus Uncharacterized conserved protein [Funct	93.34
TIGR00622	112	ssl1 transcription factor ssl1. This family is bas	93.3
PF05290	140	Baculo_IE-1: Baculovirus immediate-early protein (	92.69
PF15050	133	SCIMP: SCIMP protein	92.37
KOG3161	861	consensus Predicted E3 ubiquitin ligase [Posttrans	91.67
KOG3899	381	consensus Uncharacterized conserved protein [Funct	91.46
PF01102	122	Glycophorin_A: Glycophorin A; InterPro: IPR001195	91.34
PF07975	51	C1_4: TFIIH C1-like domain; InterPro: IPR004595 Al	91.12
KOG3113	293	consensus Uncharacterized conserved protein [Funct	90.72
KOG2807	378	consensus RNA polymerase II transcription initiati	90.38
KOG4367	699	consensus Predicted Zn-finger protein [Function un	90.11
PF10571	26	UPF0547: Uncharacterised protein family UPF0547; I	89.35
KOG0802	543	consensus E3 ubiquitin ligase [Posttranslational m	88.98
PF13901	202	DUF4206: Domain of unknown function (DUF4206)	88.92
KOG1815	444	consensus Predicted E3 ubiquitin ligase [Posttrans	88.42
KOG1829	580	consensus Uncharacterized conserved protein, conta	88.23
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	87.96
KOG4362	684	consensus Transcriptional regulator BRCA1 [Replica	87.88
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	87.8
KOG3005	276	consensus GIY-YIG type nuclease [General function	87.77
KOG0269	839	consensus WD40 repeat-containing protein [Function	87.7
KOG4718	235	consensus Non-SMC (structural maintenance of chrom	87.54
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	87.08
PF15176	102	LRR19-TM: Leucine-rich repeat family 19 TM domain	86.69
PF02439	38	Adeno_E3_CR2: Adenovirus E3 region protein CR2; In	86.55
COG5109	396	Uncharacterized conserved protein, contains RING Z	86.18
PF02891	50	zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR0041	85.9
smart00249	47	PHD PHD zinc finger. The plant homeodomain (PHD) f	85.52
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	84.57
KOG1812	384	consensus Predicted E3 ubiquitin ligase [Posttrans	84.38
PHA03029	92	hypothetical protein; Provisional	83.19
PF15179	197	Myc_target_1: Myc target protein 1	83.18
PF01363	69	FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc f	83.08
KOG3842	429	consensus Adaptor protein Pellino [Signal transduc	83.03
KOG0824	324	consensus Predicted E3 ubiquitin ligase [Posttrans	82.57
PF02009	299	Rifin_STEVOR: Rifin/stevor family; InterPro: IPR00	82.46
PF12273	130	RCR: Chitin synthesis regulation, resistance to Co	82.13
KOG0825	1134	consensus PHD Zn-finger protein [General function	81.95
KOG3039	303	consensus Uncharacterized conserved protein [Funct	81.83
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	81.65
PF00628	51	PHD: PHD-finger; InterPro: IPR019787 Zinc finger (	81.52
PF06906	57	DUF1272: Protein of unknown function (DUF1272); In	81.31
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	81.08

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

Probab=99.88  E-value=6.5e-23  Score=151.89  Aligned_cols=81  Identities=35%  Similarity=0.867  Sum_probs=67.5

Q ss_pred             cCCCCHHHHhhCCceeecCCCCCCCCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC-CccccccccccCC
Q 038049           51 NSGLKRKEMVALPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH-SSCPTCRQRLKPS  129 (141)
Q Consensus        51 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~-~~CP~CR~~~~~~  129 (141)
                      .+.+.++.+.++|..+|+....+...  .+|+||||+|+++|+++.|| |+|.||..||+.||.+. ..||+|++++...
T Consensus       204 ~~r~~k~~l~~~p~~~f~~~~~~~~~--~~CaIClEdY~~GdklRiLP-C~H~FH~~CIDpWL~~~r~~CPvCK~di~~~  280 (348)
T KOG4628|consen  204 RNRLIKRLLKKLPVRTFTKGDDEDAT--DTCAICLEDYEKGDKLRILP-CSHKFHVNCIDPWLTQTRTFCPVCKRDIRTD  280 (348)
T ss_pred             hhhhHHHHHhhCCcEEeccccccCCC--ceEEEeecccccCCeeeEec-CCCchhhccchhhHhhcCccCCCCCCcCCCC
Confidence            34456788899999999986555444  68999999999999999999 99999999999999876 5599999988755


Q ss_pred             CCCCC
Q 038049          130 DAMPS  134 (141)
Q Consensus       130 ~~~~~  134 (141)
                      ...+.
T Consensus       281 ~~~~~  285 (348)
T KOG4628|consen  281 SGSEP  285 (348)
T ss_pred             CCCCC
Confidence            44433

>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=99.78  E-value=6.8e-20  Score=98.86  Aligned_cols=44  Identities=50%  Similarity=1.217  Sum_probs=40.4

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCcccccc
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCR  123 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR  123 (141)
                      ++|+||++++.+++.+..++ |||.||.+||.+|++++.+||+||
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            36999999999999999998 999999999999999999999998

...

>PHA02929 N1R/p28-like protein; Provisional

Probab=99.66  E-value=7e-17  Score=115.15  Aligned_cols=76  Identities=29%  Similarity=0.607  Sum_probs=57.1

Q ss_pred             CCCCHHHHhhCCceeecCCCCCCCCCcccccccccccccCCc----eeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           52 SGLKRKEMVALPTVTYANSGSSPSSASAGCAICLLDFIDGDE----IRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        52 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~----v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      ++..+..++.+|.....-........+.+|+||++.+.+++.    +..++.|+|.||.+||.+|+..+.+||+||.++.
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            455677788888886554333233456889999999866431    2344459999999999999999999999999875

>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=99.61  E-value=4.3e-16  Score=92.58  Aligned_cols=45  Identities=42%  Similarity=0.938  Sum_probs=35.6

Q ss_pred             cccccccccccccC----------CceeecCCCCCcccHhhHHHHHcCCCcccccc
Q 038049           78 SAGCAICLLDFIDG----------DEIRLLPKCNHRFHVACIDKWLLSHSSCPTCR  123 (141)
Q Consensus        78 ~~~C~ICl~~~~~~----------~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR  123 (141)
                      ++.|+||++++.+.          -.+...+ |||.||..||.+|++.+.+||+||
T Consensus        19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR   73 (73)
T PF12678_consen   19 DDNCAICREPLEDPCPECQAPQDECPIVWGP-CGHIFHFHCISQWLKQNNTCPLCR   73 (73)
T ss_dssp             CSBETTTTSBTTSTTCCHHHCTTTS-EEEET-TSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred             CCcccccChhhhChhhhhcCCccccceEecc-cCCCEEHHHHHHHHhcCCcCCCCC
Confidence            34599999999332          2344555 999999999999999999999998

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

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

Probab=99.58  E-value=1.5e-15  Score=112.51  Aligned_cols=63  Identities=29%  Similarity=0.729  Sum_probs=48.0

Q ss_pred             hhCCceeecCCCCCCCCCccccccccccc-ccC---------CceeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           60 VALPTVTYANSGSSPSSASAGCAICLLDF-IDG---------DEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        60 ~~~~~~~~~~~~~~~~~~~~~C~ICl~~~-~~~---------~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      +..|..+..+.    ..++..|.||||++ .++         .+...+| |||+||-+|+..|++++++||+||.++.
T Consensus       273 ~~~~t~t~eql----~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLp-CGHilHl~CLknW~ERqQTCPICr~p~i  345 (491)
T COG5243         273 AMYPTATEEQL----TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLP-CGHILHLHCLKNWLERQQTCPICRRPVI  345 (491)
T ss_pred             hhcchhhhhhh----cCCCCeEEEecccccCCCCccCcccccCCccccc-ccceeeHHHHHHHHHhccCCCcccCccc
Confidence            33444444433    45668899999994 333         1346788 9999999999999999999999999953

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

Probab=99.58  E-value=1.1e-15  Score=110.63  Aligned_cols=52  Identities=52%  Similarity=1.276  Sum_probs=47.4

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHc-CCCccccccccccC
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL-SHSSCPTCRQRLKP  128 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~~~~  128 (141)
                      +...+|+|||+.|..+|.++.+| |.|.||..|++.|+. -+..||+||.++++
T Consensus       321 ~~GveCaICms~fiK~d~~~vlP-C~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP  373 (374)
T COG5540         321 DKGVECAICMSNFIKNDRLRVLP-CDHRFHVGCVDKWLLGYSNKCPVCRTAIPP  373 (374)
T ss_pred             CCCceEEEEhhhhcccceEEEec-cCceechhHHHHHHhhhcccCCccCCCCCC
Confidence            34588999999999999999999 999999999999998 56789999999875

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

Probab=99.54  E-value=6e-15  Score=106.14  Aligned_cols=53  Identities=32%  Similarity=0.824  Sum_probs=46.0

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDA  131 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~  131 (141)
                      ......|++||+...++   .-+| |||+||+.||.+|...+..||+||....+.+.
T Consensus       236 ~~a~~kC~LCLe~~~~p---SaTp-CGHiFCWsCI~~w~~ek~eCPlCR~~~~pskv  288 (293)
T KOG0317|consen  236 PEATRKCSLCLENRSNP---SATP-CGHIFCWSCILEWCSEKAECPLCREKFQPSKV  288 (293)
T ss_pred             CCCCCceEEEecCCCCC---CcCc-CcchHHHHHHHHHHccccCCCcccccCCCcce
Confidence            45568899999987666   7888 99999999999999999999999998877653

>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional

Probab=99.43  E-value=8.6e-14  Score=95.84  Aligned_cols=54  Identities=30%  Similarity=0.735  Sum_probs=43.0

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC----------------CCccccccccccCCCCCC
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS----------------HSSCPTCRQRLKPSDAMP  133 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~----------------~~~CP~CR~~~~~~~~~~  133 (141)
                      .++.+|+||++.+.++   .+++ |||.||+.||..|+..                ...||+||+.+......|
T Consensus        16 ~~~~~CpICld~~~dP---VvT~-CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvP   85 (193)
T PLN03208         16 GGDFDCNICLDQVRDP---VVTL-CGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVP   85 (193)
T ss_pred             CCccCCccCCCcCCCc---EEcC-CCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEE
Confidence            4567899999998665   5677 9999999999999852                346999999987655443

>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=99.40  E-value=1.5e-13  Score=75.82  Aligned_cols=46  Identities=35%  Similarity=0.865  Sum_probs=38.7

Q ss_pred             cccccccccccccCCceeecCCCCCc-ccHhhHHHHHcCCCcccccccccc
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHR-FHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      +..|.||++...   .+..+| |||. |+.+|+..|+.++..||+||+++.
T Consensus         2 ~~~C~iC~~~~~---~~~~~p-CgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    2 DEECPICFENPR---DVVLLP-CGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             HSB-TTTSSSBS---SEEEET-TCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             cCCCccCCccCC---ceEEeC-CCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            467999998854   357888 9999 999999999999999999999875

...

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

Probab=99.38  E-value=3e-13  Score=70.81  Aligned_cols=39  Identities=41%  Similarity=1.057  Sum_probs=32.6

Q ss_pred             ccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccc
Q 038049           81 CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTC  122 (141)
Q Consensus        81 C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~C  122 (141)
                      |+||++.+.+  .+..++ |||.|+.+|+..|++.+..||+|
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            8999998765  445777 99999999999999999999998

>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=99.38  E-value=4e-13  Score=71.95  Aligned_cols=44  Identities=50%  Similarity=1.185  Sum_probs=36.8

Q ss_pred             cccccccccccCCceeecCCCCCcccHhhHHHHHcC-CCccccccccc
Q 038049           80 GCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRL  126 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~  126 (141)
                      +|+||++.+  .+.+...+ |||.||.+|+..|+.. +..||.||..+
T Consensus         1 ~C~iC~~~~--~~~~~~~~-C~H~~c~~C~~~~~~~~~~~Cp~C~~~~   45 (45)
T cd00162           1 ECPICLEEF--REPVVLLP-CGHVFCRSCIDKWLKSGKNTCPLCRTPI   45 (45)
T ss_pred             CCCcCchhh--hCceEecC-CCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence            599999998  34455665 9999999999999987 77899999864

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

Probab=99.30  E-value=1.1e-12  Score=92.02  Aligned_cols=55  Identities=27%  Similarity=0.653  Sum_probs=43.5

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC---CccccccccccCCCCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH---SSCPTCRQRLKPSDAMP  133 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~---~~CP~CR~~~~~~~~~~  133 (141)
                      ....-+|.||||.-+++   .++. |||+||+-||.+|+..+   +.||+|+..+..++.+|
T Consensus        44 ~~~~FdCNICLd~akdP---VvTl-CGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vvP  101 (230)
T KOG0823|consen   44 DGGFFDCNICLDLAKDP---VVTL-CGHLFCWPCLYQWLQTRPNSKECPVCKAEVSIDTVVP  101 (230)
T ss_pred             CCCceeeeeeccccCCC---EEee-cccceehHHHHHHHhhcCCCeeCCccccccccceEEe
Confidence            45567899999886555   5666 99999999999999753   55999999887665443

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

Probab=99.29  E-value=2.5e-12  Score=77.33  Aligned_cols=52  Identities=42%  Similarity=0.902  Sum_probs=38.6

Q ss_pred             ccccccccccccc--------CCc-eeecCCCCCcccHhhHHHHHcC---CCccccccccccCC
Q 038049           78 SAGCAICLLDFID--------GDE-IRLLPKCNHRFHVACIDKWLLS---HSSCPTCRQRLKPS  129 (141)
Q Consensus        78 ~~~C~ICl~~~~~--------~~~-v~~lp~C~H~Fh~~Ci~~wl~~---~~~CP~CR~~~~~~  129 (141)
                      ++.|.||...|+.        ++. ..+...|+|.||.+||..|+.+   +..||+||++..-+
T Consensus        21 dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w~~k   84 (85)
T PF12861_consen   21 DDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPWKFK   84 (85)
T ss_pred             CCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCeeeeC
Confidence            5779999988862        222 1122259999999999999986   46799999987543

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

Probab=99.29  E-value=1.8e-12  Score=87.46  Aligned_cols=58  Identities=28%  Similarity=0.590  Sum_probs=46.3

Q ss_pred             CCCCCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCC
Q 038049           72 SSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDA  131 (141)
Q Consensus        72 ~~~~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~  131 (141)
                      ...+.+-..|+|||+.+....  ....+|||+||..||..-++....||+||+.+..++.
T Consensus       125 ~~~~~~~~~CPiCl~~~sek~--~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k~~  182 (187)
T KOG0320|consen  125 PLRKEGTYKCPICLDSVSEKV--PVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHKQF  182 (187)
T ss_pred             ccccccccCCCceecchhhcc--ccccccchhHHHHHHHHHHHhCCCCCCcccccchhhh
Confidence            344555678999999986543  3433599999999999999999999999998877654

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

Probab=99.27  E-value=2.4e-12  Score=102.58  Aligned_cols=50  Identities=38%  Similarity=0.930  Sum_probs=44.4

Q ss_pred             CcccccccccccccCCc--eeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           77 ASAGCAICLLDFIDGDE--IRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~--v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      .+..|+||+|++..+.+  ...+| |||+||..|+..|++++++||.||..+.
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            46789999999988765  67888 9999999999999999999999999544

>PHA02926 zinc finger-like protein; Provisional

Probab=99.26  E-value=2.9e-12  Score=89.51  Aligned_cols=52  Identities=35%  Similarity=0.816  Sum_probs=39.2

Q ss_pred             CCcccccccccccccC-----CceeecCCCCCcccHhhHHHHHcCC------Ccccccccccc
Q 038049           76 SASAGCAICLLDFIDG-----DEIRLLPKCNHRFHVACIDKWLLSH------SSCPTCRQRLK  127 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~-----~~v~~lp~C~H~Fh~~Ci~~wl~~~------~~CP~CR~~~~  127 (141)
                      ..+.+|+||||...+.     ..-.+++.|+|.||..||..|...+      .+||+||..+.
T Consensus       168 SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~  230 (242)
T PHA02926        168 SKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR  230 (242)
T ss_pred             cCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence            3457899999886432     1223565699999999999998753      45999999775

>PF14634 zf-RING_5: zinc-RING finger domain

Probab=99.25  E-value=5.3e-12  Score=67.78  Aligned_cols=44  Identities=32%  Similarity=0.761  Sum_probs=38.1

Q ss_pred             cccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccc
Q 038049           80 GCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQ  124 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~  124 (141)
                      .|+||+++|.+.....+++ |||+|+..|+..+......||+||+
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            4999999996666677887 9999999999999866778999985

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

Probab=99.23  E-value=5.9e-12  Score=66.81  Aligned_cols=38  Identities=42%  Similarity=0.934  Sum_probs=29.4

Q ss_pred             ccccccccccCCceeecCCCCCcccHhhHHHHHcCC----Cccccc
Q 038049           81 CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH----SSCPTC  122 (141)
Q Consensus        81 C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~C  122 (141)
                      |+||++.|.++   ..++ |||.|+..||..|++..    ..||.|
T Consensus         1 CpiC~~~~~~P---v~l~-CGH~FC~~Cl~~~~~~~~~~~~~CP~C   42 (42)
T PF15227_consen    1 CPICLDLFKDP---VSLP-CGHSFCRSCLERLWKEPSGSGFSCPEC   42 (42)
T ss_dssp             ETTTTSB-SSE---EE-S-SSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred             CCccchhhCCc---cccC-CcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence            89999999887   6777 99999999999999764    359987

>smart00504 Ubox Modified RING finger domain

Probab=99.20  E-value=1.5e-11  Score=70.95  Aligned_cols=52  Identities=35%  Similarity=0.590  Sum_probs=45.0

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCCCCC
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPS  134 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~~~  134 (141)
                      -.|+||++.+.++   ..++ |||+|+..||.+|+..+..||.|+.++..++..++
T Consensus         2 ~~Cpi~~~~~~~P---v~~~-~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~~l~~~   53 (63)
T smart00504        2 FLCPISLEVMKDP---VILP-SGQTYERRAIEKWLLSHGTDPVTGQPLTHEDLIPN   53 (63)
T ss_pred             cCCcCCCCcCCCC---EECC-CCCEEeHHHHHHHHHHCCCCCCCcCCCChhhceeC
Confidence            3599999999876   5677 99999999999999988899999999977666655

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

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

Probab=99.20  E-value=8.3e-12  Score=65.96  Aligned_cols=39  Identities=49%  Similarity=1.091  Sum_probs=33.1

Q ss_pred             ccccccccccCCceeecCCCCCcccHhhHHHHHc--CCCccccc
Q 038049           81 CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL--SHSSCPTC  122 (141)
Q Consensus        81 C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~--~~~~CP~C  122 (141)
                      |+||++.+.++.  ..++ |||.|+.+|+..|++  ....||.|
T Consensus         1 C~iC~~~~~~~~--~~~~-C~H~fC~~C~~~~~~~~~~~~CP~C   41 (41)
T PF00097_consen    1 CPICLEPFEDPV--ILLP-CGHSFCRDCLRKWLENSGSVKCPLC   41 (41)
T ss_dssp             ETTTSSBCSSEE--EETT-TSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred             CCcCCccccCCC--EEec-CCCcchHHHHHHHHHhcCCccCCcC
Confidence            899999986653  5777 999999999999998  45679987

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=99.13  E-value=4.3e-11  Score=61.79  Aligned_cols=38  Identities=45%  Similarity=1.137  Sum_probs=31.9

Q ss_pred             ccccccccccCCceeecCCCCCcccHhhHHHHHc-CCCccccc
Q 038049           81 CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL-SHSSCPTC  122 (141)
Q Consensus        81 C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~C  122 (141)
                      |+||++.   ......++ |||.||..|++.|+. .+..||.|
T Consensus         1 C~iC~~~---~~~~~~~~-C~H~~c~~C~~~~~~~~~~~CP~C   39 (39)
T smart00184        1 CPICLEE---LKDPVVLP-CGHTFCRSCIRKWLKSGNNTCPIC   39 (39)
T ss_pred             CCcCccC---CCCcEEec-CCChHHHHHHHHHHHhCcCCCCCC
Confidence            7899988   34457787 999999999999998 56679987

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

>TIGR00599 rad18 DNA repair protein rad18

Probab=99.07  E-value=1.1e-10  Score=89.08  Aligned_cols=52  Identities=33%  Similarity=0.592  Sum_probs=44.1

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCC
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDA  131 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~  131 (141)
                      .....|+||++.|..+   .+++ |||.||..||..|+.....||+||..+.....
T Consensus        24 e~~l~C~IC~d~~~~P---vitp-CgH~FCs~CI~~~l~~~~~CP~Cr~~~~~~~L   75 (397)
T TIGR00599        24 DTSLRCHICKDFFDVP---VLTS-CSHTFCSLCIRRCLSNQPKCPLCRAEDQESKL   75 (397)
T ss_pred             ccccCCCcCchhhhCc---cCCC-CCCchhHHHHHHHHhCCCCCCCCCCccccccC
Confidence            4457899999999766   4677 99999999999999988889999999876543

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

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

Probab=99.02  E-value=9e-11  Score=90.15  Aligned_cols=51  Identities=33%  Similarity=0.800  Sum_probs=39.8

Q ss_pred             CcccccccccccccC--------------CceeecCCCCCcccHhhHHHHHcC-CCccccccccccC
Q 038049           77 ASAGCAICLLDFIDG--------------DEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKP  128 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~--------------~~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~  128 (141)
                      ....|+|||.++.-.              ..-..+| |.|+||.+|+..|+.+ +-.||+||.++++
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            346799999887421              1234567 9999999999999995 5589999998864

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

Probab=99.00  E-value=2.5e-10  Score=67.15  Aligned_cols=30  Identities=43%  Similarity=0.850  Sum_probs=27.4

Q ss_pred             CCCCcccHhhHHHHHcCCCccccccccccC
Q 038049           99 KCNHRFHVACIDKWLLSHSSCPTCRQRLKP  128 (141)
Q Consensus        99 ~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~  128 (141)
                      .|+|.||.+||..||.++..||++|+...-
T Consensus        53 ~CnHaFH~HCI~rWL~Tk~~CPld~q~w~~   82 (88)
T COG5194          53 VCNHAFHDHCIYRWLDTKGVCPLDRQTWVL   82 (88)
T ss_pred             ecchHHHHHHHHHHHhhCCCCCCCCceeEE
Confidence            399999999999999999999999997653

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

Probab=98.99  E-value=1.2e-10  Score=83.43  Aligned_cols=55  Identities=27%  Similarity=0.660  Sum_probs=44.6

Q ss_pred             CCCcccccccccccccCC-------ceeecCCCCCcccHhhHHHHHc--CCCccccccccccCCC
Q 038049           75 SSASAGCAICLLDFIDGD-------EIRLLPKCNHRFHVACIDKWLL--SHSSCPTCRQRLKPSD  130 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~-------~v~~lp~C~H~Fh~~Ci~~wl~--~~~~CP~CR~~~~~~~  130 (141)
                      ..++..|+||-..+....       +...+. |+|+||+.||+-|..  ++++||.|+..+..+.
T Consensus       221 hl~d~vCaVCg~~~~~s~~eegvienty~Ls-CnHvFHEfCIrGWcivGKkqtCPYCKekVdl~r  284 (328)
T KOG1734|consen  221 HLSDSVCAVCGQQIDVSVDEEGVIENTYKLS-CNHVFHEFCIRGWCIVGKKQTCPYCKEKVDLKR  284 (328)
T ss_pred             CCCcchhHhhcchheeecchhhhhhhheeee-cccchHHHhhhhheeecCCCCCchHHHHhhHhh
Confidence            445678999998886654       567787 999999999999964  5789999999886553

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

Probab=98.98  E-value=2.2e-10  Score=81.89  Aligned_cols=52  Identities=29%  Similarity=0.675  Sum_probs=42.8

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHH-HHcCCCc-cccccccccCCCC
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDK-WLLSHSS-CPTCRQRLKPSDA  131 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~-wl~~~~~-CP~CR~~~~~~~~  131 (141)
                      ..+.+|+||++....+   ..+| |||+||..||-. |-.++.. ||+||+-...++.
T Consensus       213 ~~d~kC~lC~e~~~~p---s~t~-CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk~v  266 (271)
T COG5574         213 LADYKCFLCLEEPEVP---SCTP-CGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKV  266 (271)
T ss_pred             ccccceeeeecccCCc---cccc-ccchhhHHHHHHHHHhhccccCchhhhhccchhh
Confidence            4578899999886665   6787 999999999999 9776655 9999998776653

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

Probab=98.88  E-value=4e-10  Score=65.72  Aligned_cols=51  Identities=39%  Similarity=0.855  Sum_probs=36.5

Q ss_pred             ccccccccccccc--------CCcee-ecCCCCCcccHhhHHHHHcCC---CccccccccccC
Q 038049           78 SAGCAICLLDFID--------GDEIR-LLPKCNHRFHVACIDKWLLSH---SSCPTCRQRLKP  128 (141)
Q Consensus        78 ~~~C~ICl~~~~~--------~~~v~-~lp~C~H~Fh~~Ci~~wl~~~---~~CP~CR~~~~~  128 (141)
                      +++|.||.-+|..        +|... +.-.|.|.||..||.+|+..+   ..||.||+...-
T Consensus        20 ~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~~tsq~~CPmcRq~~~~   82 (84)
T KOG1493|consen   20 DETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNTPTSQGQCPMCRQTWQF   82 (84)
T ss_pred             CCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcCccccccCCcchheeEe
Confidence            3479999888842        23211 222499999999999999764   459999997643

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

Probab=98.86  E-value=7.7e-10  Score=81.69  Aligned_cols=51  Identities=35%  Similarity=0.688  Sum_probs=45.6

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCCC
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAM  132 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~  132 (141)
                      -..|.||.+.|..+   .++| |+|.||.-||+.+|..+..||.|+.++.+....
T Consensus        23 lLRC~IC~eyf~ip---~itp-CsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~Lr   73 (442)
T KOG0287|consen   23 LLRCGICFEYFNIP---MITP-CSHTFCSLCIRKFLSYKPQCPTCCVTVTESDLR   73 (442)
T ss_pred             HHHHhHHHHHhcCc---eecc-ccchHHHHHHHHHhccCCCCCceecccchhhhh
Confidence            36799999999888   7888 999999999999999999999999988876543

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

Probab=98.82  E-value=2.7e-09  Score=58.34  Aligned_cols=42  Identities=26%  Similarity=0.740  Sum_probs=32.7

Q ss_pred             cccccccccccCCceeecCCCC-----CcccHhhHHHHHcC--CCcccccc
Q 038049           80 GCAICLLDFIDGDEIRLLPKCN-----HRFHVACIDKWLLS--HSSCPTCR  123 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~-----H~Fh~~Ci~~wl~~--~~~CP~CR  123 (141)
                      .|.||++ ..+++.....| |.     |.+|.+|+..|+..  +.+||+|+
T Consensus         1 ~CrIC~~-~~~~~~~l~~P-C~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~   49 (49)
T smart00744        1 ICRICHD-EGDEGDPLVSP-CRCKGSLKYVHQECLERWINESGNKTCEICK   49 (49)
T ss_pred             CccCCCC-CCCCCCeeEec-cccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence            3899998 34455556788 85     89999999999965  45799995

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

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

Probab=98.80  E-value=2.2e-09  Score=83.07  Aligned_cols=52  Identities=31%  Similarity=0.585  Sum_probs=41.5

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcCC-----CccccccccccCCCCCC
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH-----SSCPTCRQRLKPSDAMP  133 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~-----~~CP~CR~~~~~~~~~~  133 (141)
                      +..|+|||++...+   ..+. |||+||..||-.++...     ..||+||..+..++..|
T Consensus       186 ~~~CPICL~~~~~p---~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kdl~p  242 (513)
T KOG2164|consen  186 DMQCPICLEPPSVP---VRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKDLLP  242 (513)
T ss_pred             CCcCCcccCCCCcc---cccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhccccceee
Confidence            67899999886555   4454 99999999999998754     45999999998866443

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

Probab=98.79  E-value=9.2e-10  Score=64.77  Aligned_cols=51  Identities=31%  Similarity=0.809  Sum_probs=24.2

Q ss_pred             cccccccccccccCCc--eeec--CCCCCcccHhhHHHHHcC---CC--------ccccccccccC
Q 038049           78 SAGCAICLLDFIDGDE--IRLL--PKCNHRFHVACIDKWLLS---HS--------SCPTCRQRLKP  128 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~--v~~l--p~C~H~Fh~~Ci~~wl~~---~~--------~CP~CR~~~~~  128 (141)
                      +.+|.||++...+++.  ...-  +.|++.||..||.+|+..   .+        .||.|++++.-
T Consensus         2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~   67 (70)
T PF11793_consen    2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW   67 (70)
T ss_dssp             --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred             CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence            4679999988763322  1222  259999999999999963   11        39999998754

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

Probab=98.76  E-value=7.2e-09  Score=54.98  Aligned_cols=34  Identities=32%  Similarity=0.697  Sum_probs=21.4

Q ss_pred             ccccccccccCC-ceeecCCCCCcccHhhHHHHHcCC
Q 038049           81 CAICLLDFIDGD-EIRLLPKCNHRFHVACIDKWLLSH  116 (141)
Q Consensus        81 C~ICl~~~~~~~-~v~~lp~C~H~Fh~~Ci~~wl~~~  116 (141)
                      |+||.+ |.+.+ ...+|+ |||+|+.+|++.++.++
T Consensus         1 CpIc~e-~~~~~n~P~~L~-CGH~~c~~cl~~l~~~~   35 (43)
T PF13445_consen    1 CPICKE-FSTEENPPMVLP-CGHVFCKDCLQKLSKKS   35 (43)
T ss_dssp             -TTT-----TTSS-EEE-S-SS-EEEHHHHHHHHHH-
T ss_pred             CCcccc-ccCCCCCCEEEe-CccHHHHHHHHHHHhcC
Confidence            899999 75544 457798 99999999999999753

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

Probab=98.74  E-value=4.5e-09  Score=62.37  Aligned_cols=56  Identities=29%  Similarity=0.432  Sum_probs=43.2

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcC-CCccccccccccCCCCCCCchh
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPSDAMPSLDE  137 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~~~~~~~~~  137 (141)
                      .-.|+|+.+-|.++   .++| +||.|...+|..|+.. +..||.|++++...+..|+...
T Consensus         4 ~f~CpIt~~lM~dP---Vi~~-~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~l~pn~~L   60 (73)
T PF04564_consen    4 EFLCPITGELMRDP---VILP-SGHTYERSAIERWLEQNGGTDPFTRQPLSESDLIPNRAL   60 (73)
T ss_dssp             GGB-TTTSSB-SSE---EEET-TSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGGSEE-HHH
T ss_pred             ccCCcCcCcHhhCc---eeCC-cCCEEcHHHHHHHHHcCCCCCCCCCCcCCcccceECHHH
Confidence            35799999999887   6777 9999999999999998 8899999999998888777443

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 ....

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

Probab=98.74  E-value=4.9e-09  Score=79.92  Aligned_cols=50  Identities=36%  Similarity=0.791  Sum_probs=40.7

Q ss_pred             CCCcccccccccccccCCc-eeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           75 SSASAGCAICLLDFIDGDE-IRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~-v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      ..+-++|++||+.+++.-. +.... |.|.||..|+..|  ...+||+||--..
T Consensus       172 ~tELPTCpVCLERMD~s~~gi~t~~-c~Hsfh~~cl~~w--~~~scpvcR~~q~  222 (493)
T KOG0804|consen  172 LTELPTCPVCLERMDSSTTGILTIL-CNHSFHCSCLMKW--WDSSCPVCRYCQS  222 (493)
T ss_pred             cccCCCcchhHhhcCccccceeeee-cccccchHHHhhc--ccCcChhhhhhcC
Confidence            4567899999999977653 44454 9999999999999  5689999997555

>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1

Probab=98.73  E-value=9e-09  Score=75.94  Aligned_cols=53  Identities=23%  Similarity=0.587  Sum_probs=39.0

Q ss_pred             cccccccccc-ccCC-ceeecCCCCCcccHhhHHHHHcC-CCccccccccccCCCCC
Q 038049           79 AGCAICLLDF-IDGD-EIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPSDAM  132 (141)
Q Consensus        79 ~~C~ICl~~~-~~~~-~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~~~~  132 (141)
                      ..||+|...- ..++ .+.+.+ |||.||..|++..+.. ...||.|+.++..+.-.
T Consensus         4 ~~CP~Ck~~~y~np~~kl~i~~-CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~fr   59 (309)
T TIGR00570         4 QGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGSGSCPECDTPLRKNNFR   59 (309)
T ss_pred             CCCCcCCCCCccCcccccccCC-CCCcccHHHHHHHhcCCCCCCCCCCCccchhhcc
Confidence            5799999853 2333 333445 9999999999996644 56799999998876633

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

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

Probab=98.73  E-value=4.3e-09  Score=64.93  Aligned_cols=50  Identities=32%  Similarity=0.731  Sum_probs=36.8

Q ss_pred             Ccccccccccccc------------cCCce--eecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           77 ASAGCAICLLDFI------------DGDEI--RLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        77 ~~~~C~ICl~~~~------------~~~~v--~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      ..+.|+||...+-            ..++.  .-- .|+|.||..||..|++++..||+|.++-.
T Consensus        45 ~vDnCAICRnHIMd~CieCQa~~~~~~~EC~VaWG-~CNHaFH~hCisrWlktr~vCPLdn~eW~  108 (114)
T KOG2930|consen   45 VVDNCAICRNHIMDLCIECQANQSATSEECTVAWG-VCNHAFHFHCISRWLKTRNVCPLDNKEWV  108 (114)
T ss_pred             eechhHHHHHHHHHHHHhhccCCCCCCCceEEEee-ecchHHHHHHHHHHHhhcCcCCCcCccee
Confidence            3567999985541            12222  222 39999999999999999999999987643

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

Probab=98.69  E-value=7.4e-09  Score=75.18  Aligned_cols=49  Identities=29%  Similarity=0.526  Sum_probs=42.4

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPS  129 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~  129 (141)
                      ....|-||-+.+..+   ..++ |||.||.-||...|..+..||+||.+..+.
T Consensus        24 s~lrC~IC~~~i~ip---~~Tt-CgHtFCslCIR~hL~~qp~CP~Cr~~~~es   72 (391)
T COG5432          24 SMLRCRICDCRISIP---CETT-CGHTFCSLCIRRHLGTQPFCPVCREDPCES   72 (391)
T ss_pred             hHHHhhhhhheeecc---eecc-cccchhHHHHHHHhcCCCCCccccccHHhh
Confidence            346799999888776   5677 999999999999999999999999977644

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

Probab=98.56  E-value=1.9e-08  Score=82.80  Aligned_cols=52  Identities=33%  Similarity=0.803  Sum_probs=38.3

Q ss_pred             CCcccccccccccc-cCCce--eecCCCCCcccHhhHHHHHcC--CCcccccccccc
Q 038049           76 SASAGCAICLLDFI-DGDEI--RLLPKCNHRFHVACIDKWLLS--HSSCPTCRQRLK  127 (141)
Q Consensus        76 ~~~~~C~ICl~~~~-~~~~v--~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~CR~~~~  127 (141)
                      .+..+|+||...+. .+...  ...+.|.|.||..|+..|+.+  +.+||+||.+++
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            45789999998775 22111  122248999999999999986  467999998764

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

Probab=98.55  E-value=3.3e-08  Score=73.62  Aligned_cols=49  Identities=29%  Similarity=0.724  Sum_probs=41.0

Q ss_pred             CCcccccccccccccCCceeecCCCCCc-ccHhhHHHHHcCCCccccccccccC
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHR-FHVACIDKWLLSHSSCPTCRQRLKP  128 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~~~~  128 (141)
                      ++..+|.|||++-.   .+.++| |.|. .|.+|-+...-....||+||+++.+
T Consensus       288 ~~gkeCVIClse~r---dt~vLP-CRHLCLCs~Ca~~Lr~q~n~CPICRqpi~~  337 (349)
T KOG4265|consen  288 ESGKECVICLSESR---DTVVLP-CRHLCLCSGCAKSLRYQTNNCPICRQPIEE  337 (349)
T ss_pred             cCCCeeEEEecCCc---ceEEec-chhhehhHhHHHHHHHhhcCCCccccchHh
Confidence            44678999998843   347899 9999 9999999987678889999998864

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

Probab=98.54  E-value=1.6e-08  Score=57.50  Aligned_cols=48  Identities=29%  Similarity=0.590  Sum_probs=24.2

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCC
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDA  131 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~  131 (141)
                      -.|++|.+-+..+  +... .|.|+|+..||..-+.  ..||+|+.+...++.
T Consensus         8 LrCs~C~~~l~~p--v~l~-~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD~   55 (65)
T PF14835_consen    8 LRCSICFDILKEP--VCLG-GCEHIFCSSCIRDCIG--SECPVCHTPAWIQDI   55 (65)
T ss_dssp             TS-SSS-S--SS---B----SSS--B-TTTGGGGTT--TB-SSS--B-S-SS-
T ss_pred             cCCcHHHHHhcCC--ceec-cCccHHHHHHhHHhcC--CCCCCcCChHHHHHH
Confidence            4699999988665  3334 5999999999988544  459999999877653

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

Probab=98.54  E-value=3.3e-08  Score=72.62  Aligned_cols=46  Identities=39%  Similarity=0.797  Sum_probs=40.0

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQ  124 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~  124 (141)
                      ..+...|+||++.|..+   ..+| |||.||..|+..++.....||.||.
T Consensus        10 ~~~~~~C~iC~~~~~~p---~~l~-C~H~~c~~C~~~~~~~~~~Cp~cr~   55 (386)
T KOG2177|consen   10 LQEELTCPICLEYFREP---VLLP-CGHNFCRACLTRSWEGPLSCPVCRP   55 (386)
T ss_pred             ccccccChhhHHHhhcC---cccc-ccchHhHHHHHHhcCCCcCCcccCC
Confidence            34557899999999888   7888 9999999999999886677999994

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

Probab=98.53  E-value=3.6e-08  Score=74.09  Aligned_cols=50  Identities=30%  Similarity=0.830  Sum_probs=35.6

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcCC---CccccccccccC
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH---SSCPTCRQRLKP  128 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~---~~CP~CR~~~~~  128 (141)
                      ..|.||-+-+.....+.-...|||+||..|+..|+..-   ..||.||-.+..
T Consensus         5 A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~~~   57 (465)
T KOG0827|consen    5 AECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKLQE   57 (465)
T ss_pred             ceeeEeccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecccc
Confidence            56999944444444444443499999999999999863   569999943433

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

Probab=98.43  E-value=4.6e-08  Score=53.52  Aligned_cols=45  Identities=31%  Similarity=0.671  Sum_probs=34.2

Q ss_pred             ccccccccccccCCceeecCCCCCc-ccHhhHHHHHc-CCCcccccccccc
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHR-FHVACIDKWLL-SHSSCPTCRQRLK  127 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~-Fh~~Ci~~wl~-~~~~CP~CR~~~~  127 (141)
                      .+|.||+|.-.+  .|..+  |||. .+.+|-.+-++ .+..||+||+++.
T Consensus         8 dECTICye~pvd--sVlYt--CGHMCmCy~Cg~rl~~~~~g~CPiCRapi~   54 (62)
T KOG4172|consen    8 DECTICYEHPVD--SVLYT--CGHMCMCYACGLRLKKALHGCCPICRAPIK   54 (62)
T ss_pred             cceeeeccCcch--HHHHH--cchHHhHHHHHHHHHHccCCcCcchhhHHH
Confidence            789999987433  33333  9998 89999766555 6788999999874

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

Probab=98.40  E-value=3.4e-08  Score=73.43  Aligned_cols=53  Identities=36%  Similarity=0.647  Sum_probs=44.3

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC-CCccccccccccCCCC
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPSDA  131 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~~~  131 (141)
                      ..+..|+|||+-++..   +.++.|.|.||.+||..-++. +..||.||+.+..+..
T Consensus        41 ~~~v~c~icl~llk~t---mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Skrs   94 (381)
T KOG0311|consen   41 DIQVICPICLSLLKKT---MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKRS   94 (381)
T ss_pred             hhhhccHHHHHHHHhh---cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcccccc
Confidence            3467899999988766   667789999999999998865 6889999999987643

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

Probab=98.24  E-value=6.7e-07  Score=67.79  Aligned_cols=48  Identities=31%  Similarity=0.784  Sum_probs=37.6

Q ss_pred             cccccccccccccCC-ceeecCCCCCcccHhhHHHHHcC--CCcccccccc
Q 038049           78 SAGCAICLLDFIDGD-EIRLLPKCNHRFHVACIDKWLLS--HSSCPTCRQR  125 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~-~v~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~CR~~  125 (141)
                      ..+|+||++.+..+- .....++|||.|..+||+.|+.+  ...||.|...
T Consensus         4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~k   54 (463)
T KOG1645|consen    4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGK   54 (463)
T ss_pred             cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCCh
Confidence            468999999997654 44445579999999999999963  3459999654

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

Probab=98.21  E-value=6.8e-07  Score=67.33  Aligned_cols=52  Identities=37%  Similarity=0.852  Sum_probs=39.5

Q ss_pred             CCcccccccccccccCC----ceeecCCCCCcccHhhHHHHHc--C-----CCcccccccccc
Q 038049           76 SASAGCAICLLDFIDGD----EIRLLPKCNHRFHVACIDKWLL--S-----HSSCPTCRQRLK  127 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~----~v~~lp~C~H~Fh~~Ci~~wl~--~-----~~~CP~CR~~~~  127 (141)
                      ..+.+|.|||+...+..    .-..+|+|.|.||.+||+.|-.  +     .+.||.||....
T Consensus       159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~  221 (344)
T KOG1039|consen  159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS  221 (344)
T ss_pred             cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence            45788999998875543    1234577999999999999973  3     367999998553

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

Probab=98.18  E-value=3.3e-07  Score=74.37  Aligned_cols=51  Identities=24%  Similarity=0.432  Sum_probs=41.7

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKP  128 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~  128 (141)
                      ....|++|+..+.++......+ |+|.||..||..|-+...+||+||..+..
T Consensus       122 ~~~~CP~Ci~s~~DqL~~~~k~-c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~  172 (1134)
T KOG0825|consen  122 VENQCPNCLKSCNDQLEESEKH-TAHYFCEECVGSWSRCAQTCPVDRGEFGE  172 (1134)
T ss_pred             hhhhhhHHHHHHHHHhhccccc-cccccHHHHhhhhhhhcccCchhhhhhhe
Confidence            3556888888776665555565 99999999999999999999999997753

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

Probab=98.16  E-value=5.5e-07  Score=72.86  Aligned_cols=51  Identities=24%  Similarity=0.634  Sum_probs=40.4

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcC-CCccccccccccCCCCC
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPSDAM  132 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~~~~  132 (141)
                      --+|+.|-+...+.   .++ .|||+||..|+..-+.. +..||.|.+++..++..
T Consensus       643 ~LkCs~Cn~R~Kd~---vI~-kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv~  694 (698)
T KOG0978|consen  643 LLKCSVCNTRWKDA---VIT-KCGHVFCEECVQTRYETRQRKCPKCNAAFGANDVH  694 (698)
T ss_pred             ceeCCCccCchhhH---HHH-hcchHHHHHHHHHHHHHhcCCCCCCCCCCCccccc
Confidence            35799998665543   334 49999999999999874 67899999999887644

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

Probab=98.11  E-value=1e-06  Score=64.47  Aligned_cols=55  Identities=31%  Similarity=0.853  Sum_probs=44.4

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC-----------------------CCccccccccccCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-----------------------HSSCPTCRQRLKPSD  130 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-----------------------~~~CP~CR~~~~~~~  130 (141)
                      +-....|+|||.-|.+++...+++ |.|.||..|+..+|..                       +..||+||..+....
T Consensus       112 n~p~gqCvICLygfa~~~~ft~T~-C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~e~  189 (368)
T KOG4445|consen  112 NHPNGQCVICLYGFASSPAFTVTA-CDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKIEE  189 (368)
T ss_pred             CCCCCceEEEEEeecCCCceeeeh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccccc
Confidence            344567999999999999899998 9999999999987721                       123999999886543

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

Probab=98.06  E-value=2.5e-06  Score=65.79  Aligned_cols=57  Identities=32%  Similarity=0.703  Sum_probs=47.0

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCCCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPS  134 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~~~  134 (141)
                      .+.+..|++|+..+.++-..  +. |||.||..|+..|+..+..||.||.++...+..+.
T Consensus        18 ~~~~l~C~~C~~vl~~p~~~--~~-cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~~   74 (391)
T KOG0297|consen   18 LDENLLCPICMSVLRDPVQT--TT-CGHRFCAGCLLESLSNHQKCPVCRQELTQAEELPV   74 (391)
T ss_pred             CcccccCccccccccCCCCC--CC-CCCcccccccchhhccCcCCcccccccchhhccCc
Confidence            35557899999998777221  34 99999999999999999999999999987777763

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

Probab=98.03  E-value=2.6e-06  Score=62.35  Aligned_cols=49  Identities=24%  Similarity=0.461  Sum_probs=38.7

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcC-CCccccccccccCC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPS  129 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~  129 (141)
                      -..+|+||+....-+   ..++ |+|.||.-||.--... +.+||+||.++.+.
T Consensus         6 ~~~eC~IC~nt~n~P---v~l~-C~HkFCyiCiKGsy~ndk~~CavCR~pids~   55 (324)
T KOG0824|consen    6 KKKECLICYNTGNCP---VNLY-CFHKFCYICIKGSYKNDKKTCAVCRFPIDST   55 (324)
T ss_pred             cCCcceeeeccCCcC---cccc-ccchhhhhhhcchhhcCCCCCceecCCCCcc
Confidence            347899999775444   5666 9999999999976554 56799999999765

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

Probab=98.02  E-value=4.5e-06  Score=58.84  Aligned_cols=55  Identities=31%  Similarity=0.725  Sum_probs=45.3

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcC--------CCccccccccccCCCCCCC
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS--------HSSCPTCRQRLKPSDAMPS  134 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~--------~~~CP~CR~~~~~~~~~~~  134 (141)
                      ...|..|-..+..+|.+|..  |-|+||++|+.+|--.        ...||.|-.++.++....+
T Consensus        50 ~pNC~LC~t~La~gdt~RLv--CyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiFPp~Nlvs  112 (299)
T KOG3970|consen   50 NPNCRLCNTPLASGDTTRLV--CYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIFPPINLVS  112 (299)
T ss_pred             CCCCceeCCccccCcceeeh--hhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccCCCccccc
Confidence            35699999999999999886  9999999999999743        3459999999987654433

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

Probab=97.98  E-value=2e-06  Score=65.11  Aligned_cols=46  Identities=33%  Similarity=0.806  Sum_probs=37.8

Q ss_pred             cccccccccccccC-CceeecCCCCCcccHhhHHHHHcCC--Cccccccc
Q 038049           78 SAGCAICLLDFIDG-DEIRLLPKCNHRFHVACIDKWLLSH--SSCPTCRQ  124 (141)
Q Consensus        78 ~~~C~ICl~~~~~~-~~v~~lp~C~H~Fh~~Ci~~wl~~~--~~CP~CR~  124 (141)
                      +-.|..|-+.+... +.+.-+| |.|+||..|+.+.+.++  ++||.||+
T Consensus       365 ~L~Cg~CGe~~Glk~e~LqALp-CsHIfH~rCl~e~L~~n~~rsCP~Crk  413 (518)
T KOG1941|consen  365 ELYCGLCGESIGLKNERLQALP-CSHIFHLRCLQEILENNGTRSCPNCRK  413 (518)
T ss_pred             hhhhhhhhhhhcCCcccccccc-hhHHHHHHHHHHHHHhCCCCCCccHHH
Confidence            35699998888643 4577888 99999999999999764  67999994

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

Probab=97.91  E-value=8.1e-06  Score=62.76  Aligned_cols=49  Identities=29%  Similarity=0.735  Sum_probs=42.6

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccC
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKP  128 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~  128 (141)
                      ..+-+|.||+.-+.++   ..+| |||.|+..||+.-+.....||.||..+.+
T Consensus        82 ~sef~c~vc~~~l~~p---v~tp-cghs~c~~Cl~r~ld~~~~cp~Cr~~l~e  130 (398)
T KOG4159|consen   82 RSEFECCVCSRALYPP---VVTP-CGHSFCLECLDRSLDQETECPLCRDELVE  130 (398)
T ss_pred             cchhhhhhhHhhcCCC---cccc-ccccccHHHHHHHhccCCCCccccccccc
Confidence            4567899999888777   6778 99999999999988878889999999876

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

Probab=97.89  E-value=4.9e-06  Score=63.22  Aligned_cols=46  Identities=30%  Similarity=0.823  Sum_probs=37.9

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcC--CCcccccccccc
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS--HSSCPTCRQRLK  127 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~CR~~~~  127 (141)
                      -..|-||-+.   +..|++-| |||..|..|+..|-..  .+.||.||..+.
T Consensus       369 FeLCKICaen---dKdvkIEP-CGHLlCt~CLa~WQ~sd~gq~CPFCRcEIK  416 (563)
T KOG1785|consen  369 FELCKICAEN---DKDVKIEP-CGHLLCTSCLAAWQDSDEGQTCPFCRCEIK  416 (563)
T ss_pred             HHHHHHhhcc---CCCccccc-ccchHHHHHHHhhcccCCCCCCCceeeEec
Confidence            3469999754   55678888 9999999999999744  578999999875

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

Probab=97.89  E-value=9.2e-06  Score=43.79  Aligned_cols=45  Identities=24%  Similarity=0.682  Sum_probs=22.8

Q ss_pred             ccccccccccCCceeecC-CCCCcccHhhHHHHHc-CCCccccccccc
Q 038049           81 CAICLLDFIDGDEIRLLP-KCNHRFHVACIDKWLL-SHSSCPTCRQRL  126 (141)
Q Consensus        81 C~ICl~~~~~~~~v~~lp-~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~~  126 (141)
                      |++|.+++...+. ...| .||+..+..|...-+. .+..||.||++.
T Consensus         1 cp~C~e~~d~~d~-~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y   47 (48)
T PF14570_consen    1 CPLCDEELDETDK-DFYPCECGFQICRFCYHDILENEGGRCPGCREPY   47 (48)
T ss_dssp             -TTTS-B--CCCT-T--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred             CCCcccccccCCC-ccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence            7899999844332 3333 4999999999998876 478899999875

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

Probab=97.88  E-value=7.9e-06  Score=46.00  Aligned_cols=43  Identities=28%  Similarity=0.584  Sum_probs=27.6

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC--CCcccc
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS--HSSCPT  121 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~  121 (141)
                      .....|+|.+..|+++  ++-.. |||+|-.+.|.+|+.+  ...||+
T Consensus         9 ~~~~~CPiT~~~~~~P--V~s~~-C~H~fek~aI~~~i~~~~~~~CPv   53 (57)
T PF11789_consen    9 TISLKCPITLQPFEDP--VKSKK-CGHTFEKEAILQYIQRNGSKRCPV   53 (57)
T ss_dssp             B--SB-TTTSSB-SSE--EEESS-S--EEEHHHHHHHCTTTS-EE-SC
T ss_pred             EeccCCCCcCChhhCC--cCcCC-CCCeecHHHHHHHHHhcCCCCCCC
Confidence            3346799999998655  44454 9999999999999944  456998

>PHA02862 5L protein; Provisional

Probab=97.85  E-value=9.4e-06  Score=53.44  Aligned_cols=56  Identities=18%  Similarity=0.398  Sum_probs=42.1

Q ss_pred             ccccccccccccCCceeecCCCC-----CcccHhhHHHHHcC--CCccccccccccCCCCCCCchhhh
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCN-----HRFHVACIDKWLLS--HSSCPTCRQRLKPSDAMPSLDEIV  139 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~-----H~Fh~~Ci~~wl~~--~~~CP~CR~~~~~~~~~~~~~~~~  139 (141)
                      +.|=||.++-+++    .-| |.     ..-|.+|+.+|++.  +..||+|+.++..+..-.+..+|+
T Consensus         3 diCWIC~~~~~e~----~~P-C~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~Ik~~yKpf~kW~   65 (156)
T PHA02862          3 DICWICNDVCDER----NNF-CGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIKKTYVSFKKWN   65 (156)
T ss_pred             CEEEEecCcCCCC----ccc-ccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEEEEEccccHHHhh
Confidence            5799999884332    345 54     56899999999975  456999999998777666666663

>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=97.80  E-value=7.6e-06  Score=53.46  Aligned_cols=36  Identities=19%  Similarity=0.504  Sum_probs=30.5

Q ss_pred             cccccccccccccCCceeecCCCC------CcccHhhHHHHHc
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCN------HRFHVACIDKWLL  114 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~------H~Fh~~Ci~~wl~  114 (141)
                      ..+|.||++.+.+.+++...+ ||      |.||.+|+..|-+
T Consensus        26 ~~EC~IC~~~I~~~~GvV~vt-~~g~lnLEkmfc~~C~~rw~~   67 (134)
T PF05883_consen   26 TVECQICFDRIDNNDGVVYVT-DGGTLNLEKMFCADCDKRWRR   67 (134)
T ss_pred             CeeehhhhhhhhcCCCEEEEe-cCCeehHHHHHHHHHHHHHHh
Confidence            478999999998866777776 76      9999999999943

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.

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

Probab=97.78  E-value=8.6e-05  Score=55.13  Aligned_cols=58  Identities=16%  Similarity=0.357  Sum_probs=42.4

Q ss_pred             eecCCCCCCCCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccc
Q 038049           66 TYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRL  126 (141)
Q Consensus        66 ~~~~~~~~~~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~  126 (141)
                      .+.++.+....+...|++|+..-+++.-+. +  =|-+||..|+-.++++...||+=..+.
T Consensus       288 ~~~se~e~l~~~~~~CpvClk~r~Nptvl~-v--SGyVfCY~Ci~~Yv~~~~~CPVT~~p~  345 (357)
T KOG0826|consen  288 QYNSESELLPPDREVCPVCLKKRQNPTVLE-V--SGYVFCYPCIFSYVVNYGHCPVTGYPA  345 (357)
T ss_pred             hcccccccCCCccccChhHHhccCCCceEE-e--cceEEeHHHHHHHHHhcCCCCccCCcc
Confidence            344444555667788999998865553222 2  689999999999999999999865443

>PHA02825 LAP/PHD finger-like protein; Provisional

Probab=97.77  E-value=1.9e-05  Score=52.89  Aligned_cols=60  Identities=18%  Similarity=0.423  Sum_probs=43.1

Q ss_pred             CCCcccccccccccccCCceeecC-CCCC---cccHhhHHHHHcC--CCccccccccccCCCCCCCchhh
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLP-KCNH---RFHVACIDKWLLS--HSSCPTCRQRLKPSDAMPSLDEI  138 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp-~C~H---~Fh~~Ci~~wl~~--~~~CP~CR~~~~~~~~~~~~~~~  138 (141)
                      +..+..|-||.++..  +.  ..| .|..   .-|.+|++.|+..  ..+||.|+.++.-+....++.+|
T Consensus         5 s~~~~~CRIC~~~~~--~~--~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y~i~~~~kpl~~W   70 (162)
T PHA02825          5 SLMDKCCWICKDEYD--VV--TNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIKKNYKKCTKW   70 (162)
T ss_pred             CCCCCeeEecCCCCC--Cc--cCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeEEEEEecCCCccc
Confidence            445678999998843  22  245 2444   5699999999975  45699999999877666666666

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

Probab=97.58  E-value=1.7e-05  Score=58.81  Aligned_cols=52  Identities=31%  Similarity=0.648  Sum_probs=43.6

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCC
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSD  130 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~  130 (141)
                      ....+|.+|-+.|.+...+.   .|-|.||..||..++.....||.|...+....
T Consensus        13 n~~itC~LC~GYliDATTI~---eCLHTFCkSCivk~l~~~~~CP~C~i~ih~t~   64 (331)
T KOG2660|consen   13 NPHITCRLCGGYLIDATTIT---ECLHTFCKSCIVKYLEESKYCPTCDIVIHKTH   64 (331)
T ss_pred             ccceehhhccceeecchhHH---HHHHHHHHHHHHHHHHHhccCCccceeccCcc
Confidence            44578999999998885544   49999999999999999999999988775443

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

Probab=97.54  E-value=0.00011  Score=53.44  Aligned_cols=51  Identities=20%  Similarity=0.423  Sum_probs=38.2

Q ss_pred             CCCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC--Ccccccccccc
Q 038049           74 PSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH--SSCPTCRQRLK  127 (141)
Q Consensus        74 ~~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~--~~CP~CR~~~~  127 (141)
                      ....+.+|++|-+.-..+  -...+ |||+||.-|+..=+...  -+||.|-.+..
T Consensus       235 ~~t~~~~C~~Cg~~PtiP--~~~~~-C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~  287 (298)
T KOG2879|consen  235 TGTSDTECPVCGEPPTIP--HVIGK-CGHIYCYYCIATSRLWDASFTCPLCGENVE  287 (298)
T ss_pred             cccCCceeeccCCCCCCC--eeecc-ccceeehhhhhhhhcchhhcccCccCCCCc
Confidence            356678999998764433  23344 99999999999876643  57999988776

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

Probab=97.53  E-value=2.4e-05  Score=52.51  Aligned_cols=32  Identities=38%  Similarity=0.730  Sum_probs=28.4

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHh
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVA  107 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~  107 (141)
                      .++..+|.||||++..++.+..|| |-.+||+.
T Consensus       174 ~ddkGECvICLEdL~~GdtIARLP-CLCIYHK~  205 (205)
T KOG0801|consen  174 KDDKGECVICLEDLEAGDTIARLP-CLCIYHKQ  205 (205)
T ss_pred             cccCCcEEEEhhhccCCCceeccc-eEEEeecC
Confidence            445679999999999999999999 99999963

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

Probab=97.51  E-value=7.2e-05  Score=64.92  Aligned_cols=66  Identities=27%  Similarity=0.646  Sum_probs=47.9

Q ss_pred             hCCceeecCCCCCCCCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC----------CccccccccccC
Q 038049           61 ALPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH----------SSCPTCRQRLKP  128 (141)
Q Consensus        61 ~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~----------~~CP~CR~~~~~  128 (141)
                      -+|...-.++.. ..+.++-|.||+.+--.....+.+. |+|+||-+|.+.-|++.          -+||+|..++..
T Consensus      3470 CLPCl~Cdks~t-kQD~DDmCmICFTE~L~AAP~IqL~-C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3470 CLPCLHCDKSAT-KQDADDMCMICFTEALSAAPAIQLD-CSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINH 3545 (3738)
T ss_pred             cccccccChhhh-hcccCceEEEEehhhhCCCcceecC-CccchhHHHHHHHHHhcccCCeeEEeeeecccccchhhh
Confidence            355555333322 3455677999998877777788887 99999999999877653          149999988753

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

Probab=97.41  E-value=6.8e-05  Score=59.07  Aligned_cols=56  Identities=25%  Similarity=0.547  Sum_probs=42.6

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC-----CCccccccccccCCCCCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-----HSSCPTCRQRLKPSDAMPS  134 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-----~~~CP~CR~~~~~~~~~~~  134 (141)
                      +.+..+|-+|-++-++.   ..+. |.|.||.-|+.+++..     +-+||.|...+......|.
T Consensus       533 nk~~~~C~lc~d~aed~---i~s~-ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~LsiDlse~a  593 (791)
T KOG1002|consen  533 NKGEVECGLCHDPAEDY---IESS-CHHKFCRLCIKEYVESFMENNNVTCPVCHIGLSIDLSEPA  593 (791)
T ss_pred             ccCceeecccCChhhhh---Hhhh-hhHHHHHHHHHHHHHhhhcccCCCCccccccccccccchh
Confidence            55678899999775443   5565 9999999999999853     4679999988875544444

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

Probab=97.39  E-value=7.2e-05  Score=61.62  Aligned_cols=49  Identities=31%  Similarity=0.727  Sum_probs=37.9

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC-C------ccccccc
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH-S------SCPTCRQ  124 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~-~------~CP~CR~  124 (141)
                      .+..+|.||.+.+...+.+---..|-|+||..||..|-++. +      .||.|+.
T Consensus       189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs  244 (950)
T KOG1952|consen  189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS  244 (950)
T ss_pred             cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence            44678999999998877653322399999999999998652 1      3999984

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

Probab=97.37  E-value=1.3e-05  Score=60.06  Aligned_cols=44  Identities=30%  Similarity=0.658  Sum_probs=32.5

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      ..+.|.||+++..+   ...+| |||.-+  |...- +...+||+||+++.
T Consensus       304 ~p~lcVVcl~e~~~---~~fvp-cGh~cc--ct~cs-~~l~~CPvCR~rI~  347 (355)
T KOG1571|consen  304 QPDLCVVCLDEPKS---AVFVP-CGHVCC--CTLCS-KHLPQCPVCRQRIR  347 (355)
T ss_pred             CCCceEEecCCccc---eeeec-CCcEEE--chHHH-hhCCCCchhHHHHH
Confidence            34679999998666   47888 999965  65554 23455999999875

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

Probab=97.35  E-value=7.2e-05  Score=51.93  Aligned_cols=44  Identities=23%  Similarity=0.500  Sum_probs=38.3

Q ss_pred             cccccccccccCCceeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           80 GCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      .|.||-.+|..+   ..+. |||.||..|...-++....|-+|.+...
T Consensus       198 ~C~iCKkdy~sp---vvt~-CGH~FC~~Cai~~y~kg~~C~~Cgk~t~  241 (259)
T COG5152         198 LCGICKKDYESP---VVTE-CGHSFCSLCAIRKYQKGDECGVCGKATY  241 (259)
T ss_pred             eehhchhhccch---hhhh-cchhHHHHHHHHHhccCCcceecchhhc
Confidence            699999999877   5665 9999999999999999999999987543

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.30  E-value=0.0002  Score=51.29  Aligned_cols=55  Identities=16%  Similarity=0.268  Sum_probs=47.7

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCCC
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAM  132 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~  132 (141)
                      ..-|++|.+.+.+...+..|..|||+|..+|++..+.....||+|-.++.+++.+
T Consensus       221 ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdiI  275 (303)
T KOG3039|consen  221 RYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDII  275 (303)
T ss_pred             ceecccchhhhcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccceE
Confidence            3459999999988877766666999999999999999999999999999877654

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

Probab=97.20  E-value=0.00026  Score=38.18  Aligned_cols=40  Identities=28%  Similarity=0.865  Sum_probs=26.6

Q ss_pred             ccccccccccCCceeecCCCC-----CcccHhhHHHHHc--CCCccccc
Q 038049           81 CAICLLDFIDGDEIRLLPKCN-----HRFHVACIDKWLL--SHSSCPTC  122 (141)
Q Consensus        81 C~ICl~~~~~~~~v~~lp~C~-----H~Fh~~Ci~~wl~--~~~~CP~C  122 (141)
                      |-||++.-.+++ .-+.| |+     ...|.+|+..|+.  .+.+|++|
T Consensus         1 CrIC~~~~~~~~-~li~p-C~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C   47 (47)
T PF12906_consen    1 CRICLEGEEEDE-PLISP-CRCKGSMKYVHRSCLERWIRESGNRKCEIC   47 (47)
T ss_dssp             ETTTTEE-SSSS--EE-S-SS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred             CeEeCCcCCCCC-ceecc-cccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence            679998866655 33455 54     3689999999997  45679887

>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=97.19  E-value=0.00015  Score=45.72  Aligned_cols=33  Identities=27%  Similarity=0.706  Sum_probs=26.2

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHH
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACID  110 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~  110 (141)
                      +++..|++|-..+.. ......| |||+||..|+.
T Consensus        76 ~~~~~C~vC~k~l~~-~~f~~~p-~~~v~H~~C~~  108 (109)
T PF10367_consen   76 TESTKCSVCGKPLGN-SVFVVFP-CGHVVHYSCIK  108 (109)
T ss_pred             CCCCCccCcCCcCCC-ceEEEeC-CCeEEeccccc
Confidence            334679999999877 4555677 99999999975

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

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

Probab=97.19  E-value=0.00015  Score=55.34  Aligned_cols=35  Identities=26%  Similarity=0.785  Sum_probs=30.6

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHc
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL  114 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~  114 (141)
                      -.|.||+++..-......+| |+|+||..|+..++.
T Consensus       185 f~C~ICf~e~~G~~c~~~lp-C~Hv~Ck~C~kdY~~  219 (445)
T KOG1814|consen  185 FDCCICFEEQMGQHCFKFLP-CSHVFCKSCLKDYFT  219 (445)
T ss_pred             ccceeeehhhcCcceeeecc-cchHHHHHHHHHHHH
Confidence            56999999976657778898 999999999999984

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

Probab=97.17  E-value=0.00029  Score=52.95  Aligned_cols=65  Identities=26%  Similarity=0.553  Sum_probs=43.5

Q ss_pred             HHHhhCCceeecCCCCCCCCCcccccccccccccCCceeecCCCCCcccHhhHHHH--HcCCCccccccccc
Q 038049           57 KEMVALPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKW--LLSHSSCPTCRQRL  126 (141)
Q Consensus        57 ~~~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~w--l~~~~~CP~CR~~~  126 (141)
                      +.+..-|..+.. +..+..++..-|.||-+.+.-.   ..+| |+|..|--|--.-  |-.++.||.||..-
T Consensus        41 NnlsaEPnltts-SaddtDEen~~C~ICA~~~TYs---~~~P-C~H~~CH~Ca~RlRALY~~K~C~~CrTE~  107 (493)
T COG5236          41 NNLSAEPNLTTS-SADDTDEENMNCQICAGSTTYS---ARYP-CGHQICHACAVRLRALYMQKGCPLCRTET  107 (493)
T ss_pred             cccccCCccccc-cccccccccceeEEecCCceEE---Eecc-CCchHHHHHHHHHHHHHhccCCCcccccc
Confidence            333334444333 3334445566799998776544   7888 9999998886543  45678999999854

>PHA03096 p28-like protein; Provisional

Probab=97.09  E-value=0.00025  Score=52.42  Aligned_cols=37  Identities=27%  Similarity=0.627  Sum_probs=28.8

Q ss_pred             ccccccccccccCC----ceeecCCCCCcccHhhHHHHHcC
Q 038049           79 AGCAICLLDFIDGD----EIRLLPKCNHRFHVACIDKWLLS  115 (141)
Q Consensus        79 ~~C~ICl~~~~~~~----~v~~lp~C~H~Fh~~Ci~~wl~~  115 (141)
                      ..|.|||+......    .=..++.|.|.|+..|+..|...
T Consensus       179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~  219 (284)
T PHA03096        179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTE  219 (284)
T ss_pred             hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHh
Confidence            67999998875432    12356789999999999999854

>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=97.07  E-value=0.00034  Score=37.01  Aligned_cols=41  Identities=32%  Similarity=0.752  Sum_probs=23.1

Q ss_pred             ccccccccccCCceeecCCCCCcccHhhHHHHHcCCC--ccccc
Q 038049           81 CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS--SCPTC  122 (141)
Q Consensus        81 C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~--~CP~C  122 (141)
                      |.+|.+-...++..... .|+=.+|..|+..+++...  .||.|
T Consensus         1 C~~C~~iv~~G~~C~~~-~C~~r~H~~C~~~y~r~~~~~~CP~C   43 (43)
T PF08746_consen    1 CEACKEIVTQGQRCSNR-DCNVRLHDDCFKKYFRHRSNPKCPNC   43 (43)
T ss_dssp             -TTT-SB-SSSEE-SS---S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred             CcccchhHeeeccCCCC-ccCchHHHHHHHHHHhcCCCCCCcCC
Confidence            56777666666444333 3888999999999998765  79987

; PDB: 3NW0_A 2CT0_A.

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

Probab=97.02  E-value=0.00056  Score=51.56  Aligned_cols=49  Identities=27%  Similarity=0.585  Sum_probs=41.5

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      ..++..|+||.-.   +......| |+|.=|++||.+.+.+.+.|=.|++.+.
T Consensus       419 ~sEd~lCpICyA~---pi~Avf~P-C~H~SC~~CI~qHlmN~k~CFfCktTv~  467 (489)
T KOG4692|consen  419 DSEDNLCPICYAG---PINAVFAP-CSHRSCYGCITQHLMNCKRCFFCKTTVI  467 (489)
T ss_pred             CcccccCcceecc---cchhhccC-CCCchHHHHHHHHHhcCCeeeEecceee
Confidence            4567889999744   44457888 9999999999999999999999998775

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

Probab=96.95  E-value=0.00039  Score=49.73  Aligned_cols=50  Identities=24%  Similarity=0.527  Sum_probs=34.7

Q ss_pred             cccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCCCC
Q 038049           80 GCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMP  133 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~~  133 (141)
                      -|--|.-- ..++...++. |+|+||..|...=  ....||+|++++.......
T Consensus         5 hCn~C~~~-~~~~~f~LTa-C~HvfC~~C~k~~--~~~~C~lCkk~ir~i~l~~   54 (233)
T KOG4739|consen    5 HCNKCFRF-PSQDPFFLTA-CRHVFCEPCLKAS--SPDVCPLCKKSIRIIQLNR   54 (233)
T ss_pred             Eecccccc-CCCCceeeee-chhhhhhhhcccC--Cccccccccceeeeeeccc
Confidence            36666533 3366677776 9999999997762  2338999999986554433

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

Probab=96.94  E-value=0.00022  Score=58.85  Aligned_cols=43  Identities=23%  Similarity=0.621  Sum_probs=32.8

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccc
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRL  126 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~  126 (141)
                      ...|+.|-..++-+- |-.  .|||.||.+|+.   .+...||-|+..+
T Consensus       840 ~skCs~C~~~LdlP~-VhF--~CgHsyHqhC~e---~~~~~CP~C~~e~  882 (933)
T KOG2114|consen  840 VSKCSACEGTLDLPF-VHF--LCGHSYHQHCLE---DKEDKCPKCLPEL  882 (933)
T ss_pred             eeeecccCCccccce-eee--ecccHHHHHhhc---cCcccCCccchhh
Confidence            368999988876552 222  399999999999   4667899998743

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

Probab=96.89  E-value=0.00061  Score=46.63  Aligned_cols=32  Identities=28%  Similarity=0.822  Sum_probs=25.9

Q ss_pred             CCCCcccHhhHHHHHcCC----C-------ccccccccccCCC
Q 038049           99 KCNHRFHVACIDKWLLSH----S-------SCPTCRQRLKPSD  130 (141)
Q Consensus        99 ~C~H~Fh~~Ci~~wl~~~----~-------~CP~CR~~~~~~~  130 (141)
                      +||.-||.-|+.+||+.-    +       .||+|-.++..+.
T Consensus       189 qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~PialKm  231 (234)
T KOG3268|consen  189 QCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIALKM  231 (234)
T ss_pred             ccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcceeec
Confidence            499999999999999741    1       2999998887654

>PF14447 Prok-RING_4: Prokaryotic RING finger family 4

Probab=96.84  E-value=0.00059  Score=37.70  Aligned_cols=46  Identities=24%  Similarity=0.510  Sum_probs=33.7

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCC
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSD  130 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~  130 (141)
                      ..|..|...-   ..-.++| |||+.+..|...+  +-.-||.|.+++...+
T Consensus         8 ~~~~~~~~~~---~~~~~~p-CgH~I~~~~f~~~--rYngCPfC~~~~~~~~   53 (55)
T PF14447_consen    8 QPCVFCGFVG---TKGTVLP-CGHLICDNCFPGE--RYNGCPFCGTPFEFDD   53 (55)
T ss_pred             eeEEEccccc---ccccccc-ccceeeccccChh--hccCCCCCCCcccCCC
Confidence            4566666442   2336787 9999999998875  6677999999886543

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

Probab=96.75  E-value=0.00031  Score=51.53  Aligned_cols=42  Identities=31%  Similarity=0.676  Sum_probs=32.1

Q ss_pred             cccccccccccccCCceeecCCCCCc-ccHhhHHHHHcCCCcccccccccc
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHR-FHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      ...|.|||+.   +.....|+ |||. -|.+|-..-    ..||+||+-+.
T Consensus       300 ~~LC~ICmDa---P~DCvfLe-CGHmVtCt~CGkrm----~eCPICRqyi~  342 (350)
T KOG4275|consen  300 RRLCAICMDA---PRDCVFLE-CGHMVTCTKCGKRM----NECPICRQYIV  342 (350)
T ss_pred             HHHHHHHhcC---CcceEEee-cCcEEeehhhcccc----ccCchHHHHHH
Confidence            5779999977   44557888 9997 788885442    48999998553

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

Probab=96.71  E-value=0.00056  Score=50.27  Aligned_cols=45  Identities=27%  Similarity=0.460  Sum_probs=38.5

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      ..|-||...|..+   .++. |+|.||..|-..-+++...|++|-+...
T Consensus       242 f~c~icr~~f~~p---Vvt~-c~h~fc~~ca~~~~qk~~~c~vC~~~t~  286 (313)
T KOG1813|consen  242 FKCFICRKYFYRP---VVTK-CGHYFCEVCALKPYQKGEKCYVCSQQTH  286 (313)
T ss_pred             ccccccccccccc---hhhc-CCceeehhhhccccccCCcceecccccc
Confidence            3499999999887   5665 9999999999998888899999987654

>PF04641 Rtf2: Rtf2 RING-finger

Probab=96.68  E-value=0.002  Score=47.22  Aligned_cols=54  Identities=20%  Similarity=0.445  Sum_probs=42.0

Q ss_pred             CCCcccccccccccccCCce-eecCCCCCcccHhhHHHHHcCCCccccccccccCCC
Q 038049           75 SSASAGCAICLLDFIDGDEI-RLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSD  130 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v-~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~  130 (141)
                      ....-.|||...+|...... .+-| |||+|-..++.+- .....||+|-.++...+
T Consensus       110 ~~~~~~CPvt~~~~~~~~~fv~l~~-cG~V~s~~alke~-k~~~~Cp~c~~~f~~~D  164 (260)
T PF04641_consen  110 SEGRFICPVTGKEFNGKHKFVYLRP-CGCVFSEKALKEL-KKSKKCPVCGKPFTEED  164 (260)
T ss_pred             CCceeECCCCCcccCCceeEEEEcC-CCCEeeHHHHHhh-cccccccccCCccccCC
Confidence            45566799999999655444 4455 9999999999997 33567999999988664

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

Probab=96.63  E-value=0.00011  Score=55.74  Aligned_cols=51  Identities=27%  Similarity=0.671  Sum_probs=44.2

Q ss_pred             cccccccccccccC-CceeecCCCCCcccHhhHHHHHcCCCccccccccccCC
Q 038049           78 SAGCAICLLDFIDG-DEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPS  129 (141)
Q Consensus        78 ~~~C~ICl~~~~~~-~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~  129 (141)
                      ...|+||.+.++.. +++..+- |||.+|.+|+..|+.+...||.||+.+...
T Consensus       196 v~sl~I~~~slK~~y~k~~~~~-~g~~~~~~kL~k~L~~~~kl~~~~rel~~~  247 (465)
T KOG0827|consen  196 VGSLSICFESLKQNYDKISAIV-CGHIYHHGKLSKWLATKRKLPSCRRELPKN  247 (465)
T ss_pred             HhhhHhhHHHHHHHHHHHHHHh-hcccchhhHHHHHHHHHHHhHHHHhhhhhh
Confidence            45799999999877 6777775 999999999999999989999999988643

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

Probab=96.52  E-value=0.0024  Score=47.19  Aligned_cols=53  Identities=28%  Similarity=0.587  Sum_probs=39.2

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHc-CCCccccccc-cccCCCCCCC
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL-SHSSCPTCRQ-RLKPSDAMPS  134 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~-~~~~~~~~~~  134 (141)
                      ..|+.|..-+..+   ..+|.|+|.|+.+||..-|. ....||+|.+ ++......|+
T Consensus       275 LkCplc~~Llrnp---~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdvlld~l~pD  329 (427)
T COG5222         275 LKCPLCHCLLRNP---MKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLDGLTPD  329 (427)
T ss_pred             ccCcchhhhhhCc---ccCccccchHHHHHHhhhhhhccccCCCcccccchhhccCcc
Confidence            6799998776555   45567999999999998775 5678999965 4444444444

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

Probab=96.50  E-value=0.0015  Score=54.45  Aligned_cols=37  Identities=24%  Similarity=0.618  Sum_probs=28.0

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHc
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL  114 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~  114 (141)
                      +.+.+|.+|.-.+... .-.+.| |||.||++|+..-..
T Consensus       815 ep~d~C~~C~~~ll~~-pF~vf~-CgH~FH~~Cl~~~v~  851 (911)
T KOG2034|consen  815 EPQDSCDHCGRPLLIK-PFYVFP-CGHCFHRDCLIRHVL  851 (911)
T ss_pred             cCccchHHhcchhhcC-cceeee-ccchHHHHHHHHHHH
Confidence            3457899998777554 334666 999999999997763

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.48  E-value=0.0021  Score=48.29  Aligned_cols=56  Identities=16%  Similarity=0.422  Sum_probs=37.3

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC-CCccccccccccCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPSD  130 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~~  130 (141)
                      +++++-|+.|+++++..|+=..--+||-..|.-|...--+. +..||-||+-..++.
T Consensus        11 edeed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~den   67 (480)
T COG5175          11 EDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDEN   67 (480)
T ss_pred             ccccccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccc
Confidence            34445699999999877654332249977777775443222 567999999776543

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=96.36  E-value=0.0053  Score=33.88  Aligned_cols=35  Identities=34%  Similarity=0.852  Sum_probs=30.0

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHH
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDK  111 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~  111 (141)
                      ....|.+|-+.|.+++.+.+-|.||-.+|++|-+.
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~   38 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK   38 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence            34679999999998888888888999999999543

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

Probab=96.27  E-value=0.0024  Score=52.55  Aligned_cols=22  Identities=32%  Similarity=0.972  Sum_probs=20.9

Q ss_pred             CCCcccHhhHHHHHcCCCcccc
Q 038049          100 CNHRFHVACIDKWLLSHSSCPT  121 (141)
Q Consensus       100 C~H~Fh~~Ci~~wl~~~~~CP~  121 (141)
                      |+|+-|.+|..+|++.+..||.
T Consensus      1048 C~Hv~H~sc~~eWf~~gd~Cps 1069 (1081)
T KOG0309|consen 1048 CGHVGHTSCMMEWFRTGDVCPS 1069 (1081)
T ss_pred             ccccccHHHHHHHHhcCCcCCC
Confidence            9999999999999999999984

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

Probab=96.08  E-value=0.0015  Score=53.75  Aligned_cols=47  Identities=34%  Similarity=0.711  Sum_probs=37.2

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcC--CCccccccccccCCC
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS--HSSCPTCRQRLKPSD  130 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~CR~~~~~~~  130 (141)
                      ..|.||++    .+....++ |+|.|+.+|+..-+..  ...||.||..+..+.
T Consensus       455 ~~c~ic~~----~~~~~it~-c~h~~c~~c~~~~i~~~~~~~~~~cr~~l~~~~  503 (674)
T KOG1001|consen  455 HWCHICCD----LDSFFITR-CGHDFCVECLKKSIQQSENAPCPLCRNVLKEKK  503 (674)
T ss_pred             cccccccc----cccceeec-ccchHHHHHHHhccccccCCCCcHHHHHHHHHH
Confidence            68999998    44456666 9999999999998864  346999999776543

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

Probab=95.96  E-value=0.0064  Score=46.43  Aligned_cols=30  Identities=33%  Similarity=0.928  Sum_probs=22.3

Q ss_pred             CCCcccHhhHHHHHcCCC-------------ccccccccccCC
Q 038049          100 CNHRFHVACIDKWLLSHS-------------SCPTCRQRLKPS  129 (141)
Q Consensus       100 C~H~Fh~~Ci~~wl~~~~-------------~CP~CR~~~~~~  129 (141)
                      |.-.+|.+|+-.|+-.++             .||.||+.++-.
T Consensus       311 CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~FCil  353 (358)
T PF10272_consen  311 CRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKFCIL  353 (358)
T ss_pred             ccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccceee
Confidence            445678999999985432             499999987644

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

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

Probab=95.90  E-value=0.005  Score=45.32  Aligned_cols=43  Identities=28%  Similarity=0.698  Sum_probs=37.3

Q ss_pred             ccccccccccCCc-eeecCCCCCcccHhhHHHHHcCCCccccccc
Q 038049           81 CAICLLDFIDGDE-IRLLPKCNHRFHVACIDKWLLSHSSCPTCRQ  124 (141)
Q Consensus        81 C~ICl~~~~~~~~-v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~  124 (141)
                      |+||.+.+..... +..++ |||.-|..|+++....+.+||+|.+
T Consensus       161 cPic~e~l~~s~~~~~~~~-CgH~~h~~cf~e~~~~~y~CP~C~~  204 (276)
T KOG1940|consen  161 CPICKEYLFLSFEDAGVLK-CGHYMHSRCFEEMICEGYTCPICSK  204 (276)
T ss_pred             CchhHHHhccccccCCccC-cccchHHHHHHHHhccCCCCCcccc
Confidence            9999998876654 45676 9999999999999988899999988

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

Probab=95.83  E-value=0.0065  Score=45.20  Aligned_cols=47  Identities=34%  Similarity=0.699  Sum_probs=37.9

Q ss_pred             ccccccccccccCCc---eeecCCCCCcccHhhHHHHHcCC-Cccccccccc
Q 038049           79 AGCAICLLDFIDGDE---IRLLPKCNHRFHVACIDKWLLSH-SSCPTCRQRL  126 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~---v~~lp~C~H~Fh~~Ci~~wl~~~-~~CP~CR~~~  126 (141)
                      .+|-||-++|...+.   .+.+. |||.|+..|+..-+... ..||.||.+.
T Consensus         4 ~~c~~c~~~~s~~~~~~~p~~l~-c~h~~c~~c~~~l~~~~~i~cpfcR~~~   54 (296)
T KOG4185|consen    4 PECEICNEDYSSEDGDHIPRVLK-CGHTICQNCASKLLGNSRILCPFCRETT   54 (296)
T ss_pred             CceeecCccccccCcccCCcccc-cCceehHhHHHHHhcCceeeccCCCCcc
Confidence            579999999987643   35565 99999999999887653 5699999985

>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=95.83  E-value=0.0082  Score=40.43  Aligned_cols=33  Identities=27%  Similarity=0.621  Sum_probs=21.4

Q ss_pred             cccccccccccccCCceeecC-----------CCC-CcccHhhHHHHH
Q 038049           78 SAGCAICLLDFIDGDEIRLLP-----------KCN-HRFHVACIDKWL  113 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp-----------~C~-H~Fh~~Ci~~wl  113 (141)
                      +..|+||||---+.   .+|-           -|+ -.-|..|++++-
T Consensus         2 d~~CpICme~PHNA---VLLlCSS~~kgcRpymc~Ts~rhSNCLdqfk   46 (162)
T PF07800_consen    2 DVTCPICMEHPHNA---VLLLCSSHEKGCRPYMCDTSYRHSNCLDQFK   46 (162)
T ss_pred             CccCceeccCCCce---EEEEeccccCCccccccCCccchhHHHHHHH
Confidence            57899999874332   2221           144 346899999875

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.

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

Probab=95.67  E-value=0.064  Score=41.22  Aligned_cols=46  Identities=20%  Similarity=0.358  Sum_probs=37.6

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcCCC---ccccccc
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS---SCPTCRQ  124 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~---~CP~CR~  124 (141)
                      .-.|||=-++-.+......+. |||+...+-+..-.++..   .||+|=.
T Consensus       334 vF~CPVlKeqtsdeNPPm~L~-CGHVISkdAlnrLS~ng~~sfKCPYCP~  382 (394)
T KOG2817|consen  334 VFICPVLKEQTSDENPPMMLI-CGHVISKDALNRLSKNGSQSFKCPYCPV  382 (394)
T ss_pred             eeecccchhhccCCCCCeeee-ccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence            356999888877777778887 999999999999877654   4999943

>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=94.72  E-value=0.015  Score=31.11  Aligned_cols=30  Identities=27%  Similarity=0.722  Sum_probs=22.0

Q ss_pred             CC-CcccHhhHHHHHcCCCccccccccccCC
Q 038049          100 CN-HRFHVACIDKWLLSHSSCPTCRQRLKPS  129 (141)
Q Consensus       100 C~-H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~  129 (141)
                      |+ |..+-.|+..-+.+...||+|..+++.+
T Consensus        18 C~dHYLCl~CLt~ml~~s~~C~iC~~~LPtk   48 (50)
T PF03854_consen   18 CSDHYLCLNCLTLMLSRSDRCPICGKPLPTK   48 (50)
T ss_dssp             -SS-EEEHHHHHHT-SSSSEETTTTEE----
T ss_pred             ecchhHHHHHHHHHhccccCCCcccCcCccc
Confidence            76 9999999999999999999999988754

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.

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

Probab=94.71  E-value=0.021  Score=42.73  Aligned_cols=47  Identities=23%  Similarity=0.444  Sum_probs=35.9

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      ..+-.+|+||.+.+..+  +.+-+ =||+.|..|=.+   ....||.||.++.
T Consensus        45 ~~~lleCPvC~~~l~~P--i~QC~-nGHlaCssC~~~---~~~~CP~Cr~~~g   91 (299)
T KOG3002|consen   45 DLDLLDCPVCFNPLSPP--IFQCD-NGHLACSSCRTK---VSNKCPTCRLPIG   91 (299)
T ss_pred             chhhccCchhhccCccc--ceecC-CCcEehhhhhhh---hcccCCccccccc
Confidence            44557899999999877  23322 479999999663   4677999999987

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

Probab=94.62  E-value=0.013  Score=43.54  Aligned_cols=44  Identities=30%  Similarity=0.665  Sum_probs=29.7

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      ..|--|--.+.  -.-|+.| |.|+||.+|-..  ...+.||.|-..+.
T Consensus        91 HfCd~Cd~PI~--IYGRmIP-CkHvFCl~CAr~--~~dK~Cp~C~d~Vq  134 (389)
T KOG2932|consen   91 HFCDRCDFPIA--IYGRMIP-CKHVFCLECARS--DSDKICPLCDDRVQ  134 (389)
T ss_pred             EeecccCCcce--eeecccc-cchhhhhhhhhc--CccccCcCcccHHH
Confidence            34666643321  1126788 999999999765  34678999977653

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

Probab=94.57  E-value=0.016  Score=41.07  Aligned_cols=40  Identities=30%  Similarity=0.661  Sum_probs=30.4

Q ss_pred             ccccccccccCCceeecCCCCCc-ccHhhHHHHHcCCCccccccccccC
Q 038049           81 CAICLLDFIDGDEIRLLPKCNHR-FHVACIDKWLLSHSSCPTCRQRLKP  128 (141)
Q Consensus        81 C~ICl~~~~~~~~v~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~~~~  128 (141)
                      |-.|-+.   +..|-.+| |.|. +|..|=..    -..||+|+.....
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            7788744   66788999 9987 89999543    4669999886543

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

Probab=94.55  E-value=0.035  Score=46.37  Aligned_cols=55  Identities=25%  Similarity=0.636  Sum_probs=40.4

Q ss_pred             CCCCCCcccccccccccccCCceeecC-CCC---CcccHhhHHHHHcC--CCcccccccccc
Q 038049           72 SSPSSASAGCAICLLDFIDGDEIRLLP-KCN---HRFHVACIDKWLLS--HSSCPTCRQRLK  127 (141)
Q Consensus        72 ~~~~~~~~~C~ICl~~~~~~~~v~~lp-~C~---H~Fh~~Ci~~wl~~--~~~CP~CR~~~~  127 (141)
                      ...++++..|-||..+=.+++.+- -| +|.   ...|.+|+.+|+.-  ...|-+|+.++.
T Consensus         6 ~~mN~d~~~CRICr~e~~~d~pLf-hPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~~   66 (1175)
T COG5183           6 TPMNEDKRSCRICRTEDIRDDPLF-HPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYK   66 (1175)
T ss_pred             CCCCccchhceeecCCCCCCCcCc-ccccccchhHHHHHHHHHHHHhcCCCcceeeecceee
Confidence            345667789999998865555553 34 343   44899999999975  355999999885

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

Probab=94.49  E-value=0.017  Score=44.76  Aligned_cols=39  Identities=28%  Similarity=0.717  Sum_probs=28.5

Q ss_pred             CcccccccccccccC-CceeecCCCCCcccHhhHHHHHcCC
Q 038049           77 ASAGCAICLLDFIDG-DEIRLLPKCNHRFHVACIDKWLLSH  116 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~-~~v~~lp~C~H~Fh~~Ci~~wl~~~  116 (141)
                      ...+|.||+.+...+ +.-... .|+|.|+.+|+...+..+
T Consensus       145 ~~~~C~iC~~e~~~~~~~f~~~-~C~H~fC~~C~k~~iev~  184 (384)
T KOG1812|consen  145 PKEECGICFVEDPEAEDMFSVL-KCGHRFCKDCVKQHIEVK  184 (384)
T ss_pred             ccccCccCccccccHhhhHHHh-cccchhhhHHhHHHhhhh
Confidence            457899999555444 333434 599999999999998743

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

Probab=94.47  E-value=0.013  Score=50.98  Aligned_cols=45  Identities=31%  Similarity=0.684  Sum_probs=37.1

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCcccccccc
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQR  125 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~  125 (141)
                      ...|.||++.+.....+.   .|||.++..|...|+..+..||.|...
T Consensus      1153 ~~~c~ic~dil~~~~~I~---~cgh~~c~~c~~~~l~~~s~~~~~ksi 1197 (1394)
T KOG0298|consen 1153 HFVCEICLDILRNQGGIA---GCGHEPCCRCDELWLYASSRCPICKSI 1197 (1394)
T ss_pred             ccchHHHHHHHHhcCCee---eechhHhhhHHHHHHHHhccCcchhhh
Confidence            347999999987543333   399999999999999999999999743

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

Probab=93.55  E-value=0.049  Score=40.65  Aligned_cols=49  Identities=22%  Similarity=0.673  Sum_probs=35.7

Q ss_pred             cccccccccccccCCc-eeecCCCC-----CcccHhhHHHHHc--CCCcccccccccc
Q 038049           78 SAGCAICLLDFIDGDE-IRLLPKCN-----HRFHVACIDKWLL--SHSSCPTCRQRLK  127 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~-v~~lp~C~-----H~Fh~~Ci~~wl~--~~~~CP~CR~~~~  127 (141)
                      +..|-||.++...... ....| |.     +..|..|++.|+.  .+..|.+|.....
T Consensus        78 ~~~cRIc~~~~~~~~~~~l~~p-C~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~  134 (323)
T KOG1609|consen   78 GPICRICHEEDEESNGLLLISP-CSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI  134 (323)
T ss_pred             CCcEEEEecccccccccccccC-ccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence            5789999987654432 34555 54     6689999999997  4567999987554

>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=93.54  E-value=0.07  Score=39.41  Aligned_cols=51  Identities=25%  Similarity=0.718  Sum_probs=35.6

Q ss_pred             cccccccc-cccCCceeecCCCCCcccHhhHHHHHcC-CCccccccccccCCC
Q 038049           80 GCAICLLD-FIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPSD  130 (141)
Q Consensus        80 ~C~ICl~~-~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~~  130 (141)
                      .|++|-.. |-.++...+...|+|..|..|++.-+.. ...||.|-..+....
T Consensus         2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iLRk~n   54 (300)
T KOG3800|consen    2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVILRKNN   54 (300)
T ss_pred             CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchhhhcc
Confidence            48888754 3344433333249999999999998765 467999987765443

>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=93.38  E-value=0.023  Score=40.88  Aligned_cols=51  Identities=29%  Similarity=0.740  Sum_probs=37.5

Q ss_pred             Ccccccccccccc-cCC-ceeecCCCCCcccHhhHHHHHcCC-Cccc--ccccccc
Q 038049           77 ASAGCAICLLDFI-DGD-EIRLLPKCNHRFHVACIDKWLLSH-SSCP--TCRQRLK  127 (141)
Q Consensus        77 ~~~~C~ICl~~~~-~~~-~v~~lp~C~H~Fh~~Ci~~wl~~~-~~CP--~CR~~~~  127 (141)
                      .+..||+|..+-. .++ .+-+-|.|-|..|..|++.-+... ..||  .|.+-+.
T Consensus         9 ~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kILR   64 (314)
T COG5220           9 EDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKILR   64 (314)
T ss_pred             hcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHHH
Confidence            3467999996643 333 344566799999999999998765 5699  8876554

>KOG3053 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.34  E-value=0.056  Score=39.27  Aligned_cols=55  Identities=24%  Similarity=0.567  Sum_probs=36.5

Q ss_pred             CCCcccccccccccccCCce-eecCCCC-----CcccHhhHHHHHcCCC--------ccccccccccCCC
Q 038049           75 SSASAGCAICLLDFIDGDEI-RLLPKCN-----HRFHVACIDKWLLSHS--------SCPTCRQRLKPSD  130 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v-~~lp~C~-----H~Fh~~Ci~~wl~~~~--------~CP~CR~~~~~~~  130 (141)
                      .+.+..|=||+..=+++..- -+-| |.     |=-|..|+..|+-.+.        +||.|+++....-
T Consensus        17 ~e~eR~CWiCF~TdeDn~~a~WV~P-CrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~   85 (293)
T KOG3053|consen   17 QELERCCWICFATDEDNRLAAWVHP-CRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVF   85 (293)
T ss_pred             cccceeEEEEeccCcccchhhhccc-ccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeec
Confidence            34557799999764443221 2334 43     7799999999995322        3999999875443

>TIGR00622 ssl1 transcription factor ssl1

Probab=93.30  E-value=0.12  Score=33.07  Aligned_cols=62  Identities=21%  Similarity=0.282  Sum_probs=39.7

Q ss_pred             CCceeecCCCCCCCCCcccccccccccccCC----------ceeecCCCCCcccHhhHHHHHcCCCcccccc
Q 038049           62 LPTVTYANSGSSPSSASAGCAICLLDFIDGD----------EIRLLPKCNHRFHVACIDKWLLSHSSCPTCR  123 (141)
Q Consensus        62 ~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~----------~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR  123 (141)
                      +|...+.+...+.......|--|+..|.+..          ....-+.|++.|+.+|=.-+-+.-.+||.|-
T Consensus        39 fPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~  110 (112)
T TIGR00622        39 FPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI  110 (112)
T ss_pred             CCCcccccccccccCCCCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence            4444444332222333456999999886431          1233456999999999777766677899995

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

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

Probab=92.69  E-value=0.097  Score=34.32  Aligned_cols=53  Identities=21%  Similarity=0.383  Sum_probs=37.7

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcC---CCccccccccccCCC
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS---HSSCPTCRQRLKPSD  130 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~---~~~CP~CR~~~~~~~  130 (141)
                      -.+|-||.|.-.+..-+.--.-||-..|.-|...-++.   ...||+|+.++....
T Consensus        80 lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~  135 (140)
T PF05290_consen   80 LYECNICKETSAEERFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKSSS  135 (140)
T ss_pred             ceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence            37899999886555322222249999999988776653   577999999986543

>PF15050 SCIMP: SCIMP protein

Probab=92.37  E-value=0.47  Score=30.52  Aligned_cols=23  Identities=26%  Similarity=0.356  Sum_probs=13.8

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHH
Q 038049            5 NIMVIVAAMLCALVCALGLHSML   27 (141)
Q Consensus         5 ~~~~i~~~~l~~~~~~l~~~~~~   27 (141)
                      ++|+++++.++++-+.+|++++.
T Consensus         7 nFWiiLAVaII~vS~~lglIlyC   29 (133)
T PF15050_consen    7 NFWIILAVAIILVSVVLGLILYC   29 (133)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHH
Confidence            57777777755555555544443

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

Probab=91.67  E-value=0.065  Score=43.75  Aligned_cols=40  Identities=28%  Similarity=0.536  Sum_probs=31.8

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccc
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCP  120 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP  120 (141)
                      ..|.||+..|......-+.++|||..|..|++.-  .+.+||
T Consensus        12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp   51 (861)
T KOG3161|consen   12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP   51 (861)
T ss_pred             hhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC
Confidence            4699999999877655555579999999999986  356788

>KOG3899 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.46  E-value=0.079  Score=39.29  Aligned_cols=30  Identities=23%  Similarity=0.732  Sum_probs=23.3

Q ss_pred             CCCcccHhhHHHHHcC-------------CCccccccccccCC
Q 038049          100 CNHRFHVACIDKWLLS-------------HSSCPTCRQRLKPS  129 (141)
Q Consensus       100 C~H~Fh~~Ci~~wl~~-------------~~~CP~CR~~~~~~  129 (141)
                      |.-.+|.+|+..|+..             +-+||.||+.++..
T Consensus       325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~  367 (381)
T KOG3899|consen  325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIR  367 (381)
T ss_pred             cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEe
Confidence            6678899999988743             34599999987644

>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=91.34  E-value=0.46  Score=30.89  Aligned_cols=7  Identities=0%  Similarity=0.373  Sum_probs=2.6

Q ss_pred             HHHHHHH
Q 038049           26 MLQCVFQ   32 (141)
Q Consensus        26 ~~~~~~~   32 (141)
                      ++.|+++
T Consensus        83 li~y~ir   89 (122)
T PF01102_consen   83 LISYCIR   89 (122)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            3333333

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.

>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair

Probab=91.12  E-value=0.17  Score=27.68  Aligned_cols=42  Identities=33%  Similarity=0.800  Sum_probs=21.2

Q ss_pred             ccccccccccCC------ceeecCCCCCcccHhhHHHHH-cCCCcccccc
Q 038049           81 CAICLLDFIDGD------EIRLLPKCNHRFHVACIDKWL-LSHSSCPTCR  123 (141)
Q Consensus        81 C~ICl~~~~~~~------~v~~lp~C~H~Fh~~Ci~~wl-~~~~~CP~CR  123 (141)
                      |--|+.+|....      ....-|.|++.|+.+| +.++ ++-.+||.|-
T Consensus         2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dC-D~fiHE~LH~CPGC~   50 (51)
T PF07975_consen    2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDC-DVFIHETLHNCPGCE   50 (51)
T ss_dssp             ETTTTEE-TTS-------EEE--TTTT--B-HHH-HHTTTTTS-SSSTT-
T ss_pred             CccCCCCCCCcccccccCCeEECCCCCCccccCc-ChhhhccccCCcCCC
Confidence            455666665542      3455667999999999 3333 2346799883

It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.

>KOG3113 consensus Uncharacterized conserved protein [Function unknown]

Probab=90.72  E-value=0.25  Score=35.95  Aligned_cols=50  Identities=18%  Similarity=0.309  Sum_probs=37.4

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCC
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSD  130 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~  130 (141)
                      -.|+|=--+|.....-..+..|||+|-..-+.+-  ...+|++|.+.+.+.+
T Consensus       112 fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei--kas~C~~C~a~y~~~d  161 (293)
T KOG3113|consen  112 FICPVTGLEMNGKYRFCALRCCGCVFSERALKEI--KASVCHVCGAAYQEDD  161 (293)
T ss_pred             eecccccceecceEEEEEEeccceeccHHHHHHh--hhccccccCCcccccC
Confidence            4588877777554433333359999999999884  5788999999887665

>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]

Probab=90.38  E-value=0.23  Score=37.38  Aligned_cols=62  Identities=19%  Similarity=0.405  Sum_probs=42.8

Q ss_pred             CCceeecCCCCCCCCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccc
Q 038049           62 LPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQ  124 (141)
Q Consensus        62 ~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~  124 (141)
                      +|...+.+.......++..|-.|.++.......+.-. |.|.||.+|=.--=++-..||.|..
T Consensus       314 ~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~-Ck~~FCldCDv~iHesLh~CpgCeh  375 (378)
T KOG2807|consen  314 FPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCES-CKNVFCLDCDVFIHESLHNCPGCEH  375 (378)
T ss_pred             cCCcchhhccccccCCCcceeeeccccCCCCcEEchh-ccceeeccchHHHHhhhhcCCCcCC
Confidence            5666666555555555677999987776665555554 9999999995543344567999963

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

Probab=90.11  E-value=0.19  Score=39.39  Aligned_cols=35  Identities=26%  Similarity=0.617  Sum_probs=29.3

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS  115 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~  115 (141)
                      ++..|+||..-|.++   +++| |+|..|.-|-..-+.+
T Consensus         3 eelkc~vc~~f~~ep---iil~-c~h~lc~~ca~~~~~~   37 (699)
T KOG4367|consen    3 EELKCPVCGSFYREP---IILP-CSHNLCQACARNILVQ   37 (699)
T ss_pred             ccccCceehhhccCc---eEee-cccHHHHHHHHhhccc
Confidence            346799999998887   7888 9999999998876544

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

Probab=89.35  E-value=0.21  Score=23.32  Aligned_cols=23  Identities=22%  Similarity=0.638  Sum_probs=12.4

Q ss_pred             cccccccccccCCceeecCCCCCcc
Q 038049           80 GCAICLLDFIDGDEIRLLPKCNHRF  104 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~H~F  104 (141)
                      +|+-|-.++.  ...+.-|.|||.|
T Consensus         2 ~CP~C~~~V~--~~~~~Cp~CG~~F   24 (26)
T PF10571_consen    2 TCPECGAEVP--ESAKFCPHCGYDF   24 (26)
T ss_pred             cCCCCcCCch--hhcCcCCCCCCCC
Confidence            3666665542  2234445577766

Several members are annotated as putative helicases.

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

Probab=88.98  E-value=0.21  Score=40.49  Aligned_cols=47  Identities=36%  Similarity=0.950  Sum_probs=38.5

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCC
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSD  130 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~  130 (141)
                      .....|.+|+.+.    ..+.++ |.   |..|+..|+-.+..||+|+..+...+
T Consensus       477 ~~~~~~~~~~~~~----~~~~~~-~~---~~~~l~~~~~~~~~~pl~~~~~~~~~  523 (543)
T KOG0802|consen  477 EPNDVCAICYQEM----SARITP-CS---HALCLRKWLYVQEVCPLCHTYMKEDD  523 (543)
T ss_pred             cccCcchHHHHHH----Hhcccc-cc---chhHHHhhhhhccccCCCchhhhccc
Confidence            3456799999887    446676 88   99999999999999999999876554

>PF13901 DUF4206: Domain of unknown function (DUF4206)

Probab=88.92  E-value=0.26  Score=34.81  Aligned_cols=40  Identities=40%  Similarity=0.828  Sum_probs=27.5

Q ss_pred             ccccccccc-----cccCCceeecCCCCCcccHhhHHHHHcCCCccccccc
Q 038049           79 AGCAICLLD-----FIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQ  124 (141)
Q Consensus        79 ~~C~ICl~~-----~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~  124 (141)
                      -.|-+|-++     |+. +.+..-+.|+.+||..|..     +..||-|-+
T Consensus       153 fiCe~C~~~~~IfPF~~-~~~~~C~~C~~v~H~~C~~-----~~~CpkC~R  197 (202)
T PF13901_consen  153 FICEICNSDDIIFPFQI-DTTVRCPKCKSVFHKSCFR-----KKSCPKCAR  197 (202)
T ss_pred             CCCccCCCCCCCCCCCC-CCeeeCCcCccccchhhcC-----CCCCCCcHh
Confidence            457777642     222 3455556799999999976     277999954

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

Probab=88.42  E-value=0.29  Score=38.71  Aligned_cols=38  Identities=29%  Similarity=0.587  Sum_probs=30.5

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS  115 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~  115 (141)
                      .....+|-||.+.+..  .+..+. |||.|+..|...++.+
T Consensus        67 ~~~~~~c~ic~~~~~~--~~~~~~-c~H~~c~~cw~~yl~~  104 (444)
T KOG1815|consen   67 KKGDVQCGICVESYDG--EIIGLG-CGHPFCPPCWTGYLGT  104 (444)
T ss_pred             CCccccCCcccCCCcc--hhhhcC-CCcHHHHHHHHHHhhh
Confidence            4556889999999765  444555 9999999999999965

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

Probab=88.23  E-value=0.15  Score=41.46  Aligned_cols=26  Identities=31%  Similarity=0.861  Sum_probs=19.2

Q ss_pred             eecCCCCCcccHhhHHHHHcCCCccccccc
Q 038049           95 RLLPKCNHRFHVACIDKWLLSHSSCPTCRQ  124 (141)
Q Consensus        95 ~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~  124 (141)
                      +.. .|+++||..|+..   .+..||-|-+
T Consensus       533 rC~-~C~avfH~~C~~r---~s~~CPrC~R  558 (580)
T KOG1829|consen  533 RCS-TCLAVFHKKCLRR---KSPCCPRCER  558 (580)
T ss_pred             eHH-HHHHHHHHHHHhc---cCCCCCchHH
Confidence            344 4999999999665   4455999954

>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3

Probab=87.96  E-value=0.56  Score=23.13  Aligned_cols=37  Identities=24%  Similarity=0.510  Sum_probs=24.4

Q ss_pred             ccccccccccCCceeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           81 CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        81 C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      |..|-..+.+.+.....  =+..||.+|        ..|..|+.++.
T Consensus         2 C~~C~~~i~~~~~~~~~--~~~~~H~~C--------f~C~~C~~~L~   38 (39)
T smart00132        2 CAGCGKPIRGGELVLRA--LGKVWHPEC--------FKCSKCGKPLG   38 (39)
T ss_pred             ccccCCcccCCcEEEEe--CCccccccC--------CCCcccCCcCc
Confidence            77888777665333222  467899988        56777776653

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

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

Probab=87.88  E-value=0.14  Score=42.16  Aligned_cols=45  Identities=31%  Similarity=0.739  Sum_probs=36.0

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcC---CCcccccccccc
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS---HSSCPTCRQRLK  127 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~---~~~CP~CR~~~~  127 (141)
                      .+|+||+..+.++   ..+. |.|.|+..|+..-+..   ...||+|+..+.
T Consensus        22 lEc~ic~~~~~~p---~~~k-c~~~~l~~~~n~~f~~~~~~~~~~lc~~~~e   69 (684)
T KOG4362|consen   22 LECPICLEHVKEP---SLLK-CDHIFLKFCLNKLFESKKGPKQCALCKSDIE   69 (684)
T ss_pred             ccCCceeEEeecc---chhh-hhHHHHhhhhhceeeccCccccchhhhhhhh
Confidence            6799999999887   4454 9999999998876654   356999997665

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

Probab=87.80  E-value=0.18  Score=42.05  Aligned_cols=43  Identities=21%  Similarity=0.546  Sum_probs=31.3

Q ss_pred             cccccccccccccC----CceeecCCCCCcccHhhHHHHHcCCCccccc
Q 038049           78 SAGCAICLLDFIDG----DEIRLLPKCNHRFHVACIDKWLLSHSSCPTC  122 (141)
Q Consensus        78 ~~~C~ICl~~~~~~----~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~C  122 (141)
                      +..|+-|.+.....    +.+...- |||+||..|+..-..+++ |-.|
T Consensus       784 e~rc~~c~~~~l~~~~~~~~~~v~~-c~h~yhk~c~~~~~~~~~-~~~~  830 (846)
T KOG2066|consen  784 EERCSSCFEPNLPSGAAFDSVVVFH-CGHMYHKECLMMESLRNA-CNIE  830 (846)
T ss_pred             hhhhhhhcccccccCcccceeeEEE-ccchhhhcccccHHHhcc-cChh
Confidence            35799999887533    3456665 999999999998876655 4444

>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]

Probab=87.77  E-value=0.33  Score=35.60  Aligned_cols=48  Identities=29%  Similarity=0.734  Sum_probs=34.9

Q ss_pred             ccccccccccccCCceeec---CCCCCcccHhhHHHHHcC---------CCccccccccc
Q 038049           79 AGCAICLLDFIDGDEIRLL---PKCNHRFHVACIDKWLLS---------HSSCPTCRQRL  126 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~l---p~C~H~Fh~~Ci~~wl~~---------~~~CP~CR~~~  126 (141)
                      .+|.+|..++.+.+..+.+   |.|+-++|..|+.+.+..         +..||.|++.+
T Consensus       183 ~~celc~~ei~e~~~~~a~c~~~~c~~~~h~~CLa~~~~~~e~g~~~p~eg~cp~C~~~~  242 (276)
T KOG3005|consen  183 VECELCEKEILETDWSRATCPNPDCDSLNHLTCLAEELLEVEPGQLIPLEGMCPKCEKFL  242 (276)
T ss_pred             hhhHHHHHHhccccceeccCCCCCCCchhhhhhhhHHHhccCCCceeccCCCCCchhcee
Confidence            5899999999655544332   258999999999995432         23499999854

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

Probab=87.70  E-value=0.4  Score=39.96  Aligned_cols=42  Identities=26%  Similarity=0.554  Sum_probs=30.2

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCcccc
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPT  121 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~  121 (141)
                      ...|.+|-..+.. .. ...+.|||.=|.+|+..|+...+.||.
T Consensus       779 ~~~CtVC~~vi~G-~~-~~c~~C~H~gH~sh~~sw~~~~s~ca~  820 (839)
T KOG0269|consen  779 SAKCTVCDLVIRG-VD-VWCQVCGHGGHDSHLKSWFFKASPCAK  820 (839)
T ss_pred             hcCceeecceeee-eE-eecccccccccHHHHHHHHhcCCCCcc
Confidence            3468888655422 11 223369999999999999998888766

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

Probab=87.54  E-value=0.33  Score=34.40  Aligned_cols=45  Identities=33%  Similarity=0.792  Sum_probs=34.7

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccc
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQ  124 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~  124 (141)
                      +-..|.+|..-.-.+  ++.-. ||=.+|..|+..++.+...||.|..
T Consensus       180 nlk~Cn~Ch~LvIqg--~rCg~-c~i~~h~~c~qty~q~~~~cphc~d  224 (235)
T KOG4718|consen  180 NLKNCNLCHCLVIQG--IRCGS-CNIQYHRGCIQTYLQRRDICPHCGD  224 (235)
T ss_pred             HHHHHhHhHHHhhee--eccCc-ccchhhhHHHHHHhcccCcCCchhc
Confidence            346799998665443  34343 8888999999999999999999954

>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=87.08  E-value=0.57  Score=25.63  Aligned_cols=40  Identities=23%  Similarity=0.487  Sum_probs=27.8

Q ss_pred             ccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCC
Q 038049           81 CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSD  130 (141)
Q Consensus        81 C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~  130 (141)
                      |+-|-..+.+.+.+...  -|..||.+|        -.|-.|++++....
T Consensus         1 C~~C~~~I~~~~~~~~~--~~~~~H~~C--------f~C~~C~~~l~~~~   40 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKA--MGKFWHPEC--------FKCSKCGKPLNDGD   40 (58)
T ss_dssp             BTTTSSBESSSSEEEEE--TTEEEETTT--------SBETTTTCBTTTSS
T ss_pred             CCCCCCCccCcEEEEEe--CCcEEEccc--------cccCCCCCccCCCe
Confidence            66677777655544322  678899888        67888888886654

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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....

>PF15176 LRR19-TM: Leucine-rich repeat family 19 TM domain

Probab=86.69  E-value=1.6  Score=27.21  Aligned_cols=33  Identities=21%  Similarity=0.216  Sum_probs=24.4

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Q 038049            5 NIMVIVAAMLCALVCALGLHSMLQCVFQCTQRA   37 (141)
Q Consensus         5 ~~~~i~~~~l~~~~~~l~~~~~~~~~~~~~~~~   37 (141)
                      .|-+++++++.+++..+++++.+.|-.+++.+.
T Consensus        16 sW~~LVGVv~~al~~SlLIalaaKC~~~~k~~~   48 (102)
T PF15176_consen   16 SWPFLVGVVVTALVTSLLIALAAKCPVWYKYLA   48 (102)
T ss_pred             ccHhHHHHHHHHHHHHHHHHHHHHhHHHHHHHh
Confidence            567788888888888888888887765554443

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

Probab=86.55  E-value=2.9  Score=21.26  Aligned_cols=6  Identities=50%  Similarity=0.811  Sum_probs=2.2

Q ss_pred             HHHHHH
Q 038049            8 VIVAAM   13 (141)
Q Consensus         8 ~i~~~~   13 (141)
                      ++++++
T Consensus         8 IIv~V~   13 (38)
T PF02439_consen    8 IIVAVV   13 (38)
T ss_pred             HHHHHH
Confidence            333333

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

>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]

Probab=86.18  E-value=3.9  Score=30.99  Aligned_cols=44  Identities=18%  Similarity=0.316  Sum_probs=32.5

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcCCC---ccccc
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS---SCPTC  122 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~---~CP~C  122 (141)
                      --.||+=-+.-.+......+. |||+.-..-++..-+++.   .||+|
T Consensus       336 ~FiCPVlKe~~t~ENpP~ml~-CgHVIskeal~~LS~nG~~~FKCPYC  382 (396)
T COG5109         336 LFICPVLKELCTDENPPVMLE-CGHVISKEALSVLSQNGVLSFKCPYC  382 (396)
T ss_pred             eeeccccHhhhcccCCCeeee-ccceeeHHHHHHHhhcCcEEeeCCCC
Confidence            356888766655555556776 999999999998765542   49999

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

Probab=85.90  E-value=0.72  Score=24.98  Aligned_cols=43  Identities=21%  Similarity=0.472  Sum_probs=18.4

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcCC-----Ccccccccc
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH-----SSCPTCRQR  125 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~-----~~CP~CR~~  125 (141)
                      ..|+|-...+..  .+|-.. |.|.-+-| ++.|+...     -.||+|.++
T Consensus         3 L~CPls~~~i~~--P~Rg~~-C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~~   50 (50)
T PF02891_consen    3 LRCPLSFQRIRI--PVRGKN-CKHLQCFD-LESFLESNQRTPKWKCPICNKP   50 (50)
T ss_dssp             SB-TTTSSB-SS--EEEETT---SS--EE-HHHHHHHHHHS---B-TTT---
T ss_pred             eeCCCCCCEEEe--CccCCc-CcccceEC-HHHHHHHhhccCCeECcCCcCc
Confidence            358887777644  356565 99884322 33455332     259999864

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

>smart00249 PHD PHD zinc finger

Probab=85.52  E-value=0.53  Score=24.17  Aligned_cols=31  Identities=19%  Similarity=0.524  Sum_probs=21.0

Q ss_pred             cccccccccccCCceeecCCCCCcccHhhHHH
Q 038049           80 GCAICLLDFIDGDEIRLLPKCNHRFHVACIDK  111 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~  111 (141)
                      .|.+|......+..+.-- .|+..||..|+..
T Consensus         1 ~C~~C~~~~~~~~~i~C~-~C~~~~H~~C~~~   31 (47)
T smart00249        1 YCSVCGKPDDGGELLQCD-GCDRWYHQTCLGP   31 (47)
T ss_pred             CcccCCCcCCCCCEEECC-CCCchhhhhhCCC
Confidence            377887766333333333 5999999999865

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

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=84.57  E-value=0.71  Score=23.30  Aligned_cols=26  Identities=38%  Similarity=0.814  Sum_probs=16.2

Q ss_pred             ccccccccccccCCc--------eeecCCCCCccc
Q 038049           79 AGCAICLLDFIDGDE--------IRLLPKCNHRFH  105 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~--------v~~lp~C~H~Fh  105 (141)
                      .+|+=|...|..++.        ++ -+.|+|+|.
T Consensus         3 i~CP~C~~~f~v~~~~l~~~~~~vr-C~~C~~~f~   36 (37)
T PF13719_consen    3 ITCPNCQTRFRVPDDKLPAGGRKVR-CPKCGHVFR   36 (37)
T ss_pred             EECCCCCceEEcCHHHcccCCcEEE-CCCCCcEee
Confidence            468888877765442        33 334888875

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

Probab=84.38  E-value=0.44  Score=37.02  Aligned_cols=44  Identities=20%  Similarity=0.495  Sum_probs=31.7

Q ss_pred             cccccccccccccCCc--eeecCCCCCcccHhhHHHHHcCCCccccc
Q 038049           78 SAGCAICLLDFIDGDE--IRLLPKCNHRFHVACIDKWLLSHSSCPTC  122 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~--v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~C  122 (141)
                      -..|+.|.-.++-.+.  -..-. |||.|++.|...|...+..|..|
T Consensus       306 wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C~~~~~~~~~~~~~~  351 (384)
T KOG1812|consen  306 WRQCPKCKFMIELSEGCNHMTCR-CGHQFCYMCGGDWKTHNGECYEC  351 (384)
T ss_pred             cCcCcccceeeeecCCcceEEee-ccccchhhcCcchhhCCccccCc
Confidence            3569999876655443  23444 99999999999998777766443

>PHA03029 hypothetical protein; Provisional

Probab=83.19  E-value=2.5  Score=24.91  Aligned_cols=29  Identities=10%  Similarity=0.290  Sum_probs=14.3

Q ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038049            4 LNIMVIVAAMLCALVCALGLHSMLQCVFQ   32 (141)
Q Consensus         4 ~~~~~i~~~~l~~~~~~l~~~~~~~~~~~   32 (141)
                      ..++..++++++.+++++.+..++.-+..
T Consensus         4 ~ei~~~ii~~iiyiilila~igiiwg~ll   32 (92)
T PHA03029          4 AEIVFLIIAIIIYIILILAIIGIIWGFLL   32 (92)
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444455555555555555555544433

>PF15179 Myc_target_1: Myc target protein 1

Probab=83.18  E-value=3.1  Score=28.92  Aligned_cols=26  Identities=12%  Similarity=0.121  Sum_probs=11.3

Q ss_pred             CCCccHHHHHHHHHHHHHHHHHHHHH
Q 038049            1 SADLNIMVIVAAMLCALVCALGLHSM   26 (141)
Q Consensus         1 s~~~~~~~i~~~~l~~~~~~l~~~~~   26 (141)
                      |||+.-+++.+-+-.++.++||.++.
T Consensus        15 ~f~~~~lIlaF~vSm~iGLviG~li~   40 (197)
T PF15179_consen   15 NFDWEDLILAFCVSMAIGLVIGALIW   40 (197)
T ss_pred             hcchhhHHHHHHHHHHHHHHHHHHHH
Confidence            45444444444444444444443333

>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=83.08  E-value=0.58  Score=26.83  Aligned_cols=38  Identities=18%  Similarity=0.336  Sum_probs=18.6

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHH
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWL  113 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl  113 (141)
                      .+...|.+|...|.--..-..-..||++|+.+|.....
T Consensus         7 ~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~   44 (69)
T PF01363_consen    7 SEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRI   44 (69)
T ss_dssp             GG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEE
T ss_pred             CCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEE
Confidence            34577999999995432222222599999999987554

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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....

>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]

Probab=83.03  E-value=1.8  Score=32.70  Aligned_cols=53  Identities=23%  Similarity=0.520  Sum_probs=36.1

Q ss_pred             Cccccccccccccc---------------C-CceeecCCCCCcccHhhHHHHHcC---------CCccccccccccCCC
Q 038049           77 ASAGCAICLLDFID---------------G-DEIRLLPKCNHRFHVACIDKWLLS---------HSSCPTCRQRLKPSD  130 (141)
Q Consensus        77 ~~~~C~ICl~~~~~---------------~-~~v~~lp~C~H~Fh~~Ci~~wl~~---------~~~CP~CR~~~~~~~  130 (141)
                      .+.+|++|+..-..               + -.-...| |||+--++=..-|-+.         +..||.|-+.+..+.
T Consensus       340 ~~r~CPmC~~~gp~V~L~lG~E~~f~vD~G~pthaF~P-CGHv~sekt~~YWs~iplPhGT~~f~a~CPFC~~~L~ge~  417 (429)
T KOG3842|consen  340 RERECPMCRVVGPYVPLWLGCEAGFYVDAGPPTHAFNP-CGHVCSEKTVKYWSQIPLPHGTHAFHAACPFCATQLAGEQ  417 (429)
T ss_pred             ccCcCCeeeeecceeeeeccccceeEecCCCcccccCC-cccccchhhhhHhhcCcCCCccccccccCcchhhhhccCC
Confidence            46899999954210               0 0112466 9999999999999754         234999988876554

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

Probab=82.57  E-value=0.46  Score=35.48  Aligned_cols=49  Identities=24%  Similarity=0.565  Sum_probs=39.6

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRL  126 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~  126 (141)
                      ......|-||...+..+....   +|.|.|+..|-..|......||.||.-.
T Consensus       102 ~~~~~~~~~~~g~l~vpt~~q---g~w~qf~~~~p~~~~~~~~~~~d~~~~~  150 (324)
T KOG0824|consen  102 QQDHDICYICYGKLTVPTRIQ---GCWHQFCYVCPKSNFAMGNDCPDCRGKI  150 (324)
T ss_pred             cCCccceeeeeeeEEeccccc---CceeeeeecCCchhhhhhhccchhhcCc
Confidence            445677999998887764332   4999999999999999999999998744

>PF02009 Rifin_STEVOR: Rifin/stevor family; InterPro: IPR002858 Malaria is still a major cause of mortality in many areas of the world

Probab=82.46  E-value=2.5  Score=31.81  Aligned_cols=13  Identities=0%  Similarity=0.258  Sum_probs=5.8

Q ss_pred             HHHHHHHHHHhcc
Q 038049           23 LHSMLQCVFQCTQ   35 (141)
Q Consensus        23 ~~~~~~~~~~~~~   35 (141)
                      ++.++++++|+||
T Consensus       271 IMvIIYLILRYRR  283 (299)
T PF02009_consen  271 IMVIIYLILRYRR  283 (299)
T ss_pred             HHHHHHHHHHHHH
Confidence            3444444555444

Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see []. Several multicopy gene families have been described in Plasmodium falciparum, including the stevor family of subtelomeric open reading frames and the rif interspersed repetitive elements. Both families contain three predicted transmembrane segments. It has been proposed that stevor and rif are members of a larger superfamily that code for variant surface antigens [].

>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=82.13  E-value=1.1  Score=29.27  Aligned_cols=10  Identities=10%  Similarity=0.019  Sum_probs=4.9

Q ss_pred             HHHhcccccC
Q 038049           30 VFQCTQRALT   39 (141)
Q Consensus        30 ~~~~~~~~~~   39 (141)
                      +++.+||.++
T Consensus        20 ~~~~rRR~r~   29 (130)
T PF12273_consen   20 YCHNRRRRRR   29 (130)
T ss_pred             HHHHHHHhhc
Confidence            4445555444

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 [].

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

Probab=81.95  E-value=1.1  Score=37.76  Aligned_cols=52  Identities=12%  Similarity=0.166  Sum_probs=35.3

Q ss_pred             CCcccccccccccccCCc---eeecCCCCCcccHhhHHHHHcC------CCcccccccccc
Q 038049           76 SASAGCAICLLDFIDGDE---IRLLPKCNHRFHVACIDKWLLS------HSSCPTCRQRLK  127 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~---v~~lp~C~H~Fh~~Ci~~wl~~------~~~CP~CR~~~~  127 (141)
                      ....+|.+|..++.+++.   +-.+.+|+|.||..||..|..+      +-.|+.|.+-+.
T Consensus        94 a~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~  154 (1134)
T KOG0825|consen   94 AESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEESEKHTAHYFCEECVG  154 (1134)
T ss_pred             ccccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhccccccccccHHHHhh
Confidence            345678888888776322   2222259999999999999843      234788877553

>KOG3039 consensus Uncharacterized conserved protein [Function unknown]

Probab=81.83  E-value=1.1  Score=32.70  Aligned_cols=37  Identities=19%  Similarity=0.263  Sum_probs=30.7

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS  115 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~  115 (141)
                      ..+.+.|+.||.++.++   .++| =||+|..+||-+++..
T Consensus        40 iK~FdcCsLtLqPc~dP---vit~-~GylfdrEaILe~ila   76 (303)
T KOG3039|consen   40 IKPFDCCSLTLQPCRDP---VITP-DGYLFDREAILEYILA   76 (303)
T ss_pred             cCCcceeeeecccccCC---ccCC-CCeeeeHHHHHHHHHH
Confidence            45567899999988777   6777 8999999999999754

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=81.65  E-value=0.91  Score=22.80  Aligned_cols=26  Identities=35%  Similarity=0.686  Sum_probs=16.3

Q ss_pred             ccccccccccccCCc--------eeecCCCCCccc
Q 038049           79 AGCAICLLDFIDGDE--------IRLLPKCNHRFH  105 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~--------v~~lp~C~H~Fh  105 (141)
                      .+|+=|...|..++.        ++-. .|||.|+
T Consensus         3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~-~C~~~f~   36 (36)
T PF13717_consen    3 ITCPNCQAKYEIDDEKIPPKGRKVRCS-KCGHVFF   36 (36)
T ss_pred             EECCCCCCEEeCCHHHCCCCCcEEECC-CCCCEeC
Confidence            467888877765543        3333 4888874

>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=81.52  E-value=0.74  Score=24.61  Aligned_cols=44  Identities=32%  Similarity=0.622  Sum_probs=28.4

Q ss_pred             cccccccccccCCceeecCCCCCcccHhhHHHHHc------CCCccccccc
Q 038049           80 GCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL------SHSSCPTCRQ  124 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~------~~~~CP~CR~  124 (141)
                      .|.||...-..++.+.-- .|+-.||..|+..=..      ..-.||.|+.
T Consensus         1 ~C~vC~~~~~~~~~i~C~-~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~   50 (51)
T PF00628_consen    1 YCPVCGQSDDDGDMIQCD-SCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP   50 (51)
T ss_dssp             EBTTTTSSCTTSSEEEBS-TTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred             eCcCCCCcCCCCCeEEcC-CCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence            388998844444444444 5999999999876432      1335888753

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 ....

>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length

Probab=81.31  E-value=2.5  Score=23.48  Aligned_cols=45  Identities=27%  Similarity=0.654  Sum_probs=31.5

Q ss_pred             cccccccccccCC-ceeecCCCC--CcccHhhHHHHHcCCCccccccccccCC
Q 038049           80 GCAICLLDFIDGD-EIRLLPKCN--HRFHVACIDKWLLSHSSCPTCRQRLKPS  129 (141)
Q Consensus        80 ~C~ICl~~~~~~~-~v~~lp~C~--H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~  129 (141)
                      .|--|-.++..+. ..++   |+  ..|+.+|.+.-|  +..||.|.-.+...
T Consensus         7 nCE~C~~dLp~~s~~A~I---CSfECTFC~~C~e~~l--~~~CPNCgGelv~R   54 (57)
T PF06906_consen    7 NCECCDKDLPPDSPEAYI---CSFECTFCADCAETML--NGVCPNCGGELVRR   54 (57)
T ss_pred             CccccCCCCCCCCCcceE---EeEeCcccHHHHHHHh--cCcCcCCCCccccC
Confidence            4666766665554 2332   55  459999999976  68899998877654

This family contains a number of conserved cysteine residues and its function is unknown.

>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length

Probab=81.08  E-value=0.13  Score=30.01  Aligned_cols=40  Identities=25%  Similarity=0.502  Sum_probs=20.3

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      ..|+.|..++....        +|..+..|-.. +.....||-|.+++.
T Consensus         2 ~~CP~C~~~L~~~~--------~~~~C~~C~~~-~~~~a~CPdC~~~Le   41 (70)
T PF07191_consen    2 NTCPKCQQELEWQG--------GHYHCEACQKD-YKKEAFCPDCGQPLE   41 (70)
T ss_dssp             -B-SSS-SBEEEET--------TEEEETTT--E-EEEEEE-TTT-SB-E
T ss_pred             CcCCCCCCccEEeC--------CEEECcccccc-ceecccCCCcccHHH
Confidence            46899987765442        55566666554 244567999988764

Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	141
1iym_A	55	Ring-H2 Finger Domain Of El5 Length = 55		1e-11
1x4j_A	75	Solution Structure Of Ring Finger In Ring Finger Pr		2e-08
2ect_A	78	Solution Structure Of The Zinc Finger, C3hc4 Type (		6e-08
2kiz_A	69	Solution Structure Of Arkadia Ring-H2 Finger Domain		1e-06
2l0b_A	91	Solution Nmr Structure Of Zinc Finger Domain Of E3		2e-05
2ep4_A	74	Solution Structure Of Ring Finger From Human Ring F		1e-04

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

Iteration: 1
 Score = 65.1 bits (157), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 25/43 (58%), Positives = 31/43 (72%)
Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCR 123
           CA+CL +  DG+E R LP+C H FH  C+D WL SHS+CP CR
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCR 50

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

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 23/51 (45%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDA 131
           C +C+ DF     +R+LP CNH FH  C+DKWL ++ +CP CR    PS  
Sbjct: 26  CVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGPSSG 75

>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 = 52.8 bits (125), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 23/46 (50%), Positives = 29/46 (63%), Gaps = 1/46 (2%)
Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRL 126
           C +C  D+  G+ +R LP CNH FH +CI  WL  H SCP CR+ L
Sbjct: 18  CPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSL 62

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

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 20/43 (46%), Positives = 29/43 (67%), Gaps = 1/43 (2%)
Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCR 123
           C ICL    +G+++R LP C H FH  C+D+WL+++  CP CR
Sbjct: 17  CTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICR 58

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKP 128
           C IC  +++ GD    LP C+H FH  C+  WL    +CP CR    P
Sbjct: 43  CPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCMFPP 89

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/42 (47%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTC 122
           CA+CL DF   DE+ + P C H FH  C+ KWL     CP C
Sbjct: 18  CAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLC 58

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	141
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	3e-26
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	4e-25
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	2e-24
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	1e-23
2ect_A	78	Ring finger protein 126; metal binding protein, st	1e-22
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	2e-21
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	4e-18
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	9e-17
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	1e-16
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	2e-12
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	2e-12
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	6e-12
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	1e-11
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	3e-11
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	4e-11
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	4e-11
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	3e-09
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	1e-08
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	2e-08
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	2e-08
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	5e-08
4epo_C	149	E3 ubiquitin-protein ligase RNF8; coiled-coil, E3	6e-08
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	6e-08
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	2e-07
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	6e-07
3nw0_A	238	Non-structural maintenance of chromosomes element	1e-06
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	3e-06
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	6e-06
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	1e-05
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	3e-05
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	8e-05
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	8e-05
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	9e-05
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	1e-04
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	1e-04
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	2e-04
1z6u_A	150	NP95-like ring finger protein isoform B; structura	2e-04
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	3e-04
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	4e-04
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	4e-04
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	5e-04
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	6e-04
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	9e-04

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

 Score = 92.8 bits (231), Expect = 3e-26
 Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 61  ALPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCP 120
            LP+  +  + ++  S    C +C+ DF     +R+LP CNH FH  C+DKWL ++ +CP
Sbjct: 8   QLPSYRF--NPNNHQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCP 64

Query: 121 TCRQRLKPSDA 131
            CR    PS  
Sbjct: 65  ICRADSGPSSG 75

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

 Score = 89.6 bits (223), Expect = 4e-25
 Identities = 25/46 (54%), Positives = 32/46 (69%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRL 126
           CA+CL +  DG+E R LP+C H FH  C+D WL SHS+CP CR  +
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

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

 Score = 88.9 bits (221), Expect = 2e-24
 Identities = 23/82 (28%), Positives = 34/82 (41%), Gaps = 2/82 (2%)

Query: 47  SRRLNSGLKRKEMVALPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHV 106
               N    ++ + ALP +       +       C IC  +++ GD    LP C+H FH 
Sbjct: 10  HMVANPPASKESIDALPEILVTEDHGAVGQEMC-CPICCSEYVKGDVATELP-CHHYFHK 67

Query: 107 ACIDKWLLSHSSCPTCRQRLKP 128
            C+  WL    +CP CR    P
Sbjct: 68  PCVSIWLQKSGTCPVCRCMFPP 89

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

 Score = 86.7 bits (215), Expect = 1e-23
 Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 72  SSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDA 131
            +       C ICL    +G+++R LP C H FH  C+D+WL+++  CP CR  ++    
Sbjct: 8   GTEEDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQLP 66

Query: 132 MPS 134
             S
Sbjct: 67  SES 69

>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 = 84.0 bits (208), Expect = 1e-22
 Identities = 28/68 (41%), Positives = 37/68 (54%), Gaps = 5/68 (7%)

Query: 68  ANSGSSPSSASAG----CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCR 123
            +SGSS +    G    C +C  D+  G+ +R LP CNH FH +CI  WL  H SCP CR
Sbjct: 1   GSSGSSGTEEHVGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCR 59

Query: 124 QRLKPSDA 131
           + L   + 
Sbjct: 60  KSLTGQNT 67

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

 Score = 81.0 bits (200), Expect = 2e-21
 Identities = 20/54 (37%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPS 134
           CA+CL DF   DE+ + P C H FH  C+ KWL     CP C   +     +  
Sbjct: 18  CAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLSG 70

>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 = 71.9 bits (177), Expect = 4e-18
 Identities = 17/49 (34%), Positives = 22/49 (44%)

Query: 75  SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCR 123
           SS S+GC ICL D      +  +  C H  H  C ++ L     CP C 
Sbjct: 2   SSGSSGCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLCS 50

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

 Score = 68.6 bits (168), Expect = 9e-17
 Identities = 24/67 (35%), Positives = 32/67 (47%), Gaps = 9/67 (13%)

Query: 68  ANSGSSPSSASAG----CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCR 123
            +SGSS           C IC+    DG    +LP C H F   CIDKW   H +CP CR
Sbjct: 1   GSSGSSGRVKQLTDEEECCICM----DGRADLILP-CAHSFCQKCIDKWSDRHRNCPICR 55

Query: 124 QRLKPSD 130
            ++  ++
Sbjct: 56  LQMTGAN 62

>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 = 1e-16
 Identities = 14/48 (29%), Positives = 23/48 (47%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKP 128
           C  C  +    D + +  +CNH FH  C+  W+  ++ CP C+Q    
Sbjct: 29  CLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVV 76

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

 Score = 57.8 bits (140), Expect = 2e-12
 Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 3/53 (5%)

Query: 75  SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK 127
           ++ +  C ICL D  +      LP C H F   CI +W+  + +CP C+  ++
Sbjct: 2   ATVAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVE 51

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

 Score = 57.6 bits (139), Expect = 2e-12
 Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 10/68 (14%)

Query: 71  GSSPSSASAG-------CAICLLDFIDGDEIRLLP---KCNHRFHVACIDKWLLSHSSCP 120
           GSS SS +         C IC+  + +  +   L    +C H F   C+   L + ++CP
Sbjct: 1   GSSGSSGTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCP 60

Query: 121 TCRQRLKP 128
           TCR+++  
Sbjct: 61  TCRKKINH 68

>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 = 57.5 bits (138), Expect = 6e-12
 Identities = 12/44 (27%), Positives = 16/44 (36%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQ 124
           C          +       CNH FH  CI +WL +   CP   +
Sbjct: 54  CQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 97

>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 = 55.6 bits (134), Expect = 1e-11
 Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 3/67 (4%)

Query: 70  SGSSPSSASAGCAICLLDFIDGDEIRLLP---KCNHRFHVACIDKWLLSHSSCPTCRQRL 126
           +     S +  C IC+  + +  +   L    +C H F   C+   L + ++CPTCR+++
Sbjct: 2   TTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61

Query: 127 KPSDAMP 133
                 P
Sbjct: 62  NHKRYHP 68

>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 = 56.0 bits (134), Expect = 3e-11
 Identities = 12/44 (27%), Positives = 16/44 (36%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQ 124
           C          +       CNH FH  CI +WL +   CP   +
Sbjct: 65  CQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 108

>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 = 55.3 bits (133), Expect = 4e-11
 Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 6/62 (9%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL-SHSSCPTCRQRLKPSDAMPS--LDE 137
           C IC+    D    RL P C+     +CI +WL    + CP CR  L+  + +     +E
Sbjct: 25  CFICMEKLRDA---RLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQLRELVNCRWAEE 81

Query: 138 IV 139
           + 
Sbjct: 82  VT 83

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

 Score = 54.0 bits (130), Expect = 4e-11
 Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 3/56 (5%)

Query: 81  CAICLLDFIDGDEIRLLP---KCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMP 133
           C IC+  + +  +   L    +C H F   C+   L + ++CPTCR+++      P
Sbjct: 6   CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHP 61

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

 Score = 52.9 bits (126), Expect = 3e-09
 Identities = 18/83 (21%), Positives = 31/83 (37%), Gaps = 15/83 (18%)

Query: 62  LPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLL----PKCNHRFHVACIDKWLLS-- 115
           +P  +         +    C IC    +DG E+ L+     KC  + H  C+++W  +  
Sbjct: 292 MPDWSDGPKLDEEDNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLM 351

Query: 116 ---------HSSCPTCRQRLKPS 129
                       CP C+ +L  S
Sbjct: 352 DGKTFLEVSFGQCPFCKAKLSTS 374

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

 Score = 48.2 bits (115), Expect = 1e-08
 Identities = 13/56 (23%), Positives = 22/56 (39%), Gaps = 3/56 (5%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPSLD 136
           C+IC    ID      + +C H F  +CI +     + CP C   +  +  +    
Sbjct: 18  CSICKGYLIDA---TTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLSGPS 70

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

 Score = 47.6 bits (113), Expect = 2e-08
 Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 5/46 (10%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH--SSCPTCRQ 124
           C IC    I G   +    C  R H+ C+ K+  S+    CP C  
Sbjct: 18  CNICHSLLIQG---QSCETCGIRMHLPCVAKYFQSNAEPRCPHCND 60

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

 Score = 50.5 bits (120), Expect = 2e-08
 Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 5/59 (8%)

Query: 76  SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS-SCPTCRQRLKPSDAMP 133
           S    C IC  +  D   +++ P C H    +C+  W  S    CP CR  +K ++ + 
Sbjct: 330 STFQLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIV 384

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

 Score = 46.7 bits (111), Expect = 5e-08
 Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMP--SLDEI 138
           C IC   F       ++P+C+H +   CI K+L   + CPTC   +   D      LDE+
Sbjct: 25  CGICFEYFNIA---MIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLKNNRILDEL 81

Query: 139 V 139
           V
Sbjct: 82  V 82

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

 Score = 47.7 bits (113), Expect = 6e-08
 Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 4/59 (6%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPSLDEIV 139
           C IC   FI+     +   C H F   CI++W+     CP CR+ +K       LD  +
Sbjct: 67  CIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDIKSKTYSLVLDNCI 121

>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 = 46.7 bits (111), Expect = 6e-08
 Identities = 14/55 (25%), Positives = 26/55 (47%), Gaps = 3/55 (5%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPSL 135
           C +C   FID      + +C H F   CI ++L +   CP C  ++  +  + ++
Sbjct: 18  CVLCGGYFID---ATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNI 69

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

 Score = 44.8 bits (106), Expect = 2e-07
 Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 4/57 (7%)

Query: 68  ANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQ 124
           ++ GS        C IC   F +     ++ KC H F  +C  +   +   C  C Q
Sbjct: 5   SSGGSEEEEIPFRCFICRQAFQNP----VVTKCRHYFCESCALEHFRATPRCYICDQ 57

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

 Score = 43.3 bits (102), Expect = 6e-07
 Identities = 19/70 (27%), Positives = 27/70 (38%), Gaps = 8/70 (11%)

Query: 68  ANSGSSPSSASAG----CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCR 123
            +SGSS ++A +     CAICL   +    + L   C H F   C+         C  CR
Sbjct: 1   GSSGSSGNTAPSLTVPECAICLQTCVH--PVSL--PCKHVFCYLCVKGASWLGKRCALCR 56

Query: 124 QRLKPSDAMP 133
           Q +       
Sbjct: 57  QEIPEDFLDS 66

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

 Score = 45.5 bits (107), Expect = 1e-06
 Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 5/46 (10%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSS--CPTCRQ 124
           C IC    I G        C  R H+ C+ K+  S++   CP C  
Sbjct: 183 CNICHSLLIQGQSC---ETCGIRMHLPCVAKYFQSNAEPRCPHCND 225

>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 = 42.5 bits (99), Expect = 3e-06
 Identities = 13/62 (20%), Positives = 22/62 (35%), Gaps = 19/62 (30%)

Query: 81  CAICLLDFIDGDE--------------IRLLPKCNHRFHVACIDKWLLSHS-----SCPT 121
           C IC+                      +  L KC+H FH+ C+     + +      CP+
Sbjct: 28  CIICMEKLAVASGYSDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPS 87

Query: 122 CR 123
           C+
Sbjct: 88  CK 89

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

 Score = 42.1 bits (98), Expect = 6e-06
 Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 3/59 (5%)

Query: 73  SPSSASAGCAICLLDFIDGDEIRLLP---KCNHRFHVACIDKWLLSHSSCPTCRQRLKP 128
           +  S +  C IC+  + +  +   L    +C H F   C+   L + ++CPTCR+++  
Sbjct: 2   AMGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH 60

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

 Score = 39.7 bits (93), Expect = 1e-05
 Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 5/53 (9%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS--SCPTCRQRLKPSDA 131
           C IC     D     ++P C + +   CI   LL     +CPTC Q     DA
Sbjct: 18  CLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA 67

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

 Score = 40.3 bits (94), Expect = 3e-05
 Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 7/63 (11%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWL-LSHSSCPTCRQRLKPSDAM---PSLD 136
           C ICL    +        +C HRF   CI   L   +  CPTCR++L    ++   P+ D
Sbjct: 57  CPICLDMLKNT---MTTKECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFD 113

Query: 137 EIV 139
            ++
Sbjct: 114 ALI 116

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

 Score = 38.8 bits (90), Expect = 8e-05
 Identities = 16/63 (25%), Positives = 21/63 (33%), Gaps = 8/63 (12%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS-SCPTCRQRLKPSDAMP---SLD 136
           C  C               C H     C+D+   +   SCP CR  L  S AM     L 
Sbjct: 55  CICCQELVFRPITT----VCQHNVCKDCLDRSFRAQVFSCPACRYDLGRSYAMQVNQPLQ 110

Query: 137 EIV 139
            ++
Sbjct: 111 TVL 113

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

 Score = 37.5 bits (87), Expect = 8e-05
 Identities = 13/51 (25%), Positives = 19/51 (37%), Gaps = 5/51 (9%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS-SCPTCRQRLKPSD 130
           C  C L            +C HRF  +C+   L S S  C  C++ +    
Sbjct: 18  CEKCHLVLCS----PKQTECGHRFCESCMAALLSSSSPKCTACQESIVKDK 64

>2bay_A PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin ligase, E3 ligase; 1.50A {Saccharomyces cerevisiae} SCOP: g.44.1.2 PDB: 1n87_A Length = 61

 Score = 37.3 bits (87), Expect = 9e-05
 Identities = 9/53 (16%), Positives = 19/53 (35%), Gaps = 3/53 (5%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMP 133
           CAI            L PK    F  + +++++    + P   + L   + + 
Sbjct: 6   CAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVE 55

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A Length = 968

 Score = 40.1 bits (93), Expect = 1e-04
 Identities = 13/38 (34%), Positives = 16/38 (42%)

Query: 96  LLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMP 133
           +LP        + I   LLS S+ P  R  LK  D  P
Sbjct: 906 ILPASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTP 943

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

 Score = 38.3 bits (89), Expect = 1e-04
 Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 5/55 (9%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSS-CPTCRQRLKPSDAMPS 134
           C ICL+   +     +   C HRF  ACI K +      CP   + L  +   P 
Sbjct: 21  CPICLMALREA----VQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPD 71

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

 Score = 37.1 bits (86), Expect = 2e-04
 Identities = 19/64 (29%), Positives = 26/64 (40%), Gaps = 8/64 (12%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH--SSCPTCRQRLKPSDAMP---SL 135
           C IC     D     ++P C + +   CI   LL     +CPTC Q     DA+     L
Sbjct: 16  CLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDALIANKFL 72

Query: 136 DEIV 139
            + V
Sbjct: 73  RQAV 76

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

 Score = 38.1 bits (88), Expect = 2e-04
 Identities = 13/63 (20%), Positives = 19/63 (30%), Gaps = 8/63 (12%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWL-LSHSSCPTCRQRLKPSDAM---PSLD 136
           C  C              +C H     C+ +       SCP CR  L  +  M     L 
Sbjct: 81  CVCCQELVYQPVTT----ECFHNVCKDCLQRSFKAQVFSCPACRHDLGQNYIMIPNEILQ 136

Query: 137 EIV 139
            ++
Sbjct: 137 TLL 139

>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 Length = 100

 Score = 37.0 bits (86), Expect = 3e-04
 Identities = 9/27 (33%), Positives = 13/27 (48%)

Query: 107 ACIDKWLLSHSSCPTCRQRLKPSDAMP 133
           + I + LL+  + P  RQ L  S   P
Sbjct: 54  SIILRHLLNSPTDPFNRQTLTESMLEP 80

>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase, UBL conjugation pathway; NMR {Mus musculus} Length = 85

 Score = 36.2 bits (84), Expect = 4e-04
 Identities = 9/27 (33%), Positives = 13/27 (48%)

Query: 107 ACIDKWLLSHSSCPTCRQRLKPSDAMP 133
           + I + LL+  + P  RQ L  S   P
Sbjct: 39  SIILRHLLNSPTDPFNRQMLTESMLEP 65

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

 Score = 36.2 bits (84), Expect = 4e-04
 Identities = 14/47 (29%), Positives = 19/47 (40%), Gaps = 3/47 (6%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS---SCPTCRQ 124
           C IC+  F +      L  C H     C++K L S      CP C +
Sbjct: 18  CPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFCSK 64

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

 Score = 36.8 bits (85), Expect = 5e-04
 Identities = 13/61 (21%), Positives = 20/61 (32%), Gaps = 7/61 (11%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMP--SLDEI 138
           C+ C     +      L  C H F   C+   +   + CP C       D      LD +
Sbjct: 25  CSRCTNILREP---VCLGGCEHIFCSNCVSDCI--GTGCPVCYTPAWIQDLKINRQLDSM 79

Query: 139 V 139
           +
Sbjct: 80  I 80

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

 Score = 36.4 bits (84), Expect = 6e-04
 Identities = 18/51 (35%), Positives = 22/51 (43%), Gaps = 5/51 (9%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWL-LSHSSCPTCRQRLKPSD 130
           C IC     D  E      C H F   CI + L +  S CP+CR    P+D
Sbjct: 26  CQICEHILADPVETS----CKHLFCRICILRCLKVMGSYCPSCRYPCFPTD 72

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

 Score = 35.1 bits (80), Expect = 9e-04
 Identities = 10/52 (19%), Positives = 17/52 (32%), Gaps = 1/52 (1%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPSDA 131
           C +C+      D       C ++    C  +     +  CP CR+      A
Sbjct: 14  CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPA 65

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	141
2l0b_A	91	E3 ubiquitin-protein ligase praja-1; zinc finger,	99.84
1x4j_A	75	Ring finger protein 38; structural genomics, NPPSF	99.81
2kiz_A	69	E3 ubiquitin-protein ligase arkadia; ring-H2 finge	99.78
2ect_A	78	Ring finger protein 126; metal binding protein, st	99.78
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	99.77
2ep4_A	74	Ring finger protein 24; zinc binding, ubiquitin, E	99.77
2ecl_A	81	Ring-box protein 2; RNF7, ring domian, zinc-bindin	99.73
3ng2_A	71	RNF4, snurf, ring finger protein 4; ring domain, E	99.71
2ecm_A	55	Ring finger and CHY zinc finger domain- containing	99.7
2ea6_A	69	Ring finger protein 4; RNF4, RES4-26, ring domain,	99.69
1v87_A	114	Deltex protein 2; ring-H2 domain, zinc-binding dom	99.69
2xeu_A	64	Ring finger protein 4; transcription, zinc-finger,	99.68
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	99.67
3dpl_R	106	Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST	99.66
2ecn_A	70	Ring finger protein 141; RNF141, ring domain, zinc	99.64
2d8s_A	80	Cellular modulator of immune recognition; C-MIR, m	99.64
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	99.64
1chc_A	68	Equine herpes virus-1 ring domain; viral protein;	99.61
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	99.61
2ct2_A	88	Tripartite motif protein 32; zinc-finger protein H	99.61
2yur_A	74	Retinoblastoma-binding protein 6; P53-associated c	99.6
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	99.59
4a0k_B	117	E3 ubiquitin-protein ligase RBX1; ligase-DNA-bindi	99.59
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	99.59
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	99.57
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	99.57
2ecw_A	85	Tripartite motif-containing protein 30; metal bind	99.56
2ecv_A	85	Tripartite motif-containing protein 5; metal bindi	99.55
2egp_A	79	Tripartite motif-containing protein 34; ZF-C3HC4 d	99.55
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.55
3lrq_A	100	E3 ubiquitin-protein ligase TRIM37; structural gen	99.54
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	99.52
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	99.52
2ysj_A	63	Tripartite motif-containing protein 31; ring-type	99.51
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	99.51
3fl2_A	124	E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA	99.49
2ecj_A	58	Tripartite motif-containing protein 39; TRIM39, ri	99.49
2ckl_A	108	Polycomb group ring finger protein 4; BMI1, RING1B	99.48
3ztg_A	92	E3 ubiquitin-protein ligase RBBP6; PACT, U-BOX, mR	99.48
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	99.47
1jm7_A	112	BRCA1, breast cancer type 1 susceptibility protein	99.45
1rmd_A	116	RAG1; V(D)J recombination, antibody, MAD, ring fin	99.45
3hct_A	118	TNF receptor-associated factor 6; cross-brace, bet	99.44
1z6u_A	150	NP95-like ring finger protein isoform B; structura	99.42
2ckl_B	165	Ubiquitin ligase protein RING2; BMI1, RING1B, poly	99.41
3l11_A	115	E3 ubiquitin-protein ligase RNF168; E3 ligase, rin	99.4
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	99.39
1e4u_A	78	Transcriptional repressor NOT4; gene regulation, t	99.38
2vje_A	64	E3 ubiquitin-protein ligase MDM2; proto-oncogene,	99.38
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	99.38
2kr4_A	85	Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ri	99.37
2vje_B	63	MDM4 protein; proto-oncogene, phosphorylation, alt	99.37
1wgm_A	98	Ubiquitin conjugation factor E4A; ubiquitinating e	99.35
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	99.33
2y1n_A	389	E3 ubiquitin-protein ligase; ligase-transferase co	99.31
3knv_A	141	TNF receptor-associated factor 2; cross-brace, alt	99.31
4ic3_A	74	E3 ubiquitin-protein ligase XIAP; ring domain, zin	99.24
3k1l_B	381	Fancl; UBC, ring, RWD, ligase; HET: MAL CIT; 3.20A	99.24
3hcs_A	170	TNF receptor-associated factor 6; cross-brace, bet	99.22
2yu4_A	94	E3 SUMO-protein ligase NSE2; SP-ring domain, struc	99.19
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	99.15
2ea5_A	68	Cell growth regulator with ring finger domain prot	99.15
1wim_A	94	KIAA0161 protein; ring finger domain, UBCM4-intera	99.13
1vyx_A	60	ORF K3, K3RING; zinc-binding protein, ring domain,	99.12
2ecg_A	75	Baculoviral IAP repeat-containing protein 4; BIRC4	99.12
2f42_A	179	STIP1 homology and U-box containing protein 1; cha	99.08
2yho_A	79	E3 ubiquitin-protein ligase mylip; ligase, E2 liga	99.02
3htk_C	267	E3 SUMO-protein ligase MMS21; SUMO E3 ligase, SPL-	98.87
2bay_A	61	PRE-mRNA splicing factor PRP19; U-BOX, ubiquitin l	98.86
3t6p_A	345	Baculoviral IAP repeat-containing protein 2; ring,	98.84
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	98.65
3nw0_A	238	Non-structural maintenance of chromosomes element	98.55
1wil_A	89	KIAA1045 protein; ring finger domain, structural g	96.92
2lri_C	66	Autoimmune regulator; Zn binding protein domain, a	96.83
2jun_A	101	Midline-1; B-BOX, TRIM, ring finger, alternative s	96.79
2ko5_A	99	Ring finger protein Z; lassa fever virus-Z, negati	96.03
2l5u_A	61	Chromodomain-helicase-DNA-binding protein 4; CHD4,	94.93
1we9_A	64	PHD finger family protein; structural genomics, PH	94.61
2k16_A	75	Transcription initiation factor TFIID subunit 3; p	93.89
1mm2_A	61	MI2-beta; PHD, zinc finger, protein scaffold, DNA	93.8
1fp0_A	88	KAP-1 corepressor; PHD domain, C3HC4 type zinc bin	93.79
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	93.76
3u5n_A	207	E3 ubiquitin-protein ligase TRIM33; TRIM33, PHD, b	93.68
1f62_A	51	Transcription factor WSTF; Zn-finger; NMR {Homo sa	93.43
2yql_A	56	PHD finger protein 21A; PHD domain, structural gen	93.42
2l2t_A	44	Receptor tyrosine-protein kinase ERBB-4; transmemb	93.33
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	93.09
3o36_A	184	Transcription intermediary factor 1-alpha; TRIM24,	93.08
3lqh_A	183	Histone-lysine N-methyltransferase MLL; PHD finger	92.96
3m62_A	968	Ubiquitin conjugation factor E4; armadillo-like re	92.89
2l43_A	88	N-teminal domain from histone H3.3, linker, PHD1 f	92.49
2puy_A	60	PHD finger protein 21A; PHD finger, histone CODE,	92.49
2ku3_A	71	Bromodomain-containing protein 1; PHD finger, chro	92.14
2e6r_A	92	Jumonji/ARID domain-containing protein 1D; PHD dom	91.66
1wep_A	79	PHF8; structural genomics, PHD domain, riken struc	91.23
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	91.14
2vpb_A	65	Hpygo1, pygopus homolog 1; gene regulation, WNT si	91.1
1xwh_A	66	Autoimmune regulator; PHD domain, Zn binding domai	90.99
2lv9_A	98	Histone-lysine N-methyltransferase MLL5; zinc fing	90.44
2klu_A	70	T-cell surface glycoprotein CD4; cell membrane, di	89.75
2ri7_A	174	Nucleosome-remodeling factor subunit BPTF; zinc fi	89.56
2lbm_A	142	Transcriptional regulator ATRX; metal binding prot	89.49
2ks1_B	44	Epidermal growth factor receptor; ERBB1, ERBB2, tr	89.17
4gne_A	107	Histone-lysine N-methyltransferase NSD3; zinc fing	88.83
1wen_A	71	Inhibitor of growth family, member 4; ING1-like pr	88.78
2xb1_A	105	Pygopus homolog 2, B-cell CLL/lymphoma 9-like Pro;	88.76
1wem_A	76	Death associated transcription factor 1; structura	88.26
2yt5_A	66	Metal-response element-binding transcription facto	87.65
3ql9_A	129	Transcriptional regulator ATRX; zinc finger, trans	87.55
2jwa_A	44	Receptor tyrosine-protein kinase ERBB-2; transmemb	87.34
3v43_A	112	Histone acetyltransferase KAT6A; MOZ, PHD finger,	87.03
2ro1_A	189	Transcription intermediary factor 1-beta; KAP, TIF	86.32
1weu_A	91	Inhibitor of growth family, member 4; structural g	85.85
3shb_A	77	E3 ubiquitin-protein ligase UHRF1; unmodified hist	85.49
1wee_A	72	PHD finger family protein; structural genomics, PH	85.36
2kgg_A	52	Histone demethylase jarid1A; PHD finger, histone m	85.34
2yw8_A	82	RUN and FYVE domain-containing protein 1; structur	85.15
2knc_A	54	Integrin alpha-IIB; transmembrane signaling, prote	85.09
2l8s_A	54	Integrin alpha-1; transmembrane region, detergent	85.0
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	84.83
1wfk_A	88	Zinc finger, FYVE domain containing 19; riken stru	84.52
1z2q_A	84	LM5-1; membrane protein, FYVE domain, zinc-finger;	84.34
1z60_A	59	TFIIH basal transcription factor complex P44 subun	84.21
1weo_A	93	Cellulose synthase, catalytic subunit (IRX3); stru	84.05
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	83.96
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	83.88
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	83.73
1wew_A	78	DNA-binding family protein; structural genomics, P	83.58
1joc_A	125	EEA1, early endosomal autoantigen 1; FYVE domain,	83.51
3o70_A	68	PHD finger protein 13; PHF13, structural genomics	82.96
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	82.88
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	82.65
1y02_A	120	CARP2, FYVE-ring finger protein sakura; zinc-bindi	82.62
3t7l_A	90	Zinc finger FYVE domain-containing protein 16; str	82.54
2co8_A	82	NEDD9 interacting protein with calponin homology a	82.45
1vfy_A	73	Phosphatidylinositol-3-phosphate binding FYVE doma	82.36
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	82.35
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	82.2
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	81.59
2vnf_A	60	ING 4, P29ING4, inhibitor of growth protein 4; ace	81.44
1wev_A	88	Riken cDNA 1110020M19; structural genomics, PHD do	81.43
1x4u_A	84	Zinc finger, FYVE domain containing 27 isoform B;	81.34
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	81.27
3asl_A	70	E3 ubiquitin-protein ligase UHRF1; histone reader	80.67

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

Probab=99.84  E-value=2.6e-21  Score=119.23  Aligned_cols=78  Identities=29%  Similarity=0.714  Sum_probs=67.5

Q ss_pred             hhcCCCCHHHHhhCCceeecCCCCCCCCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccC
Q 038049           49 RLNSGLKRKEMVALPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKP  128 (141)
Q Consensus        49 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~  128 (141)
                      ....+.+++.++.+|...+..... ..+++.+|+||+++|..++.++.+| |||.||..||..|+..+.+||+||+++..
T Consensus        12 ~~~~~~s~~~i~~lp~~~~~~~~~-~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~Fh~~Ci~~wl~~~~~CP~Cr~~~~~   89 (91)
T 2l0b_A           12 VANPPASKESIDALPEILVTEDHG-AVGQEMCCPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCRCMFPP   89 (91)
T ss_dssp             SCCCCCCHHHHHTSCEEECCTTCS-SSSSCSEETTTTEECCTTCEEEEET-TTEEEEHHHHHHHHTTTCBCTTTCCBSSC
T ss_pred             cCCCCCCHHHHHhCCCeeeccccc-ccCCCCCCcccChhhcCCCcEEecC-CCChHHHHHHHHHHHcCCcCcCcCccCCC
Confidence            446778999999999998876543 3455678999999999999899999 99999999999999999999999998865

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

Probab=99.81  E-value=4.9e-21  Score=113.89  Aligned_cols=70  Identities=37%  Similarity=0.870  Sum_probs=58.4

Q ss_pred             HHhhCCceeecCCCCCCCCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCC
Q 038049           58 EMVALPTVTYANSGSSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSD  130 (141)
Q Consensus        58 ~~~~~~~~~~~~~~~~~~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~  130 (141)
                      .++.+|..++....  ...++.+|+||++++..++.++.+| |||.||.+||..|+..+.+||+||+++....
T Consensus         5 ~i~~lp~~~~~~~~--~~~~~~~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~w~~~~~~CP~Cr~~~~~~~   74 (75)
T 1x4j_A            5 SSGQLPSYRFNPNN--HQSEQTLCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICRADSGPSS   74 (75)
T ss_dssp             CCSSCCCEEBCSSS--CSSSCCEETTTTEECCBTCEEEEET-TTEEEETTHHHHHHHHCSSCTTTCCCCCCCC
T ss_pred             hHhhCCcEEecCcc--ccCCCCCCeECCcccCCCCeEEEEC-CCCHhHHHHHHHHHHcCCcCcCcCCcCCCCC
Confidence            34567777776532  2345578999999999999999999 9999999999999999999999999987654

>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=99.78  E-value=2e-19  Score=105.15  Aligned_cols=57  Identities=35%  Similarity=0.934  Sum_probs=50.2

Q ss_pred             CCCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCC
Q 038049           74 PSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDA  131 (141)
Q Consensus        74 ~~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~  131 (141)
                      ....+.+|+||++.+..++.+..+| |||.||..||..|+..+.+||+||+.+.....
T Consensus        10 ~~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   66 (69)
T 2kiz_A           10 EEDTEEKCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDIEAQLP   66 (69)
T ss_dssp             STTCCCSBTTTTBCCCSSSCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCSBSCSCCC
T ss_pred             cCCCCCCCeeCCccccCCCcEEEeC-CCCHHHHHHHHHHHHcCCCCcCcCccccCcCC
Confidence            3455678999999998888889998 99999999999999999999999999876544

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

Probab=99.78  E-value=2.3e-19  Score=107.32  Aligned_cols=61  Identities=38%  Similarity=0.865  Sum_probs=53.4

Q ss_pred             CCCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCCCCCc
Q 038049           74 PSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPSL  135 (141)
Q Consensus        74 ~~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~~~~  135 (141)
                      ...++.+|+||++.|..++.+..++ |||.||..||..|+..+.+||+||+.+......++.
T Consensus        11 ~~~~~~~C~IC~~~~~~~~~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~   71 (78)
T 2ect_A           11 HVGSGLECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSLTGQNTATNP   71 (78)
T ss_dssp             TSSSSCCCTTTTSCCCTTSCEEECT-TSCEEETTTTHHHHTTTCSCTTTCCCCCCSCSCCCC
T ss_pred             cCCCCCCCeeCCccccCCCCEEEeC-CCCeecHHHHHHHHHcCCcCcCcCCccCCcccCCCC
Confidence            3455678999999999988888898 999999999999999999999999999877666543

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

Probab=99.77  E-value=1.5e-19  Score=101.11  Aligned_cols=51  Identities=49%  Similarity=1.152  Sum_probs=46.1

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      ++.+|+||++++.+++.+..++.|||.||.+||..|+.++.+||+||+++.
T Consensus         4 ~~~~C~IC~~~~~~~~~~~~~~~C~H~f~~~Ci~~w~~~~~~CP~Cr~~~~   54 (55)
T 1iym_A            4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCcCccCCccccCCCceEECCCCCCcccHHHHHHHHHcCCcCcCCCCEeE
Confidence            457899999999998888888779999999999999999999999999864

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

Probab=99.77  E-value=4.5e-19  Score=104.99  Aligned_cols=58  Identities=34%  Similarity=0.767  Sum_probs=50.7

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMP  133 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~~  133 (141)
                      ...+.+|+||++++..++.+..+| |||.||.+||..|+..+.+||+||+++.......
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~-C~H~f~~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~   69 (74)
T 2ep4_A           12 LNLHELCAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPVLQLAQLS   69 (74)
T ss_dssp             CCCSCBCSSSCCBCCSSSCEEEET-TTEEEEHHHHHHHHHHCSBCTTTCCBCSSCCSCC
T ss_pred             CCCCCCCcCCCcccCCCCcEEEcC-CCCEecHHHHHHHHHcCCcCCCcCcccccccccC
Confidence            344678999999999998888898 9999999999999999999999999997655443

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

Probab=99.73  E-value=1.3e-18  Score=104.84  Aligned_cols=53  Identities=32%  Similarity=0.809  Sum_probs=42.7

Q ss_pred             Cccccccccccccc-----------CCceeecCCCCCcccHhhHHHHHcCCCccccccccccCC
Q 038049           77 ASAGCAICLLDFID-----------GDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPS  129 (141)
Q Consensus        77 ~~~~C~ICl~~~~~-----------~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~  129 (141)
                      ++.+|+||+++|.+           ++.++.++.|||.||.+||+.|+.++.+||+||+++..+
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            44668888888854           344556656999999999999999999999999987643

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

Probab=99.71  E-value=4.9e-18  Score=99.58  Aligned_cols=57  Identities=26%  Similarity=0.612  Sum_probs=47.9

Q ss_pred             CCCcccccccccccccC----CceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCCC
Q 038049           75 SSASAGCAICLLDFIDG----DEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAM  132 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~----~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~  132 (141)
                      ..++.+|+||++.+.++    +.+..++ |||.||.+||..|+.++.+||+||+++..++..
T Consensus         7 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   67 (71)
T 3ng2_A            7 PSGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKRYH   67 (71)
T ss_dssp             CTTCCBCTTTCCBHHHHHTTTCCEEECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCCCSCC
T ss_pred             CCCCCCCcccChhhhccccccCCeEeCC-CCChHhHHHHHHHHHcCCCCCCCCCccChhhee
Confidence            34557899999999764    4456777 999999999999999999999999999876654

>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=99.70  E-value=7.3e-18  Score=94.11  Aligned_cols=51  Identities=35%  Similarity=0.757  Sum_probs=43.5

Q ss_pred             CCcccccccccccccCC-ceeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           76 SASAGCAICLLDFIDGD-EIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~-~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      .++.+|+||++++.+++ .+..++ |||.||.+||..|+..+.+||+||+++.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   54 (55)
T 2ecm_A            3 SGSSGCPICLEDIHTSRVVAHVLP-CGHLLHRTCYEEMLKEGYRCPLCSGPSS   54 (55)
T ss_dssp             SCCCSCTTTCCCCCTTTSCEEECT-TSCEEETTHHHHHHHHTCCCTTSCCSSC
T ss_pred             CCCCcCcccChhhcCCCcCeEecC-CCCcccHHHHHHHHHcCCcCCCCCCcCC
Confidence            34578999999996644 467777 9999999999999999999999999874

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

Probab=99.69  E-value=1.3e-17  Score=97.19  Aligned_cols=53  Identities=28%  Similarity=0.681  Sum_probs=44.9

Q ss_pred             CCCcccccccccccccC----CceeecCCCCCcccHhhHHHHHcCCCccccccccccC
Q 038049           75 SSASAGCAICLLDFIDG----DEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKP  128 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~----~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~  128 (141)
                      ..+..+|+||++.+.++    +.+..++ |||.||.+||..|+..+.+||+||+++..
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   68 (69)
T 2ea6_A           12 PSGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINH   68 (69)
T ss_dssp             TTCCCCCTTTCCCHHHHTTTTCCEEECS-SSCEEEHHHHHHHHHHCSSCTTTCCCCCC
T ss_pred             CCCCCCCcccCccccccccccCCeEeCC-CCChhcHHHHHHHHHcCCCCCCCCCccCc
Confidence            44567899999999764    3446777 99999999999999999999999998864

>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=99.69  E-value=2.5e-17  Score=105.11  Aligned_cols=53  Identities=25%  Similarity=0.583  Sum_probs=43.3

Q ss_pred             cccccccccccccCC---------------ceeecCCCCCcccHhhHHHHH-----cCCCccccccccccCCCC
Q 038049           78 SAGCAICLLDFIDGD---------------EIRLLPKCNHRFHVACIDKWL-----LSHSSCPTCRQRLKPSDA  131 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~---------------~v~~lp~C~H~Fh~~Ci~~wl-----~~~~~CP~CR~~~~~~~~  131 (141)
                      +.+|+||+++|..+.               .+..++ |||.||.+||..|+     ..+.+||+||+.+..+.+
T Consensus        25 ~~~C~ICl~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~Fh~~Ci~~wl~~~~~~~~~~CP~CR~~~~~~~g   97 (114)
T 1v87_A           25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTG   97 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCSS
T ss_pred             CCcCccCChhhcCcccccccccccccCcccceecCC-CCCcccHHHHHHHHHcccCCCCCcCCCCCCccCCCCC
Confidence            368999999997653               344677 99999999999999     456789999999976653

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

Probab=99.68  E-value=1.5e-17  Score=95.55  Aligned_cols=54  Identities=28%  Similarity=0.632  Sum_probs=45.7

Q ss_pred             CcccccccccccccC----CceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCC
Q 038049           77 ASAGCAICLLDFIDG----DEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDA  131 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~----~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~  131 (141)
                      ++.+|+||++.+.++    +.+..++ |||.||.+|+..|+.++.+||+||+++..++.
T Consensus         2 ~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~   59 (64)
T 2xeu_A            2 AMVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   59 (64)
T ss_dssp             CCCBCTTTCCBHHHHHHTTCCEEEET-TSCEEEHHHHHHHHHHCSBCTTTCCBCTTTCE
T ss_pred             CCCCCCccChhhhCccccCCCEEeCC-CCCchhHHHHHHHHHcCCCCCCCCccCCccce
Confidence            346899999999764    4456777 99999999999999999999999999887653

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

Probab=99.67  E-value=8.7e-17  Score=94.61  Aligned_cols=58  Identities=22%  Similarity=0.521  Sum_probs=47.9

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCCCCCc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPSL  135 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~~~~  135 (141)
                      ..++.+|+||++.+.++  +..++ |||.||..||..|+..+..||+||+++...+..++.
T Consensus        12 ~~~~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~~~~~~   69 (72)
T 2djb_A           12 LTPYILCSICKGYLIDA--TTITE-CLHTFCKSCIVRHFYYSNRCPKCNIVVHQTQPLSGP   69 (72)
T ss_dssp             CCGGGSCTTTSSCCSSC--EECSS-SCCEECHHHHHHHHHHCSSCTTTCCCCCSSCSCCCC
T ss_pred             cCCCCCCCCCChHHHCc--CEECC-CCCHHHHHHHHHHHHcCCcCCCcCcccCcccccccC
Confidence            45567899999998764  33346 999999999999999889999999999887766543

>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=99.66  E-value=5.6e-17  Score=102.17  Aligned_cols=50  Identities=32%  Similarity=0.709  Sum_probs=42.5

Q ss_pred             CcccccccccccccCC---------------ceeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           77 ASAGCAICLLDFIDGD---------------EIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~---------------~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      ++..|+||++.|...-               .+..++ |+|.||.+||..|+.++.+||+||+++.
T Consensus        36 ~~d~CaIC~~~~~~~c~~C~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~Cr~~~~  100 (106)
T 3dpl_R           36 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWE  100 (106)
T ss_dssp             CSCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCC
T ss_pred             CCCCCccCChhHhCcCchhhccccccCCccceEeecc-cCcEECHHHHHHHHHcCCcCcCCCCcce
Confidence            4577999999987541               356677 9999999999999999999999999864

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

Probab=99.64  E-value=6.7e-17  Score=94.53  Aligned_cols=53  Identities=36%  Similarity=0.845  Sum_probs=45.2

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAM  132 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~  132 (141)
                      ..++.+|+||++.+.+    ..+| |||.||..|+..|+.++.+||+||+++...+..
T Consensus        12 ~~~~~~C~IC~~~~~~----~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~~   64 (70)
T 2ecn_A           12 LTDEEECCICMDGRAD----LILP-CAHSFCQKCIDKWSDRHRNCPICRLQMTGANES   64 (70)
T ss_dssp             CCCCCCCSSSCCSCCS----EEET-TTEEECHHHHHHSSCCCSSCHHHHHCTTCCCCC
T ss_pred             CCCCCCCeeCCcCccC----cccC-CCCcccHHHHHHHHHCcCcCCCcCCcccCCCcc
Confidence            3445789999999866    5677 999999999999999999999999999866543

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

Probab=99.64  E-value=1.7e-16  Score=95.15  Aligned_cols=56  Identities=27%  Similarity=0.657  Sum_probs=45.9

Q ss_pred             CCCcccccccccccccCCceeecCCCC-----CcccHhhHHHHHcCC--CccccccccccCCCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCN-----HRFHVACIDKWLLSH--SSCPTCRQRLKPSDAM  132 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~-----H~Fh~~Ci~~wl~~~--~~CP~CR~~~~~~~~~  132 (141)
                      ..++..|.||++++.+++.+ ++| |+     |.||.+||+.|+..+  .+||+||..+..+...
T Consensus        12 ~~~~~~C~IC~~~~~~~~~l-~~p-C~C~Gs~h~fH~~Cl~~Wl~~~~~~~CplCr~~~~~~~~~   74 (80)
T 2d8s_A           12 PSSQDICRICHCEGDDESPL-ITP-CHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMETKL   74 (80)
T ss_dssp             CTTSCCCSSSCCCCCSSSCE-ECS-SSCCSSSCCEETTHHHHHHHHHCCSBCSSSCCBCCCCCCS
T ss_pred             CCCCCCCeEcCccccCCCee-Eec-cccCCcCCeeCHHHHHHHHhhCCCCCCCCCCCeeecCccc
Confidence            34557899999999877766 588 96     999999999999865  5899999999765543

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

Probab=99.64  E-value=9.7e-17  Score=94.16  Aligned_cols=51  Identities=31%  Similarity=0.623  Sum_probs=43.8

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPS  129 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~  129 (141)
                      ..++.+|+||++.+.+.   ..++ |||.||..||..|+..+..||+||+.+...
T Consensus        12 ~~~~~~C~IC~~~~~~~---~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   62 (71)
T 2d8t_A           12 SLTVPECAICLQTCVHP---VSLP-CKHVFCYLCVKGASWLGKRCALCRQEIPED   62 (71)
T ss_dssp             SSSCCBCSSSSSBCSSE---EEET-TTEEEEHHHHHHCTTCSSBCSSSCCBCCHH
T ss_pred             CCCCCCCccCCcccCCC---EEcc-CCCHHHHHHHHHHHHCCCcCcCcCchhCHh
Confidence            45567899999998654   5677 999999999999999999999999998644

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

Probab=99.61  E-value=1.8e-16  Score=92.19  Aligned_cols=49  Identities=33%  Similarity=0.830  Sum_probs=42.3

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKP  128 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~  128 (141)
                      .+.+|+||++.+.+  .+..+| |||.||.+|+..|+.++.+||+||+++..
T Consensus         4 ~~~~C~IC~~~~~~--~~~~~~-C~H~fc~~Ci~~~~~~~~~CP~Cr~~~~~   52 (68)
T 1chc_A            4 VAERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCCeeCCccccC--CcEecC-CCCeeHHHHHHHHHhCcCcCcCCChhhHh
Confidence            45789999999864  346787 99999999999999989999999998864

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

Probab=99.61  E-value=7e-16  Score=89.18  Aligned_cols=52  Identities=23%  Similarity=0.562  Sum_probs=43.1

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHc-CCCccccccccccCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL-SHSSCPTCRQRLKPSD  130 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~~~~~~  130 (141)
                      ..++.+|+||++.+.++   ..++ |||.||..||..|+. .+..||+||+++..++
T Consensus        12 ~~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~   64 (66)
T 2ecy_A           12 VEDKYKCEKCHLVLCSP---KQTE-CGHRFCESCMAALLSSSSPKCTACQESIVKDK   64 (66)
T ss_dssp             CCCCEECTTTCCEESSC---CCCS-SSCCCCHHHHHHHHTTSSCCCTTTCCCCCTTT
T ss_pred             CCcCCCCCCCChHhcCe---eECC-CCCHHHHHHHHHHHHhCcCCCCCCCcCCChhh
Confidence            34567899999999766   3467 999999999999994 5678999999987654

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

Probab=99.61  E-value=7.7e-16  Score=93.68  Aligned_cols=54  Identities=28%  Similarity=0.629  Sum_probs=45.6

Q ss_pred             CCCcccccccccccccCCc-eeecCCCCCcccHhhHHHHHcCC---CccccccccccCC
Q 038049           75 SSASAGCAICLLDFIDGDE-IRLLPKCNHRFHVACIDKWLLSH---SSCPTCRQRLKPS  129 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~-v~~lp~C~H~Fh~~Ci~~wl~~~---~~CP~CR~~~~~~  129 (141)
                      ..+..+|+||++.|.+.+. ...++ |||.||..|+..|+..+   ..||+||+++...
T Consensus        12 ~~~~~~C~IC~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~   69 (88)
T 2ct2_A           12 LREVLECPICMESFTEEQLRPKLLH-CGHTICRQCLEKLLASSINGVRCPFCSKITRIT   69 (88)
T ss_dssp             CCSCCBCTTTCCBCCTTSSCEEECS-SSCEEEHHHHHHHHHHCSSCBCCTTTCCCBCCS
T ss_pred             ccCCCCCccCCccccccCCCeEECC-CCChhhHHHHHHHHHcCCCCcCCCCCCCcccch
Confidence            4456789999999988664 56777 99999999999999875   7899999988654

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

Probab=99.60  E-value=1e-15  Score=90.47  Aligned_cols=53  Identities=30%  Similarity=0.590  Sum_probs=43.2

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC--CccccccccccCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH--SSCPTCRQRLKPSD  130 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~--~~CP~CR~~~~~~~  130 (141)
                      ..++.+|+||++.+.++   ..++.|||.||..||..|+..+  ..||+||+++...+
T Consensus        12 ~~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~~~~   66 (74)
T 2yur_A           12 IPDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPD   66 (74)
T ss_dssp             SCGGGSCSSSCCCCTTC---EECSSSCCEECTTHHHHHHHHSSSSCCSSSCCSSCCTT
T ss_pred             CCCCCCCcCCChHHhCC---eEcCCCCCHHHHHHHHHHHHhcCCCcCCCCCCcCCCcc
Confidence            45567899999999765   4565599999999999999865  68999999865444

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

Probab=99.59  E-value=7.6e-16  Score=92.52  Aligned_cols=49  Identities=22%  Similarity=0.464  Sum_probs=42.5

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      .....+|+||++.+.++   ..++ |||.||..||..|+.....||+||+++.
T Consensus        12 ~~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           12 EEIPFRCFICRQAFQNP---VVTK-CRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             CCCCSBCSSSCSBCCSE---EECT-TSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCCCCCcCCCchhcCe---eEcc-CCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            34457899999998664   4677 9999999999999998999999999986

>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=99.59  E-value=1.2e-16  Score=102.06  Aligned_cols=51  Identities=31%  Similarity=0.709  Sum_probs=0.9

Q ss_pred             CcccccccccccccC-------------C--ceeecCCCCCcccHhhHHHHHcCCCccccccccccC
Q 038049           77 ASAGCAICLLDFIDG-------------D--EIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKP  128 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~-------------~--~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~  128 (141)
                      +++.|+||+++|.+.             +  .+..++ |+|.||.+||..|+.++.+||+||+++..
T Consensus        47 ~~d~CaICl~~~~~~c~~C~~~~~~~~~~~~~v~~~~-C~H~FH~~CI~~Wl~~~~~CP~Cr~~~~~  112 (117)
T 4a0k_B           47 VVDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEF  112 (117)
T ss_dssp             CC-----------------------------------------------------------------
T ss_pred             CCCcCeECChhhcCcChhhhcccccccccccccccCC-cCceEcHHHHHHHHHcCCcCCCCCCeeee
Confidence            357899999999752             2  233345 99999999999999999999999998643

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

Probab=99.59  E-value=1.3e-15  Score=89.58  Aligned_cols=52  Identities=23%  Similarity=0.529  Sum_probs=42.8

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHc---CCCccccccccccCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL---SHSSCPTCRQRLKPSD  130 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~---~~~~CP~CR~~~~~~~  130 (141)
                      ..++.+|+||++.+.++   ..++ |||.||.+|+..|+.   .+..||+||+++..++
T Consensus        17 ~~~~~~C~IC~~~~~~~---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~   71 (73)
T 2ysl_A           17 LQEEVICPICLDILQKP---VTID-CGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNA   71 (73)
T ss_dssp             CCCCCBCTTTCSBCSSE---EECT-TCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCCCC
T ss_pred             CccCCEeccCCcccCCe---EEcC-CCChhhHHHHHHHHHcCCCCCCCCCCCCcCCccc
Confidence            44567899999998754   5567 999999999999996   4568999999987654

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

Probab=99.57  E-value=1.7e-15  Score=90.31  Aligned_cols=56  Identities=23%  Similarity=0.469  Sum_probs=46.5

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC-CCccccccccccCCCCCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPSDAMPS  134 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~~~~~~  134 (141)
                      ..++..|+||++.+.++   ..++ |||.||..||..|+.. +.+||+||+++...+..++
T Consensus         5 ~~~~~~C~IC~~~~~~P---v~~~-CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~~~l~~n   61 (78)
T 1t1h_A            5 FPEYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPN   61 (78)
T ss_dssp             CSSSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEEC
T ss_pred             CcccCCCCCccccccCC---EEcC-CCCeecHHHHHHHHHHCcCCCCCCcCCCChhhCccC
Confidence            34457899999999765   5567 9999999999999987 7889999999987665544

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

Probab=99.57  E-value=7.2e-16  Score=101.55  Aligned_cols=49  Identities=35%  Similarity=0.850  Sum_probs=42.6

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCC
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSD  130 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~  130 (141)
                      +.+|+||++.+.++   ..+| |||.||..||..|+..+.+||+||+++....
T Consensus        53 ~~~C~iC~~~~~~~---~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~  101 (138)
T 4ayc_A           53 ELQCIICSEYFIEA---VTLN-CAHSFCSYCINEWMKRKIECPICRKDIKSKT  101 (138)
T ss_dssp             HSBCTTTCSBCSSE---EEET-TSCEEEHHHHHHHTTTCSBCTTTCCBCCCEE
T ss_pred             cCCCcccCcccCCc---eECC-CCCCccHHHHHHHHHcCCcCCCCCCcCCCCC
Confidence            35799999998664   5677 9999999999999999999999999986543

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

Probab=99.56  E-value=3.5e-15  Score=90.01  Aligned_cols=55  Identities=31%  Similarity=0.555  Sum_probs=45.3

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC------CCccccccccccCCCCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS------HSSCPTCRQRLKPSDAMP  133 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~------~~~CP~CR~~~~~~~~~~  133 (141)
                      ..++.+|+||++.+.++   ..++ |||.||..|+..|+..      ...||.||+++..++..+
T Consensus        16 ~~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~   76 (85)
T 2ecw_A           16 IKEEVTCPICLELLKEP---VSAD-CNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLKP   76 (85)
T ss_dssp             CCTTTSCTTTCSCCSSC---EECT-TSCCBCHHHHHHHHHHSBCTTSCBCCTTTCCCCCTTCCEE
T ss_pred             CccCCCCcCCChhhCcc---eeCC-CCCHHHHHHHHHHHHhccCCCCCCCCCCCCCcCCHHhCCc
Confidence            34567899999998776   4677 9999999999999987      678999999988665433

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

Probab=99.55  E-value=4.2e-15  Score=89.68  Aligned_cols=56  Identities=32%  Similarity=0.647  Sum_probs=46.1

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC------CCccccccccccCCCCCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS------HSSCPTCRQRLKPSDAMPS  134 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~------~~~CP~CR~~~~~~~~~~~  134 (141)
                      ..+..+|+||++.+.++   ..++ |||.||..|+..|+..      ...||.||+.+...+..++
T Consensus        16 ~~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~~~~CP~Cr~~~~~~~~~~n   77 (85)
T 2ecv_A           16 VKEEVTCPICLELLTQP---LSLD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRPN   77 (85)
T ss_dssp             CCCCCCCTTTCSCCSSC---BCCS-SSCCBCTTHHHHHHHHHHHTTSCCCCTTTCCSSCSSSCCCS
T ss_pred             ccCCCCCCCCCcccCCc---eeCC-CCCHHHHHHHHHHHHHhhcCCCCCcCCCCCCccCHHhcCcc
Confidence            34567899999998765   4567 9999999999999987      7789999999987655444

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

Probab=99.55  E-value=8.1e-16  Score=91.81  Aligned_cols=55  Identities=27%  Similarity=0.463  Sum_probs=44.7

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC-------CCccccccccccCCCCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-------HSSCPTCRQRLKPSDAMP  133 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-------~~~CP~CR~~~~~~~~~~  133 (141)
                      ..++.+|+||++.+.++   ..++ |||.||.+||..|+..       ...||.||+++..++..+
T Consensus         9 ~~~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~   70 (79)
T 2egp_A            9 VQEEVTCPICLELLTEP---LSLD-CGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEHLQA   70 (79)
T ss_dssp             CCCCCEETTTTEECSSC---CCCS-SSCCCCHHHHSCCCCCCSSSCCCCCCCSSSCCCCCSSGGGT
T ss_pred             cccCCCCcCCCcccCCe---eECC-CCCHHHHHHHHHHHHhcccCCCCCCcCCCCCCcCCHhhCCc
Confidence            34567899999999775   4577 9999999999999986       567999999987654333

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

Probab=99.55  E-value=2.1e-15  Score=98.18  Aligned_cols=55  Identities=27%  Similarity=0.640  Sum_probs=46.5

Q ss_pred             CCcccccccccccccC----CceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCC
Q 038049           76 SASAGCAICLLDFIDG----DEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDA  131 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~----~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~  131 (141)
                      .++.+|+||++.+.++    +.+..++ |||.||.+||..|+..+.+||+||+.+..++.
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l   63 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKRY   63 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEET-TCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCE
T ss_pred             CCCCCCcccChhhhCccccccCeEecC-CCChhhHHHHHHHHHhCCCCCCCCCcCccccc
Confidence            3457899999999764    4456777 99999999999999999999999999876553

>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=99.54  E-value=1.1e-15  Score=95.45  Aligned_cols=52  Identities=27%  Similarity=0.654  Sum_probs=42.9

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC-CccccccccccCCCC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH-SSCPTCRQRLKPSDA  131 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~-~~CP~CR~~~~~~~~  131 (141)
                      ++.+|+||++.+.++  +..++ |||.||..||..|+..+ ..||+||+++...+.
T Consensus        21 ~~~~C~IC~~~~~~p--~~~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~~l   73 (100)
T 3lrq_A           21 EVFRCFICMEKLRDA--RLCPH-CSKLCCFSCIRRWLTEQRAQCPHCRAPLQLREL   73 (100)
T ss_dssp             HHTBCTTTCSBCSSE--EECTT-TCCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGC
T ss_pred             CCCCCccCCccccCc--cccCC-CCChhhHHHHHHHHHHCcCCCCCCCCcCCHHHh
Confidence            357799999999654  33377 99999999999999887 699999999876543

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

Probab=99.52  E-value=4.9e-15  Score=85.32  Aligned_cols=55  Identities=22%  Similarity=0.550  Sum_probs=43.5

Q ss_pred             ccccccccc-ccccCCce-eecCCCCCcccHhhHHHHHcC-CCccccccccccCCCCCC
Q 038049           78 SAGCAICLL-DFIDGDEI-RLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPSDAMP  133 (141)
Q Consensus        78 ~~~C~ICl~-~~~~~~~v-~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~~~~~  133 (141)
                      +.+|+||++ .+.++... ..++ |||.||..||..|+.+ +..||+||+++..++..+
T Consensus         3 ~~~C~IC~~~~~~~~~~~~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~   60 (65)
T 1g25_A            3 DQGCPRCKTTKYRNPSLKLMVNV-CGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRV   60 (65)
T ss_dssp             TTCCSTTTTHHHHCSSCCEEECT-TCCCEEHHHHHHHHHTTSSSCTTTCCCCSSCCCEE
T ss_pred             CCcCCcCCCCccCCCccCeecCC-CCCHhHHHHHHHHHHcCCCcCCCCCCcccccccee
Confidence            467999999 77766543 3466 9999999999999765 467999999998765443

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

Probab=99.52  E-value=2.9e-15  Score=93.25  Aligned_cols=55  Identities=27%  Similarity=0.596  Sum_probs=44.5

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCCCCC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPS  134 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~~~  134 (141)
                      ++.+|+||++.+.++  +..++ |||.||..||..|+..+..||+||+.+...+..++
T Consensus        21 ~~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~~l~~n   75 (99)
T 2y43_A           21 DLLRCGICFEYFNIA--MIIPQ-CSHNYCSLCIRKFLSYKTQCPTCCVTVTEPDLKNN   75 (99)
T ss_dssp             HHTBCTTTCSBCSSE--EECTT-TCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCEEC
T ss_pred             CCCCcccCChhhCCc--CEECC-CCCHhhHHHHHHHHHCCCCCCCCCCcCChhhCCcC
Confidence            346799999998764  33346 99999999999999999999999999886544443

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

Probab=99.51  E-value=2e-14  Score=82.20  Aligned_cols=44  Identities=27%  Similarity=0.572  Sum_probs=37.1

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHc---CCCccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL---SHSSCPTC  122 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~---~~~~CP~C  122 (141)
                      ..++.+|+||++.+.++   ..++ |||.||..||..|+.   .+..||+|
T Consensus        17 ~~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   63 (63)
T 2ysj_A           17 LQEEVICPICLDILQKP---VTID-CGHNFCLKCITQIGETSCGFFKCPLC   63 (63)
T ss_dssp             CCCCCBCTTTCSBCSSC---EECT-TSSEECHHHHHHHHHHCSSCCCCSCC
T ss_pred             CccCCCCCcCCchhCCe---EEeC-CCCcchHHHHHHHHHcCCCCCcCcCC
Confidence            44567899999998765   5667 999999999999998   45689998

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

Probab=99.51  E-value=2.4e-14  Score=84.15  Aligned_cols=52  Identities=29%  Similarity=0.688  Sum_probs=43.1

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC--CccccccccccCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH--SSCPTCRQRLKPS  129 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~--~~CP~CR~~~~~~  129 (141)
                      .+...+|+||.+.+.+++...   .|+|.||.+||..||+++  .+||+||+++..+
T Consensus        12 ~~~i~~C~IC~~~i~~g~~C~---~C~h~fH~~Ci~kWl~~~~~~~CP~Cr~~w~~~   65 (74)
T 2ct0_A           12 PDAVKICNICHSLLIQGQSCE---TCGIRMHLPCVAKYFQSNAEPRCPHCNDYWPHE   65 (74)
T ss_dssp             SSSSCBCSSSCCBCSSSEECS---SSCCEECHHHHHHHSTTCSSCCCTTTCSCCCSC
T ss_pred             cCCCCcCcchhhHcccCCccC---CCCchhhHHHHHHHHHhcCCCCCCCCcCcCCCC
Confidence            344578999999998765443   499999999999999987  7899999988644

>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=99.49  E-value=1.5e-14  Score=93.51  Aligned_cols=48  Identities=25%  Similarity=0.517  Sum_probs=41.3

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC-CccccccccccC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH-SSCPTCRQRLKP  128 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~-~~CP~CR~~~~~  128 (141)
                      ++..|+||++.+.++   ..+| |||.||..||..|+..+ ..||+||+++..
T Consensus        51 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   99 (124)
T 3fl2_A           51 ETFQCICCQELVFRP---ITTV-CQHNVCKDCLDRSFRAQVFSCPACRYDLGR   99 (124)
T ss_dssp             HHTBCTTTSSBCSSE---EECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCT
T ss_pred             cCCCCCcCChHHcCc---EEee-CCCcccHHHHHHHHhHCcCCCCCCCccCCC
Confidence            356799999999765   5667 99999999999999854 489999999987

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

Probab=99.49  E-value=2.5e-14  Score=80.34  Aligned_cols=44  Identities=32%  Similarity=0.854  Sum_probs=36.4

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHc---CCCccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL---SHSSCPTC  122 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~---~~~~CP~C  122 (141)
                      ..++.+|+||++.+.++   ..++ |||.||.+||..|+.   .+..||+|
T Consensus        12 ~~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~C   58 (58)
T 2ecj_A           12 LQVEASCSVCLEYLKEP---VIIE-CGHNFCKACITRWWEDLERDFPCPVC   58 (58)
T ss_dssp             SCCCCBCSSSCCBCSSC---CCCS-SCCCCCHHHHHHHTTSSCCSCCCSCC
T ss_pred             cccCCCCccCCcccCcc---EeCC-CCCccCHHHHHHHHHhcCCCCCCCCC
Confidence            34557899999999776   4577 999999999999954   56789998

>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=99.48  E-value=1.9e-14  Score=90.92  Aligned_cols=50  Identities=28%  Similarity=0.681  Sum_probs=42.7

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPS  129 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~  129 (141)
                      ++.+|+||++.+.++  +..++ |||.||..||..|+..+..||.||+.+...
T Consensus        14 ~~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~~   63 (108)
T 2ckl_A           14 PHLMCVLCGGYFIDA--TTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVHKT   63 (108)
T ss_dssp             GGTBCTTTSSBCSSE--EEETT-TCCEEEHHHHHHHHTSCSBCTTTCCBSCSS
T ss_pred             CcCCCccCChHHhCc--CEeCC-CCChhhHHHHHHHHHhCCcCcCCCcccccc
Confidence            457899999998654  44447 999999999999999999999999998765

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

Probab=99.48  E-value=3.9e-14  Score=86.88  Aligned_cols=50  Identities=30%  Similarity=0.593  Sum_probs=41.3

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC--CCcccccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS--HSSCPTCRQRLK  127 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~CR~~~~  127 (141)
                      ..++..|+||++.|.++   ..+|.|||.||..||..|+..  +..||+||+++.
T Consensus        10 ~~~~~~C~IC~~~~~~p---~~~~~CgH~fC~~Ci~~~~~~~~~~~CP~Cr~~~~   61 (92)
T 3ztg_A           10 IPDELLCLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDV   61 (92)
T ss_dssp             CCTTTEETTTTEECSSC---EECTTTCCEECHHHHHHHHHHCTTCCCTTTCCSSC
T ss_pred             CCcCCCCCCCChhhcCc---eECCCCCCHHHHHHHHHHHHhcCCCcCcCCCCcCC
Confidence            44567899999999866   456559999999999999964  368999999974

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

Probab=99.47  E-value=1.4e-14  Score=94.20  Aligned_cols=54  Identities=28%  Similarity=0.665  Sum_probs=45.5

Q ss_pred             CCcccccccccccccC----CceeecCCCCCcccHhhHHHHHcCCCccccccccccCCC
Q 038049           76 SASAGCAICLLDFIDG----DEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSD  130 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~----~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~  130 (141)
                      ++..+|+||++.+.+.    .....++ |||.||..||+.|+..+.+||+||+++..++
T Consensus        70 ~~~~~C~iC~~~~~~~~~~~~~~~~~~-CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~  127 (133)
T 4ap4_A           70 SGTVSCPICMDGYSEIVQNGRLIVSTE-CGHVFCSQCLRDSLKNANTCPTCRKKINHKR  127 (133)
T ss_dssp             SSSCBCTTTCCBHHHHHHTTCCEEEET-TSBEEEHHHHHHHHHHCSBCTTTCCBCCGGG
T ss_pred             CCCCCCCCCCCccccccccCcceEeCC-CCChhhHHHHHHHHHcCCCCCCCCCcCChhc
Confidence            4567899999998763    3345666 9999999999999999999999999987654

>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=99.45  E-value=3.9e-14  Score=89.79  Aligned_cols=52  Identities=25%  Similarity=0.517  Sum_probs=43.1

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcCCC---ccccccccccCCCCCC
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS---SCPTCRQRLKPSDAMP  133 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~---~CP~CR~~~~~~~~~~  133 (141)
                      ..+|+||++.+.++   ..++ |||.||..||..|+..+.   .||+||.++......+
T Consensus        21 ~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~~~~   75 (112)
T 1jm7_A           21 ILECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQE   75 (112)
T ss_dssp             HTSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBC
T ss_pred             CCCCcccChhhcCe---EECC-CCCHHHHHHHHHHHHhCCCCCCCcCCCCcCCHhhcCc
Confidence            46799999998765   4567 999999999999998654   8999999998765444

>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=99.45  E-value=1.4e-14  Score=92.57  Aligned_cols=54  Identities=33%  Similarity=0.563  Sum_probs=44.7

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcC-CCccccccccccCCCCCCC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPSDAMPS  134 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~~~~~~  134 (141)
                      ++..|+||++.+.++   ..++ |||.||..||..|+.. +.+||+||+++...+..+.
T Consensus        22 ~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~   76 (116)
T 1rmd_A           22 KSISCQICEHILADP---VETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLESP   76 (116)
T ss_dssp             HHTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCBCC
T ss_pred             CCCCCCCCCcHhcCc---EEcC-CCCcccHHHHHHHHhHCcCcCCCCCCCCCHhhcccc
Confidence            356799999998665   4577 9999999999999986 7789999999987664443

>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=99.44  E-value=2.7e-14  Score=91.58  Aligned_cols=57  Identities=32%  Similarity=0.654  Sum_probs=46.1

Q ss_pred             CCCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCC-ccccccccccCCCCCCC
Q 038049           74 PSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS-SCPTCRQRLKPSDAMPS  134 (141)
Q Consensus        74 ~~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~-~CP~CR~~~~~~~~~~~  134 (141)
                      ...++..|+||++.+.++   ..++ |||.||..||..|+..+. .||+||.++...+..++
T Consensus        14 ~~~~~~~C~IC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~   71 (118)
T 3hct_A           14 PLESKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPD   71 (118)
T ss_dssp             CCCGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGCEEC
T ss_pred             CCCCCCCCCcCChhhcCe---EECC-cCChhhHHHHHHHHhhCCCCCCCCCCCcCHHhcccC
Confidence            345567899999998765   5577 999999999999998764 99999999877554443

>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=99.42  E-value=8.8e-14  Score=92.76  Aligned_cols=49  Identities=24%  Similarity=0.499  Sum_probs=42.2

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCC-ccccccccccCC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS-SCPTCRQRLKPS  129 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~-~CP~CR~~~~~~  129 (141)
                      +...|+||++.+.++   ..+| |||.||..||..|+..+. .||+||.++...
T Consensus        77 ~~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  126 (150)
T 1z6u_A           77 QSFMCVCCQELVYQP---VTTE-CFHNVCKDCLQRSFKAQVFSCPACRHDLGQN  126 (150)
T ss_dssp             HHTBCTTTSSBCSSE---EECT-TSCEEEHHHHHHHHHTTCCBCTTTCCBCCTT
T ss_pred             cCCEeecCChhhcCC---EEcC-CCCchhHHHHHHHHHhCCCcCCCCCccCCCC
Confidence            346899999998765   4577 999999999999998764 899999999877

>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=99.41  E-value=1.1e-13  Score=93.51  Aligned_cols=51  Identities=35%  Similarity=0.675  Sum_probs=42.2

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC-CCccccccccccCC
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPS  129 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~  129 (141)
                      .+...|+||++.+.++  +..++ |||.||..||..|+.. +..||+||.++...
T Consensus        52 ~~~~~C~IC~~~~~~p--~~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~  103 (165)
T 2ckl_B           52 HSELMCPICLDMLKNT--MTTKE-CLHRFCADCIITALRSGNKECPTCRKKLVSK  103 (165)
T ss_dssp             HHHHBCTTTSSBCSSE--EEETT-TCCEEEHHHHHHHHHTTCCBCTTTCCBCCSG
T ss_pred             CCCCCCcccChHhhCc--CEeCC-CCChhHHHHHHHHHHhCcCCCCCCCCcCCCc
Confidence            3456899999998763  44457 9999999999999987 78899999998643

>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=99.40  E-value=3.9e-14  Score=90.36  Aligned_cols=50  Identities=30%  Similarity=0.720  Sum_probs=42.5

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC-CCccccccccccC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKP  128 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~  128 (141)
                      ..++.+|+||++.+.++   ..++ |||.||..||..|+.. +..||.||+.+..
T Consensus        12 ~~~~~~C~iC~~~~~~p---~~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (115)
T 3l11_A           12 SLSECQCGICMEILVEP---VTLP-CNHTLCKPCFQSTVEKASLCCPFCRRRVSS   62 (115)
T ss_dssp             CHHHHBCTTTCSBCSSC---EECT-TSCEECHHHHCCCCCTTTSBCTTTCCBCHH
T ss_pred             CCCCCCCccCCcccCce---eEcC-CCCHHhHHHHHHHHhHCcCCCCCCCcccCc
Confidence            45567899999998765   5667 9999999999999976 6789999998863

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

Probab=99.39  E-value=1.1e-13  Score=77.39  Aligned_cols=49  Identities=22%  Similarity=0.502  Sum_probs=40.9

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCC
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDA  131 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~  131 (141)
                      .++.+|+||++.+.++   ..+| |||.||..|+..|   ...||+||+.+..+..
T Consensus         4 ~~~~~C~IC~~~~~~p---~~l~-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~~   52 (56)
T 1bor_A            4 FQFLRCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGAD   52 (56)
T ss_dssp             CCCSSCSSSCSSCBCC---SCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCSS
T ss_pred             ccCCCceEeCCccCCe---EEcC-CCCcccHHHHccC---CCCCCcCCcEeecCCc
Confidence            4457799999999876   6788 9999999999884   6789999999876543

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

Probab=99.38  E-value=6e-13  Score=79.22  Aligned_cols=55  Identities=16%  Similarity=0.379  Sum_probs=42.2

Q ss_pred             CCCcccccccccccccCCce-eecCCCCCcccHhhHHHHHcC-CCccccccccccCCC
Q 038049           75 SSASAGCAICLLDFIDGDEI-RLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPSD  130 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v-~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~~  130 (141)
                      ..++.+|+||++.+...+.. .-++ |||.||..|+..++.. +..||.||+++....
T Consensus         8 ~~~~~~CpICle~~~~~d~~~~p~~-CGH~fC~~Cl~~~~~~~~~~CP~CR~~~~~~~   64 (78)
T 1e4u_A            8 KEDPVECPLCMEPLEIDDINFFPCT-CGYQICRFCWHRIRTDENGLCPACRKPYPEDP   64 (78)
T ss_dssp             CCCCCBCTTTCCBCCTTTTTCCSST-TSCCCCHHHHHHHTTSSCSBCTTTCCBCSSCS
T ss_pred             cccCCcCCccCccCccccccccccC-CCCCcCHHHHHHHHhcCCCCCCCCCCccCCCc
Confidence            34567899999988644332 2245 9999999999999753 578999999997654

>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=99.38  E-value=1.3e-13  Score=79.18  Aligned_cols=50  Identities=26%  Similarity=0.430  Sum_probs=40.4

Q ss_pred             CCCcccccccccccccCCcee-ecCCCCCc-ccHhhHHHHHcCCCcccccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIR-LLPKCNHR-FHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~-~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      ..++.+|+||++...+.  +. .+| |||. |+.+|+..|...+..||+||+++.
T Consensus         5 ~~~~~~C~IC~~~~~~~--~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~   56 (64)
T 2vje_A            5 LNAIEPCVICQGRPKNG--CIVHGK-TGHLMACFTCAKKLKKRNKPCPVCRQPIQ   56 (64)
T ss_dssp             CGGGSCCTTTSSSCSCE--EEEETT-EEEEEECHHHHHHHHHTTCCCTTTCCCCC
T ss_pred             CCCcCCCCcCCCCCCCE--EEECCC-CCChhhHHHHHHHHHHcCCcCCCcCcchh
Confidence            34567899999886443  22 238 9999 899999999998899999999875

>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=99.38  E-value=1.9e-13  Score=85.23  Aligned_cols=57  Identities=21%  Similarity=0.135  Sum_probs=49.5

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCCCCCch
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPSLD  136 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~~~~~  136 (141)
                      .++-.|+||++.|.++   ..++ |||.|+..||..|+..+.+||.||.++...+..|+..
T Consensus        27 p~~~~CpI~~~~m~dP---V~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~L~pn~~   83 (100)
T 2kre_A           27 PDEFRDPLMDTLMTDP---VRLP-SGTIMDRSIILRHLLNSPTDPFNRQTLTESMLEPVPE   83 (100)
T ss_dssp             STTTBCTTTCSBCSSE---EEET-TTEEEEHHHHHHHTTSCSBCSSSCCBCCTTSSEECHH
T ss_pred             cHhhCCcCccCcccCC---eECC-CCCEEchHHHHHHHHcCCCCCCCCCCCChhhceECHH
Confidence            4457899999999887   6777 9999999999999998899999999998877777643

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

Probab=99.37  E-value=2.5e-13  Score=82.22  Aligned_cols=57  Identities=21%  Similarity=0.128  Sum_probs=49.0

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCCCCCch
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPSLD  136 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~~~~~  136 (141)
                      .++-.|+||++.|.++   ..++ |||.|+..||..|+..+.+||.||.++...+..++..
T Consensus        12 p~~~~CpI~~~~m~dP---V~~~-cGhtf~r~~I~~~l~~~~~cP~~~~~l~~~~l~pn~~   68 (85)
T 2kr4_A           12 PDEFRDPLMDTLMTDP---VRLP-SGTVMDRSIILRHLLNSPTDPFNRQMLTESMLEPVPE   68 (85)
T ss_dssp             CTTTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHCSBCTTTCCBCCGGGCEECHH
T ss_pred             chheECcccCchhcCC---eECC-CCCEECHHHHHHHHhcCCCCCCCcCCCChHhcchHHH
Confidence            3457899999999887   6787 9999999999999998899999999998777666643

>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=99.37  E-value=1.7e-13  Score=78.38  Aligned_cols=51  Identities=22%  Similarity=0.442  Sum_probs=40.5

Q ss_pred             CCCcccccccccccccCCceeecCCCCCc-ccHhhHHHHHcCCCcccccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHR-FHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      .+.+.+|.||++...+. .+..+| |||. |+.+|+..|...+..||+||+++.
T Consensus         4 ~~~~~~C~IC~~~~~~~-~~~~~p-CgH~~~C~~C~~~~~~~~~~CPiCR~~i~   55 (63)
T 2vje_B            4 QNLLKPCSLCEKRPRDG-NIIHGR-TGHLVTCFHCARRLKKAGASCPICKKEIQ   55 (63)
T ss_dssp             GGGGSBCTTTSSSBSCE-EEEETT-EEEEEECHHHHHHHHHTTCBCTTTCCBCC
T ss_pred             CCcCCCCcccCCcCCCe-EEEecC-CCCHhHHHHHHHHHHHhCCcCCCcCchhh
Confidence            44567899999875443 122348 9998 999999999988889999999875

>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme, KIAA0126, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.44.1.2

Probab=99.35  E-value=6.8e-13  Score=82.34  Aligned_cols=57  Identities=21%  Similarity=0.188  Sum_probs=49.2

Q ss_pred             CCcccccccccccccCCceeecCCCC-CcccHhhHHHHHcCCCccccccccccCCCCCCCch
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCN-HRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPSLD  136 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~-H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~~~~~  136 (141)
                      .++-.|+||++.|.++   ..++ || |.|+..||..|+..+.+||.||.++...+..|+..
T Consensus        20 p~~~~CpI~~~~m~dP---V~~~-cG~htf~r~cI~~~l~~~~~cP~~~~~l~~~~L~pn~~   77 (98)
T 1wgm_A           20 CDEFLDPIMSTLMCDP---VVLP-SSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRPNTE   77 (98)
T ss_dssp             CTTTBCTTTCSBCSSE---EECT-TTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEECHH
T ss_pred             cHhcCCcCccccccCC---eECC-CCCeEECHHHHHHHHHhCCCCCCCCCCCChhhceEcHH
Confidence            3457899999999877   5677 99 99999999999998889999999998877777643

>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=99.33  E-value=2.8e-13  Score=86.66  Aligned_cols=51  Identities=22%  Similarity=0.428  Sum_probs=42.7

Q ss_pred             cccccccccccccCCceeec-CCCCCcccHhhHHHHHcCCCccccccccccCCCCCCC
Q 038049           78 SAGCAICLLDFIDGDEIRLL-PKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPS  134 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~l-p~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~~~  134 (141)
                      +..|+||++.+.++   ..+ + |||.||..||..|+.  ..||+||.++...+..++
T Consensus        22 ~~~C~IC~~~~~~p---v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~~~~n   73 (117)
T 1jm7_B           22 LLRCSRCTNILREP---VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLKIN   73 (117)
T ss_dssp             TTSCSSSCSCCSSC---BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCCCC
T ss_pred             CCCCCCCChHhhCc---cEeCC-CCCHHHHHHHHHHhc--CCCcCCCCcCcccccccc
Confidence            47799999999766   455 6 999999999999987  889999999976655554

>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=99.31  E-value=7.1e-13  Score=99.90  Aligned_cols=49  Identities=29%  Similarity=0.700  Sum_probs=41.9

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHc-CCCccccccccccCCC
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL-SHSSCPTCRQRLKPSD  130 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~~~~~~  130 (141)
                      ..+|+||++.+.+.   ..+| |||.||..|+..|+. .+.+||+||+++....
T Consensus       332 ~~~C~ICle~~~~p---v~lp-CGH~FC~~Ci~~wl~~~~~~CP~CR~~i~~~~  381 (389)
T 2y1n_A          332 FQLCKICAENDKDV---KIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTE  381 (389)
T ss_dssp             SSBCTTTSSSBCCE---EEET-TCCEECHHHHHHHHHHTCSBCTTTCCBCCEEE
T ss_pred             CCCCCccCcCCCCe---EEeC-CCChhhHHHHHHHHhcCCCCCCCCCCccCCce
Confidence            36899999997553   6788 999999999999998 6889999999887543

>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=99.31  E-value=5.8e-13  Score=87.90  Aligned_cols=51  Identities=22%  Similarity=0.354  Sum_probs=42.1

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC-CccccccccccCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH-SSCPTCRQRLKPS  129 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~-~~CP~CR~~~~~~  129 (141)
                      ..++.+|+||++.+.++   ..++ |||.||..||..|+..+ ..||+||.++..+
T Consensus        28 l~~~~~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~~~~~~   79 (141)
T 3knv_A           28 LEAKYLCSACRNVLRRP---FQAQ-CGHRYCSFCLASILSSGPQNCAACVHEGIYE   79 (141)
T ss_dssp             CCGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHGGGSCEECHHHHHTTCCC
T ss_pred             CCcCcCCCCCChhhcCc---EECC-CCCccCHHHHHHHHhcCCCCCCCCCCccccc
Confidence            44567899999999776   4577 99999999999999865 4899999986533

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

Probab=99.24  E-value=1.2e-12  Score=77.18  Aligned_cols=44  Identities=25%  Similarity=0.551  Sum_probs=37.3

Q ss_pred             CcccccccccccccCCceeecCCCCCc-ccHhhHHHHHcCCCccccccccccC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHR-FHVACIDKWLLSHSSCPTCRQRLKP  128 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~~~~  128 (141)
                      ++.+|+||++.+.+.   ..+| |||. ||..|+..|    ..||+||+++..
T Consensus        23 ~~~~C~iC~~~~~~~---~~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~   67 (74)
T 4ic3_A           23 EEKLCKICMDRNIAI---VFVP-CGHLVTCKQCAEAV----DKCPMCYTVITF   67 (74)
T ss_dssp             HHTBCTTTSSSBCCE---EEET-TCCBCCCHHHHTTC----SBCTTTCCBCSE
T ss_pred             cCCCCCCCCCCCCCE---EEcC-CCChhHHHHhhhcC----ccCCCcCcCccC
Confidence            346799999987554   6678 9999 999999998    899999998864

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

Probab=99.24  E-value=1.6e-12  Score=96.04  Aligned_cols=55  Identities=29%  Similarity=0.760  Sum_probs=42.2

Q ss_pred             CCCcccccccccccccCCcee----ecCCCCCcccHhhHHHHHcCC-----------CccccccccccCC
Q 038049           75 SSASAGCAICLLDFIDGDEIR----LLPKCNHRFHVACIDKWLLSH-----------SSCPTCRQRLKPS  129 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~----~lp~C~H~Fh~~Ci~~wl~~~-----------~~CP~CR~~~~~~  129 (141)
                      .+...+|+||++.+.++..+.    ..+.|||.||..|+.+|+++.           .+||+||+++..+
T Consensus       305 ee~~~ECaICys~~l~~g~lPdk~C~n~~C~h~FH~~CL~kWLrs~~~sRqSFnvi~G~CPyCr~pIs~s  374 (381)
T 3k1l_B          305 DNEELRCNICFAYRLDGGEVPLVSCDNAKCVLKCHAVCLEEWFKTLMDGKTFLEVSFGQCPFCKAKLSTS  374 (381)
T ss_dssp             CCSCCSCSSSCCSSCTTCCCCCBCCSCTTCCCCBCSGGGHHHHHHHHSSSCTTTCCEEECTTTCCEEEGG
T ss_pred             ccCCccCcccceeecCCCCCccccccCCccCCccchHHHHHHHHhCCCccccccccCCCCCCCCCcCCcc
Confidence            456788999999998743332    122499999999999999752           3599999998754

>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=99.22  E-value=1.9e-12  Score=87.80  Aligned_cols=56  Identities=30%  Similarity=0.617  Sum_probs=45.7

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC-CccccccccccCCCCCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH-SSCPTCRQRLKPSDAMPS  134 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~-~~CP~CR~~~~~~~~~~~  134 (141)
                      ..++..|+||++.+.++   ..++ |||.||..||..|+..+ ..||+||.++...+..++
T Consensus        15 ~~~~~~C~IC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~~~~~~~   71 (170)
T 3hcs_A           15 LESKYECPICLMALREA---VQTP-CGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPD   71 (170)
T ss_dssp             CCGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHHCSBCTTTCCBCCGGGCEEC
T ss_pred             CCCCCCCCCCChhhcCc---EECC-CCCHHHHHHHHHHHHhCCCCCCCCccCcchhhhhhh
Confidence            45567899999998766   4577 99999999999999764 499999999887654443

>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=99.19  E-value=3.7e-12  Score=78.45  Aligned_cols=57  Identities=21%  Similarity=0.415  Sum_probs=44.3

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC------Ccccc--cccc-ccCCCCCCCc
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH------SSCPT--CRQR-LKPSDAMPSL  135 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~------~~CP~--CR~~-~~~~~~~~~~  135 (141)
                      ..+..|+||++.|.++   ..++.|||.|+..||..|+..+      .+||+  |++. +...+..++.
T Consensus         5 ~~~~~CPI~~~~~~dP---V~~~~cGh~f~r~cI~~~l~~~~~~~~~~~CP~tgc~~~~l~~~~L~pn~   70 (94)
T 2yu4_A            5 SSGFTCPITKEEMKKP---VKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSDLIQDE   70 (94)
T ss_dssp             SSCCBCTTTCSBCSSE---EEESSSCCEEEHHHHHHHHHHHHTTTCCBCCCSTTCCCCCBCGGGEEECH
T ss_pred             CcEeECcCcCchhcCC---EEcCCCCCeecHHHHHHHHHHccCcCCCCCCCcCcCcccccCHhhCcCCH
Confidence            3457799999999765   4453499999999999999753      48999  9877 7666665553

>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=99.15  E-value=1.3e-11  Score=89.32  Aligned_cols=57  Identities=16%  Similarity=0.167  Sum_probs=47.5

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC-CCccccccccccCCCCCCCc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPSDAMPSL  135 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~~~~~~~  135 (141)
                      ....-.|+||++.|.++   .++| |||.|+..||..|+.. +.+||+||.++...+..|+.
T Consensus       205 ~~~~~~c~i~~~~~~dP---v~~~-~gh~f~~~~i~~~~~~~~~~cP~~~~~~~~~~l~~n~  262 (281)
T 2c2l_A          205 IPDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNL  262 (281)
T ss_dssp             CCSTTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEECH
T ss_pred             CCcccCCcCcCCHhcCC---eECC-CCCEECHHHHHHHHHHCCCCCcCCCCCCchhcCcccH
Confidence            34567899999999877   6787 9999999999999986 45599999999877776663

>2ea5_A Cell growth regulator with ring finger domain protein 1; CGRRF1, ring domain, zinc-binding domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.15  E-value=3.1e-11  Score=69.89  Aligned_cols=47  Identities=32%  Similarity=0.759  Sum_probs=38.2

Q ss_pred             CCCcccccccccccccCCceeecCCCCCc-ccHhhHHHHHcCCCccccccccccCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHR-FHVACIDKWLLSHSSCPTCRQRLKPS  129 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~~~~~  129 (141)
                      ..++..|.||++...+   +..+| |||. |+..|+..    ...||+||+.+...
T Consensus        12 ~~~~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~----~~~CP~CR~~i~~~   59 (68)
T 2ea5_A           12 EENSKDCVVCQNGTVN---WVLLP-CRHTCLCDGCVKY----FQQCPMCRQFVQES   59 (68)
T ss_dssp             CCCSSCCSSSSSSCCC---CEETT-TTBCCSCTTHHHH----CSSCTTTCCCCCCE
T ss_pred             CCCCCCCCCcCcCCCC---EEEEC-CCChhhhHHHHhc----CCCCCCCCcchhce
Confidence            4456789999987544   47888 9999 99999984    47899999988654

>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=99.13  E-value=2.8e-11  Score=74.40  Aligned_cols=48  Identities=25%  Similarity=0.688  Sum_probs=40.2

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcC--------CCcccc--cccc
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS--------HSSCPT--CRQR  125 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~--------~~~CP~--CR~~  125 (141)
                      +..+|+||++++..++.+...+ |||.||.+|+..|+..        ...||.  |+..
T Consensus         4 ~~~~C~IC~~~~~~~~~~~l~~-CgH~FC~~Cl~~~~~~~i~~g~~~~i~CP~~~C~~~   61 (94)
T 1wim_A            4 GSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACPKQ   61 (94)
T ss_dssp             SBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTCSSC
T ss_pred             CCcCCcccCcccccccceEcCC-CCCcccHHHHHHHHHHHhhcCCcccccCccccCCCC
Confidence            4568999999998777676677 9999999999999863        236999  9987

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

Probab=99.12  E-value=4.6e-11  Score=67.44  Aligned_cols=49  Identities=24%  Similarity=0.658  Sum_probs=37.7

Q ss_pred             CCcccccccccccccCCceeecCCCC--C---cccHhhHHHHHcC--CCccccccccccC
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCN--H---RFHVACIDKWLLS--HSSCPTCRQRLKP  128 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~--H---~Fh~~Ci~~wl~~--~~~CP~CR~~~~~  128 (141)
                      ++...|.||+++.  ++.+ ++| |.  |   .||.+|+..|+..  +.+||+||..+..
T Consensus         4 ~~~~~CrIC~~~~--~~~l-~~P-C~C~gs~~~~H~~Cl~~W~~~~~~~~C~~C~~~~~~   59 (60)
T 1vyx_A            4 EDVPVCWICNEEL--GNER-FRA-CGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             CSCCEETTTTEEC--SCCC-CCS-CCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCEeEEeecCC--CCce-ecC-cCCCCchhhhHHHHHHHHHHhCCCCccCCCCCeeec
Confidence            4457899999883  3333 577 65  4   8999999999964  6789999998754

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

Probab=99.12  E-value=1.8e-11  Score=72.18  Aligned_cols=44  Identities=25%  Similarity=0.556  Sum_probs=36.4

Q ss_pred             cccccccccccccCCceeecCCCCCc-ccHhhHHHHHcCCCccccccccccCC
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHR-FHVACIDKWLLSHSSCPTCRQRLKPS  129 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~~~~~  129 (141)
                      +.+|+||++.+.+.   ..+| |||. ||..|+..    ...||+||+++...
T Consensus        25 ~~~C~IC~~~~~~~---~~~p-CgH~~~C~~C~~~----~~~CP~Cr~~i~~~   69 (75)
T 2ecg_A           25 EKLCKICMDRNIAI---VFVP-CGHLVTCKQCAEA----VDKCPMCYTVITFK   69 (75)
T ss_dssp             HHSCSSSCSSCCCB---CCSS-SCCCCBCHHHHHH----CSBCTTTCCBCCCC
T ss_pred             CCCCCcCCCCCCCE---EEec-CCCHHHHHHHhhC----CCCCccCCceecCc
Confidence            46799999987554   5678 9999 99999964    47899999998754

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

Probab=99.08  E-value=4.4e-11  Score=81.55  Aligned_cols=58  Identities=16%  Similarity=0.157  Sum_probs=48.2

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC-CCccccccccccCCCCCCCch
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPSDAMPSLD  136 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~~~~~~~~  136 (141)
                      ..+.-.|+||++.|.++   .++| |||.|+..||..|+.. +.+||.||.++...+..|+..
T Consensus       103 ip~~f~CPI~~elm~DP---V~~~-~Ghtfer~~I~~~l~~~~~tcP~t~~~l~~~~L~pN~~  161 (179)
T 2f42_A          103 IPDYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPNLA  161 (179)
T ss_dssp             CCGGGBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCEECHH
T ss_pred             CcHhhcccCccccCCCC---eECC-CCCEECHHHHHHHHHhCCCCCCCCcCCCChhhCcchHH
Confidence            34567899999999876   5677 9999999999999976 457999999998877777643

>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=99.02  E-value=4.6e-11  Score=71.18  Aligned_cols=44  Identities=30%  Similarity=0.740  Sum_probs=36.3

Q ss_pred             cccccccccccccCCceeecCCCCCc-ccHhhHHHHHcCCCccccccccccCC
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHR-FHVACIDKWLLSHSSCPTCRQRLKPS  129 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~~~~~  129 (141)
                      +..|+||++.+.+   ...+| |||. |+..|+..|    ..||+||+++...
T Consensus        18 ~~~C~IC~~~~~~---~v~~p-CgH~~~C~~C~~~~----~~CP~Cr~~i~~~   62 (79)
T 2yho_A           18 AMLCMVCCEEEIN---STFCP-CGHTVCCESCAAQL----QSCPVCRSRVEHV   62 (79)
T ss_dssp             HTBCTTTSSSBCC---EEEET-TCBCCBCHHHHTTC----SBCTTTCCBCCEE
T ss_pred             CCEeEEeCcccCc---EEEEC-CCCHHHHHHHHHhc----CcCCCCCchhhCe
Confidence            4679999988644   46788 9999 999999987    4999999988643

>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=98.87  E-value=5e-10  Score=80.09  Aligned_cols=56  Identities=23%  Similarity=0.425  Sum_probs=44.7

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC--Ccccc--ccccccCCCCCCC
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH--SSCPT--CRQRLKPSDAMPS  134 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~--~~CP~--CR~~~~~~~~~~~  134 (141)
                      ..+..|+||++.|.++  |+.+. |||.|+..||..|+..+  ..||+  ||+.+...+..++
T Consensus       179 ~~el~CPIcl~~f~DP--Vts~~-CGHsFcR~cI~~~~~~~~~~~CPvtGCr~~l~~~dL~pN  238 (267)
T 3htk_C          179 KIELTCPITCKPYEAP--LISRK-CNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFVRD  238 (267)
T ss_dssp             BCCSBCTTTSSBCSSE--EEESS-SCCEEEHHHHHHHSTTCSCEECSGGGCSCEECGGGEEEC
T ss_pred             ceeeECcCccCcccCC--eeeCC-CCCcccHHHHHHHHHhCCCCCCCcccccCcCchhhCCcC
Confidence            3456899999999665  44455 99999999999999764  46999  9998877666555

>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=98.86  E-value=3.3e-10  Score=64.12  Aligned_cols=51  Identities=14%  Similarity=0.127  Sum_probs=43.3

Q ss_pred             ccccccccccccCCceeec-CCCCCcccHhhHHHHHcCCCccccccccccCCCCCC
Q 038049           79 AGCAICLLDFIDGDEIRLL-PKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMP  133 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~l-p~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~~  133 (141)
                      -.|+|+++.+.++   ..+ + +||+|...||.+|+.++.+||+.+.++...+..+
T Consensus         4 ~~CpIs~~~m~dP---V~~~~-sG~~yer~~I~~~l~~~~~cP~t~~~L~~~~Lip   55 (61)
T 2bay_A            4 MLCAISGKVPRRP---VLSPK-SRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVE   55 (61)
T ss_dssp             CCCTTTCSCCSSE---EEETT-TTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCEE
T ss_pred             EEecCCCCCCCCC---EEeCC-CCcEEcHHHHHHHHHhCCCCcCCcCCCChhhcEE
Confidence            4699999999865   455 5 9999999999999998888999999998766544

>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=98.84  E-value=4.6e-10  Score=83.85  Aligned_cols=45  Identities=24%  Similarity=0.665  Sum_probs=37.7

Q ss_pred             CcccccccccccccCCceeecCCCCCc-ccHhhHHHHHcCCCccccccccccCC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHR-FHVACIDKWLLSHSSCPTCRQRLKPS  129 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~-Fh~~Ci~~wl~~~~~CP~CR~~~~~~  129 (141)
                      ++..|+||++.+.+.   ..+| |||. ||..|+..|    ..||+||+++...
T Consensus       294 ~~~~C~IC~~~~~~~---v~lp-CgH~~fC~~C~~~~----~~CP~CR~~i~~~  339 (345)
T 3t6p_A          294 EERTCKVCMDKEVSV---VFIP-CGHLVVCQECAPSL----RKCPICRGIIKGT  339 (345)
T ss_dssp             TTCBCTTTSSSBCCE---EEET-TCCEEECTTTGGGC----SBCTTTCCBCCEE
T ss_pred             CCCCCCccCCcCCce---EEcC-CCChhHhHHHHhcC----CcCCCCCCCccCe
Confidence            356899999987554   6678 9999 999999988    7899999988643

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

Probab=98.65  E-value=1.9e-08  Score=61.42  Aligned_cols=47  Identities=26%  Similarity=0.498  Sum_probs=37.5

Q ss_pred             cccccccccccCCceeecCCCCCcccHhhHHHHHc-CCCccccccccccCC
Q 038049           80 GCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL-SHSSCPTCRQRLKPS  129 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~~~~~  129 (141)
                      .|.+|--++.  ...|+.| |+|+|+.+|+..|.+ +.++||.||.++..-
T Consensus         3 fC~~C~~Pi~--iygRmIP-CkHvFCydCa~~~~~~~~k~Cp~C~~~V~rV   50 (101)
T 3vk6_A            3 FCDKCGLPIK--VYGRMIP-CKHVFCYDCAILHEKKGDKMCPGCSDPVQRI   50 (101)
T ss_dssp             BCTTTCSBCS--EEEEEET-TCCEEEHHHHHHHHHTTCCBCTTTCCBCSEE
T ss_pred             ecCccCCCeE--EEeeecc-ccccHHHHHHHHHHhccCCCCcCcCCeeeee
Confidence            4777766653  3458898 999999999999985 468899999988643

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

Probab=98.55  E-value=9.3e-08  Score=68.00  Aligned_cols=50  Identities=30%  Similarity=0.690  Sum_probs=40.5

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCC--ccccccccccCC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS--SCPTCRQRLKPS  129 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~--~CP~CR~~~~~~  129 (141)
                      ...+|.||.+-...+.   ..+.|+|.||..|+..|++++.  .||.|+.+....
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            4678999999887662   3334999999999999998754  899999987654

>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=96.92  E-value=0.0023  Score=37.67  Aligned_cols=38  Identities=18%  Similarity=0.473  Sum_probs=26.1

Q ss_pred             CCCCCcccccccccccccCCceeecCCCCCcccHhhHHHH
Q 038049           73 SPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKW  112 (141)
Q Consensus        73 ~~~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~w  112 (141)
                      ++...+..|.||- .+..++...-- .|+-+||..|+..-
T Consensus        10 e~~~~D~~C~VC~-~~t~~~l~pCR-vC~RvfH~~CL~r~   47 (89)
T 1wil_A           10 EPVVNDEMCDVCE-VWTAESLFPCR-VCTRVFHDGCLRRM   47 (89)
T ss_dssp             CCCCCSCCCTTTC-CCCSSCCSSCS-SSSSCCCHHHHHHH
T ss_pred             cCCCCCcccCccc-cccccceeccc-cccccccHhhcccc
Confidence            3445678899994 44444333222 39999999999985

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

Probab=96.83  E-value=0.0014  Score=37.06  Aligned_cols=48  Identities=23%  Similarity=0.434  Sum_probs=33.9

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCC----ccccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS----SCPTCRQRL  126 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~----~CP~CR~~~  126 (141)
                      ......|.||.+.   ++ +..-..|...||..|++..+....    .||.|.+..
T Consensus         9 ~~~~~~C~vC~~~---~~-ll~Cd~C~~~~H~~Cl~P~l~~~P~g~W~C~~C~~~~   60 (66)
T 2lri_C            9 LAPGARCGVCGDG---TD-VLRCTHCAAAFHWRCHFPAGTSRPGTGLRCRSCSGDV   60 (66)
T ss_dssp             CCTTCCCTTTSCC---TT-CEECSSSCCEECHHHHCTTTCCCCSSSCCCTTTTTCC
T ss_pred             CCCCCCcCCCCCC---Ce-EEECCCCCCceecccCCCccCcCCCCCEECccccCCC
Confidence            3445679999742   33 444445999999999998876543    599997654

>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled coil, cytoplasm, cytoskeleton, disease mutation, ligase, metal-binding; NMR {Homo sapiens}

Probab=96.79  E-value=0.0008  Score=41.08  Aligned_cols=34  Identities=15%  Similarity=0.325  Sum_probs=26.2

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHH
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKW  112 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~w  112 (141)
                      +..|+||++.+..+....-++ |+|.|+..|+..+
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            467999998754444444476 9999999999983

>2l5u_A Chromodomain-helicase-DNA-binding protein 4; CHD4, MI2B, MI2-beta, PHD, protein binding, peptide binding metal binding protein; NMR {Homo sapiens}

Probab=94.93  E-value=0.023  Score=31.41  Aligned_cols=47  Identities=30%  Similarity=0.718  Sum_probs=32.0

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC----Ccccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH----SSCPTCRQR  125 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~CR~~  125 (141)
                      ..++..|.+|.+.   + .+..-..|...||..|+..=+...    -.||.|+..
T Consensus         8 ~~~~~~C~vC~~~---g-~ll~CD~C~~~fH~~Cl~p~l~~~p~g~W~C~~C~~~   58 (61)
T 2l5u_A            8 TDHQDYCEVCQQG---G-EIILCDTCPRAYHMVCLDPDMEKAPEGKWSCPHCEKE   58 (61)
T ss_dssp             SCCCSSCTTTSCC---S-SEEECSSSSCEEEHHHHCTTCCSCCCSSCCCTTGGGG
T ss_pred             CCCCCCCccCCCC---C-cEEECCCCChhhhhhccCCCCCCCCCCceECcccccc
Confidence            4455779999853   3 333444588999999999754332    249999753

>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=94.61  E-value=0.0086  Score=33.40  Aligned_cols=50  Identities=22%  Similarity=0.476  Sum_probs=34.0

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHc-----CCCccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL-----SHSSCPTCRQ  124 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~-----~~~~CP~CR~  124 (141)
                      +++...|++|...+.++...+.-..|..=||..|+..-..     ..-.||.|+.
T Consensus         3 ~~e~~~C~~C~~~~~~~~~mI~Cd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~   57 (64)
T 1we9_A            3 SGSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSN   57 (64)
T ss_dssp             CSSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHT
T ss_pred             CCCCCCCCCCCCccCCCCCEEEccCCCCCCCccccCcChhHhcCCCcEECCCCcC
Confidence            3455779999988765444444335888899999875322     2345999976

>2k16_A Transcription initiation factor TFIID subunit 3; protein, alternative splicing, metal-binding, nucleus, phosphoprotein, transcription regulation; NMR {Mus musculus} PDB: 2k17_A*

Probab=93.89  E-value=0.021  Score=32.80  Aligned_cols=53  Identities=19%  Similarity=0.387  Sum_probs=35.3

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC----CCccccccccccC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS----HSSCPTCRQRLKP  128 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~CR~~~~~  128 (141)
                      ..+...|.+|..... ++....-..|.--||..|+..-...    .-.||.|+..+..
T Consensus        15 ~~~~~~C~~C~~~~~-~~~mi~CD~C~~wfH~~Cv~~~~~~~~~~~w~C~~C~~~~~k   71 (75)
T 2k16_A           15 GNQIWICPGCNKPDD-GSPMIGCDDCDDWYHWPCVGIMAAPPEEMQWFCPKCANKIKK   71 (75)
T ss_dssp             SCEEECBTTTTBCCS-SCCEEECSSSSSEEEHHHHTCSSCCCSSSCCCCTTTHHHHCS
T ss_pred             CCCCcCCCCCCCCCC-CCCEEEcCCCCcccccccCCCCccCCCCCCEEChhccCchhh
Confidence            344567999987643 4334444458888999999865432    3359999876643

>1mm2_A MI2-beta; PHD, zinc finger, protein scaffold, DNA binding protein; NMR {Homo sapiens} SCOP: g.50.1.2 PDB: 2l75_A* 1mm3_A

Probab=93.80  E-value=0.02  Score=31.66  Aligned_cols=47  Identities=21%  Similarity=0.528  Sum_probs=31.0

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC----Ccccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH----SSCPTCRQR  125 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~CR~~  125 (141)
                      ..++..|.+|.+.   ++ +..-..|...||..|+..=+...    =.||.|+..
T Consensus         6 d~~~~~C~vC~~~---g~-ll~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~   56 (61)
T 1mm2_A            6 DHHMEFCRVCKDG---GE-LLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCP   56 (61)
T ss_dssp             CSSCSSCTTTCCC---SS-CBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTT
T ss_pred             cCCCCcCCCCCCC---CC-EEEcCCCCHHHcccccCCCcCcCCCCccCChhhcCc
Confidence            3455779999752   33 33333588999999998644332    249999764

>1fp0_A KAP-1 corepressor; PHD domain, C3HC4 type zinc binding domain, -structure, transcription; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=93.79  E-value=0.047  Score=32.52  Aligned_cols=52  Identities=23%  Similarity=0.498  Sum_probs=34.6

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC----CccccccccccCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH----SSCPTCRQRLKPSD  130 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~CR~~~~~~~  130 (141)
                      ..++..|.+|.+.   ++ +..-..|.-.||..|+..=+..-    -.||.|+..-..++
T Consensus        22 d~n~~~C~vC~~~---g~-LL~CD~C~~~fH~~Cl~PpL~~~P~g~W~C~~C~~~~~~ke   77 (88)
T 1fp0_A           22 DDSATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKE   77 (88)
T ss_dssp             SSSSSCCSSSCSS---SC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCSSCC
T ss_pred             CCCCCcCcCcCCC---CC-EEECCCCCCceecccCCCCCCCCcCCCcCCccccCCCccch
Confidence            4556789999854   33 33434588899999997755432    24999987544433

>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=93.76  E-value=0.11  Score=30.17  Aligned_cols=60  Identities=18%  Similarity=0.340  Sum_probs=41.7

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC-----CccccccccccCCCCCCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH-----SSCPTCRQRLKPSDAMPS  134 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~-----~~CP~CR~~~~~~~~~~~  134 (141)
                      ......|.+|.+.+++..-|..-..=+|.||-.|-+..++++     -.||-=.+--.....+||
T Consensus        12 ~~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sIk~q~~~~EvyCPSG~kCpL~gS~~PW   76 (93)
T 2cs3_A           12 NSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKAQGATGEVYCPSGEKCPLVGSNVPW   76 (93)
T ss_dssp             SCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHHHHSSSCCCCTTSSCCBCSSSSSBC
T ss_pred             CCCeeEeecchhhhccCceeeCCCccCCeeeccccHHHHHhcCCCCcEECCCCCccccCCCcCch
Confidence            345578999999998876665433456999999999998753     237766554444445555

>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=93.68  E-value=0.016  Score=40.05  Aligned_cols=47  Identities=30%  Similarity=0.530  Sum_probs=33.1

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC----Cccccccccc
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH----SSCPTCRQRL  126 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~CR~~~  126 (141)
                      .++..|.+|.+.    ..+.....|...||..|+..-+...    -.||.|+..-
T Consensus         5 ~~~~~C~~C~~~----g~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~~~   55 (207)
T 3u5n_A            5 PNEDWCAVCQNG----GDLLCCEKCPKVFHLTCHVPTLLSFPSGDWICTFCRDIG   55 (207)
T ss_dssp             SSCSSBTTTCCC----EEEEECSSSSCEECTTTSSSCCSSCCSSCCCCTTTSCSS
T ss_pred             CCCCCCCCCCCC----CceEEcCCCCCccCCccCCCCCCCCCCCCEEeCceeCcc
Confidence            445779999743    3344555699999999998765542    3499998754

>1f62_A Transcription factor WSTF; Zn-finger; NMR {Homo sapiens} SCOP: g.50.1.2

Probab=93.43  E-value=0.034  Score=29.38  Aligned_cols=44  Identities=30%  Similarity=0.694  Sum_probs=28.3

Q ss_pred             cccccccccccCCceeecCCCCCcccHhhHHHHHcCC----Cccccccc
Q 038049           80 GCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH----SSCPTCRQ  124 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~CR~  124 (141)
                      .|.+|...-..+ .+..-..|...||..|+..=+...    -.||.|+.
T Consensus         2 ~C~vC~~~~~~~-~ll~Cd~C~~~~H~~Cl~p~l~~~P~g~W~C~~C~~   49 (51)
T 1f62_A            2 RCKVCRKKGEDD-KLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCCS-CCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCCCCCCCCCCC-CEEECCCCChhhCcccCCCCcCCCCCCcEECcCccc
Confidence            488887653333 333444599999999997533332    24999865

>2yql_A PHD finger protein 21A; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=93.42  E-value=0.012  Score=31.96  Aligned_cols=46  Identities=26%  Similarity=0.681  Sum_probs=30.6

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC----Cccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH----SSCPTCRQ  124 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~CR~  124 (141)
                      ..++..|.+|.+.   ++.+ .-..|...||..|+..=+...    -.||.|++
T Consensus         6 ~~~~~~C~vC~~~---g~ll-~Cd~C~~~~H~~Cl~ppl~~~p~g~W~C~~C~~   55 (56)
T 2yql_A            6 SGHEDFCSVCRKS---GQLL-MCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQD   55 (56)
T ss_dssp             CSSCCSCSSSCCS---SCCE-ECSSSSCEECSSSSSSCCCSCCCSSCCCHHHHC
T ss_pred             CCCCCCCccCCCC---CeEE-EcCCCCcceECccCCCCcCCCCCCceEChhhhC
Confidence            4456779999863   3333 333599999999998644332    23888864

>2l2t_A Receptor tyrosine-protein kinase ERBB-4; transmembrane dimer, membrane domain, membrane protei; NMR {Homo sapiens}

Probab=93.33  E-value=0.34  Score=24.86  Aligned_cols=29  Identities=10%  Similarity=0.068  Sum_probs=13.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 038049            6 IMVIVAAMLCALVCALGLHSMLQCVFQCT   34 (141)
Q Consensus         6 ~~~i~~~~l~~~~~~l~~~~~~~~~~~~~   34 (141)
                      ...+.+.++..+++++.+...++++++++
T Consensus         9 ~~aIA~gVVgGv~~v~ii~~~~~~~~RRR   37 (44)
T 2l2t_A            9 TPLIAAGVIGGLFILVIVGLTFAVYVRRK   37 (44)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             cceEEEeehHHHHHHHHHHHHHHHHhhhh
Confidence            33444455544444444444444444433

>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=93.09  E-value=0.029  Score=34.78  Aligned_cols=48  Identities=27%  Similarity=0.531  Sum_probs=30.7

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC----CCcccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS----HSSCPTCR  123 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~CR  123 (141)
                      ..++..|.+|.+.-+..+.+.-. .|+..||..|+...+..    .-.||.|+
T Consensus         4 ~~~~~~C~~C~~~g~~~~ll~C~-~C~~~~H~~Cl~~~~~~~~~~~W~C~~C~   55 (111)
T 2ysm_A            4 GSSGANCAVCDSPGDLLDQFFCT-TCGQHYHGMCLDIAVTPLKRAGWQCPECK   55 (111)
T ss_dssp             CCCCSCBTTTCCCCCTTTSEECS-SSCCEECTTTTTCCCCTTTSTTCCCTTTC
T ss_pred             CCCCCCCcCCCCCCCCcCCeECC-CCCCCcChHHhCCccccccccCccCCcCC
Confidence            34567899998663222224444 59999999999887642    22366653

>3o36_A Transcription intermediary factor 1-alpha; TRIM24, PHD finger, bromodomain, H4K16 acetylation, breast C transcription-protein binding complex; HET: ALY; 1.70A {Homo sapiens} PDB: 3o33_A* 3o34_A* 3o35_A* 3o37_A

Probab=93.08  E-value=0.022  Score=38.49  Aligned_cols=46  Identities=28%  Similarity=0.560  Sum_probs=32.1

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC----Cccccccccc
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH----SSCPTCRQRL  126 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~CR~~~  126 (141)
                      ++..|.+|.+.   ++ +.....|.-.||..|+..-+...    -.||.|+..-
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            34679999843   43 44444589999999987765542    3499998754

>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=92.96  E-value=0.036  Score=37.61  Aligned_cols=48  Identities=25%  Similarity=0.469  Sum_probs=34.3

Q ss_pred             ccccccccccccCCc---eeecCCCCCcccHhhHHHH------Hc-----CCCccccccccc
Q 038049           79 AGCAICLLDFIDGDE---IRLLPKCNHRFHVACIDKW------LL-----SHSSCPTCRQRL  126 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~---v~~lp~C~H~Fh~~Ci~~w------l~-----~~~~CP~CR~~~  126 (141)
                      ..|+||...|.+++.   .+.-..|..=||..|+..=      +.     ..-.||.|+..-
T Consensus         3 ~~CpiC~k~Y~~~~~~~~MIqCd~C~~W~H~~Cvgi~~~~~e~~~~~pe~~~y~Cp~C~~~~   64 (183)
T 3lqh_A            3 NFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERH   64 (183)
T ss_dssp             CBCTTTCCBCTTCCTTCCEEECTTTCCEEEGGGSSCCHHHHHHHHHSHHHHCCCCTTTCCSS
T ss_pred             CcCCCCcCccCCcccCCCeEECCCCCcccchhccccCHHHHHHhhcCCCCCeeECcCCCCCC
Confidence            569999999988763   4444458899999998531      11     146799998753

>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A

Probab=92.89  E-value=0.063  Score=44.96  Aligned_cols=57  Identities=25%  Similarity=0.225  Sum_probs=48.8

Q ss_pred             CcccccccccccccCCceeecCCCC-CcccHhhHHHHHcCCCccccccccccCCCCCCCchh
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCN-HRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPSLDE  137 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~-H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~~~~~~  137 (141)
                      ++-.|+|=++-+.++   .++| -| +.|-...|..|+.++.+||.=|.++...+..|+...
T Consensus       890 ~~F~cPIs~~lM~DP---Vilp-sG~~TydR~~I~~wl~~~~tdP~Tr~~L~~~~liPN~~L  947 (968)
T 3m62_A          890 DEFLDPLMYTIMKDP---VILP-ASKMNIDRSTIKAHLLSDSTDPFNRMPLKLEDVTPNEEL  947 (968)
T ss_dssp             GGGBCTTTCSBCSSE---EECT-TTCCEEEHHHHHHHHTTCCBCTTTCCBCCGGGCEECHHH
T ss_pred             HHhCCcchhhHHhCC---eEcC-CCCEEECHHHHHHHHhcCCCCCCCCCCCCcccccccHHH
Confidence            456799999999877   6777 77 589999999999999999999999998888888543

>2l43_A N-teminal domain from histone H3.3, linker, PHD1 from bromodomain-containing protein...; PHD finger, histone CODE, transcription; NMR {Homo sapiens}

Probab=92.49  E-value=0.058  Score=32.10  Aligned_cols=56  Identities=21%  Similarity=0.370  Sum_probs=36.0

Q ss_pred             CCCccccccccccc-ccCCceeecCCCCCcccHhhHHHHHcC--CCccccccccccCCC
Q 038049           75 SSASAGCAICLLDF-IDGDEIRLLPKCNHRFHVACIDKWLLS--HSSCPTCRQRLKPSD  130 (141)
Q Consensus        75 ~~~~~~C~ICl~~~-~~~~~v~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~CR~~~~~~~  130 (141)
                      .+++..|.||.+.- .+.+.+..-..|.-.||..|+..-+.-  .=.||.|......+.
T Consensus        22 ~~~~~~C~vC~~~~s~~~~~ll~CD~C~~~fH~~Cl~p~~vP~g~W~C~~C~~~~~~~~   80 (88)
T 2l43_A           22 IDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQSRARPA   80 (88)
T ss_dssp             CCCCCCCSSCCSSSSCSEEEEEECSSSCCCCCHHHHTCSSCCSSCCCCHHHHHHTTSCC
T ss_pred             CCCCCcCCcCCCCCCCCCCCEEECCCCCchhhcccCCCCccCCCceECccccCccchhh
Confidence            34567899998653 223344444468889999999863321  234999987655443

>2puy_A PHD finger protein 21A; PHD finger, histone CODE, BRAF-HDAC complex, transcription; 1.43A {Homo sapiens}

Probab=92.49  E-value=0.013  Score=32.29  Aligned_cols=49  Identities=22%  Similarity=0.634  Sum_probs=32.7

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC----CccccccccccCC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH----SSCPTCRQRLKPS  129 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~CR~~~~~~  129 (141)
                      ++..|.+|...   ++.+ .-..|...||..|+..=+...    -.||.|+.....+
T Consensus         4 ~~~~C~vC~~~---g~ll-~Cd~C~~~fH~~Cl~ppl~~~p~g~W~C~~C~~~~~~~   56 (60)
T 2puy_A            4 HEDFCSVCRKS---GQLL-MCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQMLKK   56 (60)
T ss_dssp             CCSSCTTTCCC---SSCE-ECSSSSCEECGGGSSSCCSSCCCSCCCCHHHHHHHHHT
T ss_pred             CCCCCcCCCCC---CcEE-EcCCCCcCEECCcCCCCcCCCCCCceEChhccChhhch
Confidence            45679999853   4333 333599999999998644332    2499997765433

>2ku3_A Bromodomain-containing protein 1; PHD finger, chromatin regulator, metal-binding, finger, signaling protein; NMR {Homo sapiens}

Probab=92.14  E-value=0.057  Score=30.81  Aligned_cols=51  Identities=24%  Similarity=0.428  Sum_probs=32.9

Q ss_pred             CCCccccccccccc-ccCCceeecCCCCCcccHhhHHHHHcC--CCcccccccc
Q 038049           75 SSASAGCAICLLDF-IDGDEIRLLPKCNHRFHVACIDKWLLS--HSSCPTCRQR  125 (141)
Q Consensus        75 ~~~~~~C~ICl~~~-~~~~~v~~lp~C~H~Fh~~Ci~~wl~~--~~~CP~CR~~  125 (141)
                      ..++..|.||.+.- .+++.+..-..|.-.||..|+..-..-  .=.||.|+..
T Consensus        13 ~~~~~~C~vC~~~~s~~~~~ll~CD~C~~~~H~~Cl~~~~vP~g~W~C~~C~~~   66 (71)
T 2ku3_A           13 IDEDAVCSICMDGESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHCLQS   66 (71)
T ss_dssp             CCSSCSCSSSCCCCCCSSSCEEECSSSCCEEEHHHHTCSSCCSSCCCCHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEECCCCCCccccccCCCCcCCCCCcCCccCcCc
Confidence            44557799998653 233445454569999999999753221  2248888653

>2e6r_A Jumonji/ARID domain-containing protein 1D; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=91.66  E-value=0.027  Score=33.87  Aligned_cols=50  Identities=24%  Similarity=0.456  Sum_probs=32.9

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC----Ccccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH----SSCPTCRQR  125 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~CR~~  125 (141)
                      ..++..|.||...-.. +.+..-..|...||..|+..=+...    =.||.|+..
T Consensus        13 ~~~~~~C~vC~~~~~~-~~ll~CD~C~~~~H~~Cl~Ppl~~~P~g~W~C~~C~~~   66 (92)
T 2e6r_A           13 FIDSYICQVCSRGDED-DKLLFCDGCDDNYHIFCLLPPLPEIPRGIWRCPKCILA   66 (92)
T ss_dssp             CCCCCCCSSSCCSGGG-GGCEECTTTCCEECSSSSSSCCSSCCSSCCCCHHHHHH
T ss_pred             ccCCCCCccCCCcCCC-CCEEEcCCCCchhccccCCCCcccCCCCCcCCccCcCc
Confidence            3445679999866433 3344444599999999997533322    249999774

>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=91.23  E-value=0.25  Score=28.51  Aligned_cols=51  Identities=18%  Similarity=0.373  Sum_probs=32.5

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHc-----CCCccccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL-----SHSSCPTCRQRL  126 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~-----~~~~CP~CR~~~  126 (141)
                      +.....| ||...+.++...+.-..|..=||..|+..--.     ..-.||.|+...
T Consensus         9 ~~~~~~C-~C~~~~d~~~~MIqCd~C~~WfH~~Cvgl~~~~~~~~~~~~C~~C~~~~   64 (79)
T 1wep_A            9 ALVPVYC-LCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVF   64 (79)
T ss_dssp             CCCCCCS-TTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTS
T ss_pred             cCCccEE-EcCCccCCCCceEEcCCCCCcEEeeecCcccccccCCCeEECCCccccc
Confidence            3444556 99888754443333335888899999963211     345699998754

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=91.14  E-value=0.051  Score=33.74  Aligned_cols=45  Identities=27%  Similarity=0.573  Sum_probs=29.9

Q ss_pred             cccccccccccCCceeecCCCCCcccHhhHHHHHcCC----Cccccccc
Q 038049           80 GCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH----SSCPTCRQ  124 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~CR~  124 (141)
                      .|.+|.+.-.+++.+..-..|...||..|++.-+...    =.||.||.
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            5888886533333444444699999999987655432    24999874

>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=91.10  E-value=0.19  Score=28.10  Aligned_cols=36  Identities=28%  Similarity=0.566  Sum_probs=25.6

Q ss_pred             CCCcccccccccccccCCceeecC-CCCCcccHhhHH
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLP-KCNHRFHVACID  110 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp-~C~H~Fh~~Ci~  110 (141)
                      ++....|.+|..++.+++..+.-. .|.-=||..|+.
T Consensus         5 ~~~~~~C~~C~~p~~~~~~mI~CD~~C~~WfH~~Cvg   41 (65)
T 2vpb_A            5 SDPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTG   41 (65)
T ss_dssp             ----CBCTTTCSBCCTTSCEEEBTTTTCCEEEHHHHT
T ss_pred             CCCcCcCccCCCccCCCCCeEecccCccccCchhccC
Confidence            344567999999987776655554 588889999986

>1xwh_A Autoimmune regulator; PHD domain, Zn binding domain, apeced, nucleosome, E3 ligase, transcription; NMR {Homo sapiens} PDB: 2ke1_A 2kft_A

Probab=90.99  E-value=0.068  Score=29.93  Aligned_cols=46  Identities=28%  Similarity=0.611  Sum_probs=31.1

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC----Ccccccccc
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH----SSCPTCRQR  125 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~CR~~  125 (141)
                      .++..|.+|.+.   ++ +..-..|...||..|+..=+...    -.||.|...
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            455789999853   33 33444588999999998544332    249999753

>2lv9_A Histone-lysine N-methyltransferase MLL5; zinc finger, transcription, protein binding, NESG, northeast structural genomics consortium, SGC; NMR {Homo sapiens}

Probab=90.44  E-value=0.11  Score=31.53  Aligned_cols=47  Identities=26%  Similarity=0.475  Sum_probs=30.3

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcC---CCccccccc
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS---HSSCPTCRQ  124 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~---~~~CP~CR~  124 (141)
                      .+...| ||-.....+..|.- ..|.--||..|+..=...   .-.||.|+.
T Consensus        26 ~d~vrC-iC~~~~~~~~mi~C-d~C~~w~H~~C~~~~~~~~p~~w~C~~C~~   75 (98)
T 2lv9_A           26 TDVTRC-ICGFTHDDGYMICC-DKCSVWQHIDCMGIDRQHIPDTYLCERCQP   75 (98)
T ss_dssp             CCBCCC-TTSCCSCSSCEEEB-TTTCBEEETTTTTCCTTSCCSSBCCTTTSS
T ss_pred             CCCEEe-ECCCccCCCcEEEc-CCCCCcCcCcCCCCCccCCCCCEECCCCcC
Confidence            334567 89776555544433 359999999998753221   235999974

>2klu_A T-cell surface glycoprotein CD4; cell membrane, disulfide bond, HOST- virus interaction, immune response, immunoglobulin domain, lipoprotein; NMR {Homo sapiens}

Probab=89.75  E-value=1.4  Score=24.48  Aligned_cols=18  Identities=11%  Similarity=0.052  Sum_probs=8.5

Q ss_pred             HHHHHHHhcccccCCchh
Q 038049           26 MLQCVFQCTQRALTEPRQ   43 (141)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~   43 (141)
                      .+++..++++|.++..+.
T Consensus        27 cI~ccvkcrhRrrqAeRM   44 (70)
T 2klu_A           27 GIFFSVRSRHRRRQAERM   44 (70)
T ss_dssp             HHHHHHHSSCCSSSCTTS
T ss_pred             HHHHhhHHHHHHHHHHHH
Confidence            333355555555444443

>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=89.56  E-value=0.19  Score=33.42  Aligned_cols=50  Identities=18%  Similarity=0.423  Sum_probs=32.9

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHH-----cCCCccccccccc
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWL-----LSHSSCPTCRQRL  126 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl-----~~~~~CP~CR~~~  126 (141)
                      ++...| +|.....++.....-..|..-||..|+..--     ...-.||.|+..-
T Consensus         6 ~~~~~C-~C~~~~~~~~~mi~Cd~C~~WfH~~Cv~~~~~~~~~~~~~~C~~C~~~~   60 (174)
T 2ri7_A            6 DTKLYC-ICKTPEDESKFYIGCDRCQNWYHGRCVGILQSEAELIDEYVCPQCQSTE   60 (174)
T ss_dssp             -CCEET-TTTEECCTTSCEEECTTTCCEEEHHHHTCCHHHHTTCSSCCCHHHHHHH
T ss_pred             CCCcEe-eCCCCCCCCCCEeECCCCCchhChhhcCCchhhccCccCeecCCCcchh
Confidence            345678 9998765444444444588899999995321     1245699998743

>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A

Probab=89.49  E-value=0.59  Score=30.25  Aligned_cols=46  Identities=22%  Similarity=0.443  Sum_probs=31.7

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHc-----------CCCccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL-----------SHSSCPTCRQ  124 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~-----------~~~~CP~CR~  124 (141)
                      ...+..|.+|.+-   + .+..-..|...||..|+..=+.           ..=.||.|+.
T Consensus        60 Dg~~d~C~vC~~G---G-~LlcCD~Cpr~Fh~~Cl~p~l~~~~l~~i~~p~~~W~C~~C~~  116 (142)
T 2lbm_A           60 DGMDEQCRWCAEG---G-NLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHP  116 (142)
T ss_dssp             TSCBCSCSSSCCC---S-SEEECSSSCCEEEHHHHHHHTCHHHHHHHHTSTTCCCCTTTCC
T ss_pred             CCCCCeecccCCC---C-cEEeCCCCCCeeeHhhcCCCCChhhhhhcccCCCCCEeecccC
Confidence            4456889999843   3 3444445999999999996542           1235999974

>2ks1_B Epidermal growth factor receptor; ERBB1, ERBB2, transmembrane, heterodimer, complex, tyrosine receptor, bicelles, transferase; NMR {Homo sapiens}

Probab=89.17  E-value=0.31  Score=25.01  Aligned_cols=21  Identities=19%  Similarity=0.156  Sum_probs=7.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q 038049           12 AMLCALVCALGLHSMLQCVFQ   32 (141)
Q Consensus        12 ~~l~~~~~~l~~~~~~~~~~~   32 (141)
                      .++..+++++.+...++++++
T Consensus        16 gVVgGv~~~~ii~~~~~~~~R   36 (44)
T 2ks1_B           16 GMVGALLLLLVVALGIGLFMR   36 (44)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH
T ss_pred             ehhHHHHHHHHHHHHHHHHhh
Confidence            333333333333333333444

>4gne_A Histone-lysine N-methyltransferase NSD3; zinc finger, transcription, nuclear protein, transf nuclear protein complex; 1.47A {Homo sapiens} PDB: 4gnd_A 4gnf_A 4gng_A*

Probab=88.83  E-value=0.5  Score=29.07  Aligned_cols=49  Identities=22%  Similarity=0.462  Sum_probs=31.0

Q ss_pred             CCCcccccccccccccCCceeecC--CCCCcccHhhHHHHHcCCC----ccccccccccCC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLP--KCNHRFHVACIDKWLLSHS----SCPTCRQRLKPS  129 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp--~C~H~Fh~~Ci~~wl~~~~----~CP~CR~~~~~~  129 (141)
                      ..++..|.+|.+   .+ .+..-.  .|...||..|+.  |....    .||.|+.....+
T Consensus        12 ~~~~~~C~~C~~---~G-~ll~CD~~~Cp~~fH~~Cl~--L~~~P~g~W~Cp~c~C~~C~k   66 (107)
T 4gne_A           12 QMHEDYCFQCGD---GG-ELVMCDKKDCPKAYHLLCLN--LTQPPYGKWECPWHQCDECSS   66 (107)
T ss_dssp             CSSCSSCTTTCC---CS-EEEECCSTTCCCEECTGGGT--CSSCCSSCCCCGGGBCTTTCS
T ss_pred             CCCCCCCCcCCC---CC-cEeEECCCCCCcccccccCc--CCcCCCCCEECCCCCCCcCCC
Confidence            345577999983   23 333332  388999999998  44322    388877655544

>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=88.78  E-value=0.5  Score=26.78  Aligned_cols=47  Identities=28%  Similarity=0.607  Sum_probs=28.4

Q ss_pred             CCcccccccccccccCCceeecCC--CC-CcccHhhHHHHHcC----CCcccccccccc
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPK--CN-HRFHVACIDKWLLS----HSSCPTCRQRLK  127 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~--C~-H~Fh~~Ci~~wl~~----~~~CP~CR~~~~  127 (141)
                      .+...| ||-... .++ ...-..  |. .-||..|+.  |..    +-.||.|+..-.
T Consensus        14 ~~~~~C-~C~~~~-~g~-MI~CD~~~C~~~wfH~~Cvg--l~~~p~g~w~Cp~C~~~~~   67 (71)
T 1wen_A           14 NEPTYC-LCHQVS-YGE-MIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESG   67 (71)
T ss_dssp             TSCCCS-TTCCCS-CSS-EECCSCSSCSCCCEETTTTT--CSSCCSSCCCCTTTSSCSS
T ss_pred             CCCCEE-ECCCCC-CCC-EeEeeCCCCCCccEecccCC--cCcCCCCCEECCCCCcccc
Confidence            344567 898753 233 323223  55 579999998  333    234999987543

>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=88.76  E-value=0.065  Score=32.97  Aligned_cols=50  Identities=20%  Similarity=0.400  Sum_probs=33.9

Q ss_pred             ccccccccccccCCceeecC-CCCCcccHhhHHHHH----------cCCCccccccccccC
Q 038049           79 AGCAICLLDFIDGDEIRLLP-KCNHRFHVACIDKWL----------LSHSSCPTCRQRLKP  128 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp-~C~H~Fh~~Ci~~wl----------~~~~~CP~CR~~~~~  128 (141)
                      ..|.||...+.++.....-. .|.-=||.+|+.-=-          ..+-.||.|+..-..
T Consensus         4 ~~C~iC~~p~~~~~~mi~Cdd~C~~WfH~~CVglt~~~~~~i~~~~~~~~~Cp~C~~~~~~   64 (105)
T 2xb1_A            4 YPCGACRSEVNDDQDAILCEASCQKWFHRECTGMTESAYGLLTTEASAVWACDLCLKTKEG   64 (105)
T ss_dssp             CBCTTTCSBCCTTSCEEECTTTTCCEEEGGGTTCCHHHHHHHHHCTTEEECCHHHHHTTTT
T ss_pred             CCCCCCCCccCCCCCEEEecCCcccccccccCCcCHHHHHhhccCCCCCEECccccCcCCC
Confidence            46999999986655544443 477779999986321          023459999886543

>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=88.26  E-value=0.28  Score=28.06  Aligned_cols=48  Identities=23%  Similarity=0.365  Sum_probs=31.1

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHH---------cCCCcccccccccc
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWL---------LSHSSCPTCRQRLK  127 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl---------~~~~~CP~CR~~~~  127 (141)
                      ...| ||...+..+..|.-- .|..=||..|+..-.         ...-.||.|+..-.
T Consensus        16 ~~~C-~C~~~~~~~~MI~Cd-~C~~WfH~~Cvgl~~~~~~~l~~~~~~~~C~~C~~~~~   72 (76)
T 1wem_A           16 ALYC-ICRQPHNNRFMICCD-RCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILSG   72 (76)
T ss_dssp             CCCS-TTCCCCCSSCEEECS-SSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHSC
T ss_pred             CCEE-ECCCccCCCCEEEeC-CCCCcEeCeEEccchhhhhhccCCCCeEECcCCcCccC
Confidence            4557 898776533334333 588889999985321         24567999987543

>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=87.65  E-value=0.34  Score=26.78  Aligned_cols=53  Identities=23%  Similarity=0.515  Sum_probs=34.6

Q ss_pred             CCCccccccccccccc-CCceeecCCCCCcccHhhHHHHHc-------CCCcccccccccc
Q 038049           75 SSASAGCAICLLDFID-GDEIRLLPKCNHRFHVACIDKWLL-------SHSSCPTCRQRLK  127 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~-~~~v~~lp~C~H~Fh~~Ci~~wl~-------~~~~CP~CR~~~~  127 (141)
                      ..++..|.+|...... +..+..-..|.-.||..|+..=+.       ..=.||.|+....
T Consensus         3 ~~~~~~C~vC~~~~~~~~~~ll~Cd~C~~~~H~~C~~p~l~~~~~~p~~~W~C~~C~~~~~   63 (66)
T 2yt5_A            3 SGSSGVCTICQEEYSEAPNEMVICDKCGQGYHQLCHTPHIDSSVIDSDEKWLCRQCVFATT   63 (66)
T ss_dssp             CCCCCCBSSSCCCCCBTTBCEEECSSSCCEEETTTSSSCCCHHHHHSSCCCCCHHHHHTTS
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEECCCCChHHHhhhCCCcccccccCCCCCEECCCCcCccc
Confidence            3455779999976432 334444456999999999886331       2235999976543

>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=87.55  E-value=1  Score=28.64  Aligned_cols=46  Identities=22%  Similarity=0.465  Sum_probs=31.0

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHH------c-----CCCccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWL------L-----SHSSCPTCRQ  124 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl------~-----~~~~CP~CR~  124 (141)
                      ...+..|.+|-+    +..+..-..|-..||..|+..=+      .     ..=.|+.|+.
T Consensus        54 Dg~~~~C~vC~d----GG~LlcCd~Cpr~Fc~~Cl~~~lg~~~l~~i~~~~~~W~C~~C~~  110 (129)
T 3ql9_A           54 DGMDEQCRWCAE----GGNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHP  110 (129)
T ss_dssp             TSCBSSCTTTCC----CSEEEECSSSSCEEEHHHHHHHTCHHHHHHHTCTTSCCCCTTTCC
T ss_pred             CCCCCcCeecCC----CCeeEecCCCchhhhHHHhCCCcchhHHHHhccCCCCeEcCCcCC
Confidence            445677999984    34444444588999999999642      1     1235999965

>2jwa_A Receptor tyrosine-protein kinase ERBB-2; transmembrane helix dimer, protein kinase receptor membrane domain, ATP-binding, glycoprotein; NMR {Homo sapiens} PDB: 2ks1_A

Probab=87.34  E-value=1.9  Score=22.05  Aligned_cols=7  Identities=29%  Similarity=0.572  Sum_probs=2.6

Q ss_pred             HHHHHHH
Q 038049            9 IVAAMLC   15 (141)
Q Consensus         9 i~~~~l~   15 (141)
                      +.+.++.
T Consensus        14 Ia~~vVG   20 (44)
T 2jwa_A           14 IISAVVG   20 (44)
T ss_dssp             HHHHHHH
T ss_pred             hHHHHHH
Confidence            3333333

>3v43_A Histone acetyltransferase KAT6A; MOZ, PHD finger, transferase-structural protein; 1.47A {Homo sapiens} PDB: 2ln0_A

Probab=87.03  E-value=1.1  Score=27.62  Aligned_cols=33  Identities=21%  Similarity=0.444  Sum_probs=22.4

Q ss_pred             ccccccccccc-----ccCCceeecCCCCCcccHhhHH
Q 038049           78 SAGCAICLLDF-----IDGDEIRLLPKCNHRFHVACID  110 (141)
Q Consensus        78 ~~~C~ICl~~~-----~~~~~v~~lp~C~H~Fh~~Ci~  110 (141)
                      ...|.+|+..-     ..++.+..-..|+..||..|+.
T Consensus         5 ~~~C~~C~~~~~~~~~g~~~~Ll~C~~C~~~~H~~Cl~   42 (112)
T 3v43_A            5 IPICSFCLGTKEQNREKKPEELISCADCGNSGHPSCLK   42 (112)
T ss_dssp             CSSBTTTCCCTTCCTTSCCCCCEECTTTCCEECHHHHT
T ss_pred             CccccccCCchhhCcCCCchhceEhhhcCCCCCCchhc
Confidence            36699998653     1223344444599999999995

>2ro1_A Transcription intermediary factor 1-beta; KAP, TIF, PHD finger, bromodomain, SUMO, acetylation, alternative splicing, metal-binding, nucleus; NMR {Homo sapiens}

Probab=86.32  E-value=0.14  Score=34.82  Aligned_cols=45  Identities=27%  Similarity=0.570  Sum_probs=30.0

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcC----CCccccccccc
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS----HSSCPTCRQRL  126 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~----~~~CP~CR~~~  126 (141)
                      +..|.+|.+.   ++ +.....|...||..|+..=+..    .-.||.|+..-
T Consensus         2 ~~~C~~C~~~---g~-ll~Cd~C~~~~H~~Cl~p~l~~~p~g~W~C~~C~~~~   50 (189)
T 2ro1_A            2 ATICRVCQKP---GD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLP   50 (189)
T ss_dssp             CCCBTTTCCC---SS-CCCCTTTCCBCCSTTSTTCCSSCCCTTCCTTTTSCSC
T ss_pred             CCcCccCCCC---Cc-eeECCCCCchhccccCCCCcccCCCCCCCCcCccCCC
Confidence            3569999843   43 3333358899999999754432    22499998753

>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=85.85  E-value=0.67  Score=27.64  Aligned_cols=46  Identities=28%  Similarity=0.629  Sum_probs=27.7

Q ss_pred             CcccccccccccccCCceeecCC--CC-CcccHhhHHHHHcC----CCcccccccccc
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPK--CN-HRFHVACIDKWLLS----HSSCPTCRQRLK  127 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~--C~-H~Fh~~Ci~~wl~~----~~~CP~CR~~~~  127 (141)
                      +...| ||..... ++ ...-..  |. .-||..|+.  +..    +-.||.|+..-.
T Consensus        35 e~~yC-iC~~~~~-g~-MI~CD~~dC~~~WfH~~CVg--l~~~p~g~W~Cp~C~~~~~   87 (91)
T 1weu_A           35 EPTYC-LCHQVSY-GE-MIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQESG   87 (91)
T ss_dssp             CCBCS-TTCCBCC-SC-CCCCSCSSCSCCCCCSTTTT--CSSCCCSSCCCTTTCCCCS
T ss_pred             CCcEE-ECCCCCC-CC-EeEecCCCCCCCCEecccCC--cCcCCCCCEECcCccCcCC
Confidence            44557 9987642 33 222223  44 569999998  333    235999987543

>3shb_A E3 ubiquitin-protein ligase UHRF1; unmodified histone, methylation, UHRF1, PHD, ligase-NUCL protein complex; 1.80A {Homo sapiens}

Probab=85.49  E-value=0.1  Score=30.25  Aligned_cols=44  Identities=34%  Similarity=0.700  Sum_probs=27.2

Q ss_pred             cccccccccccCCceeecCCCCCcccHhhHHHHHcCC-----Cccccccc
Q 038049           80 GCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH-----SSCPTCRQ  124 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~-----~~CP~CR~  124 (141)
                      .|.+|...- +++.+..-..|...||..|+..-|...     =.||.|++
T Consensus        28 ~C~vC~~~~-d~~~ll~CD~C~~~yH~~Cl~PpL~~~P~g~~W~C~~C~~   76 (77)
T 3shb_A           28 ACHLCGGRQ-DPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   76 (77)
T ss_dssp             SBTTTCCCS-CGGGEEECTTTCCEEETTTSSSCCSSCCSSSCCCCTTTC-
T ss_pred             cCCccCCCC-CCcceeEeCCCCCccCcccCCCcccCCCCCCceECcCccc
Confidence            466676543 223344444588999999998655431     35888875

>1wee_A PHD finger family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=85.36  E-value=0.25  Score=27.99  Aligned_cols=50  Identities=22%  Similarity=0.303  Sum_probs=31.8

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHH----cCCCccccccccc
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWL----LSHSSCPTCRQRL  126 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl----~~~~~CP~CR~~~  126 (141)
                      .....| ||.....+++..+.-..|..=||..|+..--    .....||.|+..-
T Consensus        14 ~~~~~C-~C~~~~~~g~~mI~Cd~C~~W~H~~Cvg~~~~~~~~~~~~C~~C~~~~   67 (72)
T 1wee_A           14 NWKVDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELS   67 (72)
T ss_dssp             SSEECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHHC
T ss_pred             CcceEe-eCCCccCCCCcEEECCCCCCccCCeeeccCccccCCCcEECCCccCCC
Confidence            445668 7987765554333433588779999987532    1234599998643

>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=85.34  E-value=0.25  Score=26.13  Aligned_cols=44  Identities=18%  Similarity=0.323  Sum_probs=28.7

Q ss_pred             cccccccccccCCceeecC-CCCCcccHhhHHHHH----cCCCcccccc
Q 038049           80 GCAICLLDFIDGDEIRLLP-KCNHRFHVACIDKWL----LSHSSCPTCR  123 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp-~C~H~Fh~~Ci~~wl----~~~~~CP~CR  123 (141)
                      .|.+|...+.+++..+.-. .|.-=||..|+..--    ..+..||.|+
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            4778988876555444443 488779999976321    2456688885

>2yw8_A RUN and FYVE domain-containing protein 1; structure genomics, structural genomics, NPPSFA; 3.00A {Homo sapiens} PDB: 2yqm_A

Probab=85.15  E-value=0.72  Score=26.78  Aligned_cols=52  Identities=21%  Similarity=0.427  Sum_probs=31.3

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHc------CCCcccccccccc
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL------SHSSCPTCRQRLK  127 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~------~~~~CP~CR~~~~  127 (141)
                      .+...|.+|...|..-..----..||.+|+..|....+.      ....|-.|-..+.
T Consensus        17 ~~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~~~~l~~~~~~~RVC~~C~~~l~   74 (82)
T 2yw8_A           17 DEATHCRQCEKEFSISRRKHHCRNCGHIFCNTCSSNELALPSYPKPVRVCDSCHTLLL   74 (82)
T ss_dssp             CCCCBCTTTCCBCBTTBCCEECTTTCCEECSGGGCEEECCTTCSSCEEECHHHHHHTT
T ss_pred             ccCCcccCcCCcccCccccccCCCCCCEEChHHhCCeeecCCCCCcCEECHHHHHHHH
Confidence            344679999999864321112225999999999765321      1123666655443

>2knc_A Integrin alpha-IIB; transmembrane signaling, protein structure, cell A cleavage on PAIR of basic residues, disease mutation, disul bond, glycoprotein; NMR {Homo sapiens}

Probab=85.09  E-value=2.4  Score=22.64  Aligned_cols=23  Identities=17%  Similarity=0.176  Sum_probs=10.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q 038049            6 IMVIVAAMLCALVCALGLHSMLQ   28 (141)
Q Consensus         6 ~~~i~~~~l~~~~~~l~~~~~~~   28 (141)
                      ++++++++...+++.++++.++.
T Consensus        13 wiIi~svl~GLllL~li~~~LwK   35 (54)
T 2knc_A           13 WWVLVGVLGGLLLLTILVLAMWK   35 (54)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Confidence            33444444444444444444443

>2l8s_A Integrin alpha-1; transmembrane region, detergent micelle, CE adhesion; NMR {Homo sapiens}

Probab=85.00  E-value=3  Score=22.24  Aligned_cols=25  Identities=12%  Similarity=0.174  Sum_probs=12.3

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHH
Q 038049            5 NIMVIVAAMLCALVCALGLHSMLQC   29 (141)
Q Consensus         5 ~~~~i~~~~l~~~~~~l~~~~~~~~   29 (141)
                      .++++++++...+++.++++.++.+
T Consensus         9 ~WiIi~svl~GLLLL~Lii~~LwK~   33 (54)
T 2l8s_A            9 LWVILLSAFAGLLLLMLLILALWKI   33 (54)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            3444555555555555544444443

>1g47_A Pinch protein; LIM domain, Zn finger, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=84.83  E-value=0.76  Score=25.81  Aligned_cols=43  Identities=28%  Similarity=0.512  Sum_probs=30.7

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPS  129 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~  129 (141)
                      ....|+-|-..+...+.+...  -|..||.+|        ..|-.|+.++...
T Consensus        10 ~~~~C~~C~~~I~~~~~~~~a--~~~~~H~~C--------F~C~~C~~~L~~~   52 (77)
T 1g47_A           10 ASATCERCKGGFAPAEKIVNS--NGELYHEQC--------FVCAQCFQQFPEG   52 (77)
T ss_dssp             CCCBCSSSCCBCCSTTTCEEE--TTEEECTTT--------CCCTTTCCCCGGG
T ss_pred             CCCCchhcCCccCCCceEEEe--CccEecccc--------CeECCCCCCCCCC
Confidence            346799999988765554332  577899988        5677888777654

>1wfk_A Zinc finger, FYVE domain containing 19; riken structural genomics/proteomics initiative, RSGI, structural genomics, unknown function; NMR {Mus musculus} SCOP: g.50.1.1

Probab=84.52  E-value=0.95  Score=26.70  Aligned_cols=52  Identities=19%  Similarity=0.374  Sum_probs=33.1

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHc-------CCCcccccccccc
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL-------SHSSCPTCRQRLK  127 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~-------~~~~CP~CR~~~~  127 (141)
                      .+...|.+|...|..-..----..||++|+..|....+.       ....|-.|...+.
T Consensus         7 ~~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~~~~lp~~g~~~~RVC~~C~~~l~   65 (88)
T 1wfk_A            7 GMESRCYGCAVKFTLFKKEYGCKNCGRAFCNGCLSFSALVPRAGNTQQKVCKQCHTILT   65 (88)
T ss_dssp             CCCSBCTTTCCBCCSSSCEEECSSSCCEEETTTSCEEEEETTTTSEEEEECHHHHHHHH
T ss_pred             CcCCCCcCcCCcccCccccccCCCCCCEEChhHcCCceeccccCCCcCEECHHHHHHHH
Confidence            344679999998865422111225999999999765331       1244888876654

>1z2q_A LM5-1; membrane protein, FYVE domain, zinc-finger; NMR {Leishmania major}

Probab=84.34  E-value=0.85  Score=26.59  Aligned_cols=53  Identities=15%  Similarity=0.285  Sum_probs=32.4

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHc--------CCCccccccccccC
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL--------SHSSCPTCRQRLKP  128 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~--------~~~~CP~CR~~~~~  128 (141)
                      .+...|.+|...|..-..----..||++|+.+|....+.        ....|-.|-..+..
T Consensus        19 ~~~~~C~~C~~~Fs~~~RrHHCR~CG~v~C~~Cs~~~~~lp~~~~~~~~RVC~~C~~~l~~   79 (84)
T 1z2q_A           19 EDAPACNGCGCVFTTTVRRHHCRNCGYVLCGDCSRHRAAIPMRGITEPERVCDACYLALRS   79 (84)
T ss_dssp             TTCCBCTTTCCBCCTTSCCEECTTTCCEECTGGGCCEEEETTTTEEEEEECCHHHHHHHHT
T ss_pred             CCCCCCcCcCCccccchhcccccCCCcEEChHHhCCeEeccCCCCCCCCEECHHHHHHHhh
Confidence            345679999999865322111225999999999765421        12346666555443

>1z60_A TFIIH basal transcription factor complex P44 subunit; basic transcription factor, zinc binding protein, ring finger; NMR {Homo sapiens} SCOP: g.49.1.2

Probab=84.21  E-value=0.49  Score=25.86  Aligned_cols=43  Identities=28%  Similarity=0.438  Sum_probs=29.3

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccc
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTC  122 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~C  122 (141)
                      ..|--|...+.+. ....-+.|++.|+.+|=.--=++-.+||.|
T Consensus        16 ~~C~~C~~~~~~~-~~y~C~~C~~~FC~dCD~fiHe~Lh~CPgC   58 (59)
T 1z60_A           16 RFCYGCQGELKDQ-HVYVCAVCQNVFCVDCDVFVHDSLHSCPGC   58 (59)
T ss_dssp             CEETTTTEECTTS-EEECCTTTTCCBCHHHHHTTTTTSCSSSTT
T ss_pred             CcccccCcccCCC-ccEECCccCcCcccchhHHHHhhccCCcCC
Confidence            4599999888543 234456799999999933222334679988

>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=84.05  E-value=4.4  Score=23.98  Aligned_cols=52  Identities=21%  Similarity=0.364  Sum_probs=35.1

Q ss_pred             CcccccccccccccCCc--eeec-CCCCCcccHhhHHHHHc-CCCccccccccccC
Q 038049           77 ASAGCAICLLDFIDGDE--IRLL-PKCNHRFHVACIDKWLL-SHSSCPTCRQRLKP  128 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~--v~~l-p~C~H~Fh~~Ci~~wl~-~~~~CP~CR~~~~~  128 (141)
                      +...|.||-++......  +.+. ..|+--.|..|++-=.+ .++.||.|.+++..
T Consensus        15 ~~qiCqiCGD~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCktrYkr   70 (93)
T 1weo_A           15 DGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKR   70 (93)
T ss_dssp             SSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCC
T ss_pred             CCCccccccCccccCCCCCEEEeeeccCChhhHHHHHHHHhccCccccccCCcccc
Confidence            44779999988644322  2221 13666689999875443 47889999999863

>1wyh_A SLIM 2, skeletal muscle LIM-protein 2; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=83.96  E-value=0.85  Score=25.22  Aligned_cols=41  Identities=24%  Similarity=0.542  Sum_probs=29.3

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCC
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPS  129 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~  129 (141)
                      ..|+-|-..+.+.+.+...  -+..||.+|        ..|-.|+.+|...
T Consensus         6 ~~C~~C~~~I~~~~~~~~a--~~~~~H~~C--------F~C~~C~~~L~~~   46 (72)
T 1wyh_A            6 SGCSACGETVMPGSRKLEY--GGQTWHEHC--------FLCSGCEQPLGSR   46 (72)
T ss_dssp             CBCSSSCCBCCSSSCEECS--TTCCEETTT--------CBCTTTCCBTTTS
T ss_pred             CCCccCCCccccCccEEEE--CccccCccc--------CeECCCCCcCCCC
Confidence            5699999888765444322  678899988        5678888877654

>2cu8_A Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein, zinc-binding, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=83.88  E-value=1.3  Score=24.87  Aligned_cols=41  Identities=20%  Similarity=0.538  Sum_probs=31.2

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCC
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPS  129 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~  129 (141)
                      ...|+-|-..+.+++.+..   -+..||.+|        ..|..|+.+|...
T Consensus         9 ~~~C~~C~~~I~~~~~v~a---~~~~~H~~C--------F~C~~C~~~L~~~   49 (76)
T 2cu8_A            9 ASKCPKCDKTVYFAEKVSS---LGKDWHKFC--------LKCERCSKTLTPG   49 (76)
T ss_dssp             CCBCTTTCCBCCTTTEEEE---TTEEEETTT--------CBCSSSCCBCCTT
T ss_pred             CCCCcCCCCEeECCeEEEE---CCeEeeCCC--------CCCCCCCCccCCC
Confidence            4679999998886665542   678899988        5688888888654

>1x61_A Thyroid receptor interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=83.73  E-value=1.3  Score=24.39  Aligned_cols=39  Identities=33%  Similarity=0.721  Sum_probs=26.8

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      ..|+-|-..+...+.+...  -+..||.+|        ..|-.|+.+|.
T Consensus         6 ~~C~~C~~~I~~~~~~~~a--~~~~~H~~C--------F~C~~C~~~L~   44 (72)
T 1x61_A            6 SGCGGCGEDVVGDGAGVVA--LDRVFHVGC--------FVCSTCRAQLR   44 (72)
T ss_dssp             CCCSSSCSCCCSSSCCEEC--SSSEECTTT--------CBCSSSCCBCT
T ss_pred             CCCccCCCccCCCceEEEE--CCCeEcccC--------CcccccCCcCC
Confidence            5688888877654433322  567888888        56778888774

>1wew_A DNA-binding family protein; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: g.50.1.2

Probab=83.58  E-value=0.51  Score=27.15  Aligned_cols=50  Identities=22%  Similarity=0.387  Sum_probs=30.6

Q ss_pred             CcccccccccccccCCceeec-CCCCCcccHhhHHHHHc---------CCCcccccccccc
Q 038049           77 ASAGCAICLLDFIDGDEIRLL-PKCNHRFHVACIDKWLL---------SHSSCPTCRQRLK  127 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~l-p~C~H~Fh~~Ci~~wl~---------~~~~CP~CR~~~~  127 (141)
                      ....| ||-.....+..|.-- +.|..=||..|+.---.         .+..||.|+..-.
T Consensus        15 ~~~~C-iC~~~~~~g~MI~CD~~~C~~W~H~~CVgi~~~~~~~~~~~~~~~~C~~C~~~~~   74 (78)
T 1wew_A           15 IKVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTSG   74 (78)
T ss_dssp             CCCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCCS
T ss_pred             CCEEe-ECCCcCCCCCEEEECCccCCccccCEEEccccccccccccCCCCEECCCCCcccC
Confidence            44667 898764344333322 04888899999964211         2456999987543

>1joc_A EEA1, early endosomal autoantigen 1; FYVE domain, inositol 3-phosphate binding, membrane protein; HET: ITP; 2.20A {Homo sapiens} SCOP: g.50.1.1 h.1.21.1 PDB: 1hyi_A* 1hyj_A

Probab=83.51  E-value=0.74  Score=29.05  Aligned_cols=36  Identities=19%  Similarity=0.315  Sum_probs=24.0

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHH
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKW  112 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~w  112 (141)
                      +...|.+|...|..-..----..||++||..|....
T Consensus        68 ~~~~C~~C~~~Fs~~~RrHHCR~CG~vfC~~Cs~~~  103 (125)
T 1joc_A           68 EVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKN  103 (125)
T ss_dssp             GCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEE
T ss_pred             CCCCCcCcCCccccccccccCCCCCeEEChHHhCCc
Confidence            346799999998643211122259999999996543

>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=82.96  E-value=0.26  Score=27.75  Aligned_cols=49  Identities=20%  Similarity=0.502  Sum_probs=30.2

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhHHHHHc---CCCcccccccc
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL---SHSSCPTCRQR  125 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~---~~~~CP~CR~~  125 (141)
                      ..+...| ||..... ++..+.-..|..=||..|+..--.   ..-.||.|+.+
T Consensus        16 ~~~~~~C-iC~~~~~-~~~MIqCd~C~~WfH~~Cvgi~~~~~~~~~~C~~C~~s   67 (68)
T 3o70_A           16 FQGLVTC-FCMKPFA-GRPMIECNECHTWIHLSCAKIRKSNVPEVFVCQKCRDS   67 (68)
T ss_dssp             TTTCCCS-TTCCCCT-TCCEEECTTTCCEEETTTTTCCTTSCCSSCCCHHHHTC
T ss_pred             CCCceEe-ECCCcCC-CCCEEECCCCCccccccccCcCcccCCCcEECCCCCCC
Confidence            3445668 9987654 332333335888899999874221   23459998753

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=82.88  E-value=0.21  Score=28.90  Aligned_cols=45  Identities=24%  Similarity=0.603  Sum_probs=28.7

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcC-----CCccccccc
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-----HSSCPTCRQ  124 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-----~~~CP~CR~  124 (141)
                      ..|.+|...- ++..+..-..|...||..|+..=+..     .=.||.|++
T Consensus        27 c~C~vC~~~~-~~~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   76 (77)
T 2e6s_A           27 CSCRVCGGKH-EPNMQLLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKT   76 (77)
T ss_dssp             SSCSSSCCCC-CSTTEEECSSSCCEEETTSSSSCCSSCCCSSCCCCTTTCC
T ss_pred             CCCcCcCCcC-CCCCEEEcCCCCccccccccCCCccCCCCCCCcCCcCccC
Confidence            3688998643 23334444459999999999854332     224888864

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=82.65  E-value=0.098  Score=32.56  Aligned_cols=49  Identities=22%  Similarity=0.541  Sum_probs=31.3

Q ss_pred             cccccccccccCCceeecCCCCCcccHhhHHHHHcCC----CccccccccccCC
Q 038049           80 GCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH----SSCPTCRQRLKPS  129 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~CR~~~~~~  129 (141)
                      .|.+|...-..+ .+..-..|...||..|+..=+...    =.||.|+..+..+
T Consensus        60 ~C~~C~~~~~~~-~ll~Cd~C~~~yH~~Cl~ppl~~~P~g~W~C~~C~~~~~~k  112 (114)
T 2kwj_A           60 SCILCGTSENDD-QLLFCDDCDRGYHMYCLNPPVAEPPEGSWSCHLCWELLKEK  112 (114)
T ss_dssp             CCTTTTCCTTTT-TEEECSSSCCEEETTTSSSCCSSCCSSCCCCHHHHHHHHHT
T ss_pred             ccCcccccCCCC-ceEEcCCCCccccccccCCCccCCCCCCeECccccchhhcc
Confidence            588887653333 333444599999999998643332    2399997765443

>1y02_A CARP2, FYVE-ring finger protein sakura; zinc-binding module, phosphoinositide binding, caspase regulation, metal binding protein; 1.80A {Homo sapiens} SCOP: a.140.2.1 g.50.1.1

Probab=82.62  E-value=0.2  Score=31.60  Aligned_cols=53  Identities=15%  Similarity=0.343  Sum_probs=31.9

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccC
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKP  128 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~  128 (141)
                      .....|..|-..|..-..---...||.+||..|..........|-.|...+..
T Consensus        17 ~~~~~C~~C~~~Fs~~~RkHHCR~CG~ifC~~Cs~~~~~~vRVC~~C~~~~~~   69 (120)
T 1y02_A           17 GLEPSCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQRFRAT   69 (120)
T ss_dssp             ---CCCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHHHHHHT
T ss_pred             cccCcccCcCCccccccccccCCCCCCeeCHHHhCCCCCCceECHHHHHHHhc
Confidence            34467999999885432111222599999999977665556678888665443

>3t7l_A Zinc finger FYVE domain-containing protein 16; structural genomics consortium, SGC, lipid BIND protein, transport protein; 1.09A {Homo sapiens}

Probab=82.54  E-value=0.91  Score=26.87  Aligned_cols=51  Identities=16%  Similarity=0.396  Sum_probs=31.8

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHc------CCCcccccccccc
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL------SHSSCPTCRQRLK  127 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~------~~~~CP~CR~~~~  127 (141)
                      +...|.+|...|..-..--.-..||++|+..|...+..      ....|-.|...+.
T Consensus        19 ~~~~C~~C~~~F~~~~RrhhCr~CG~v~C~~Cs~~~~~l~~~~~~~RVC~~C~~~l~   75 (90)
T 3t7l_A           19 EAPNCMNCQVKFTFTKRRHHCRACGKVFCGVCCNRKCKLQYLEKEARVCVVCYETIS   75 (90)
T ss_dssp             GCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEEEEETTTTEEEEECHHHHHHHH
T ss_pred             cCCcCcCCCCcccchhhCccccCCCCEECCcccCCeeecCCCCCCCeECHHHHHHHH
Confidence            34679999998864322122225999999999776532      1234766665443

>2co8_A NEDD9 interacting protein with calponin homology and LIM domains; zinc finger protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=82.45  E-value=2  Score=24.59  Aligned_cols=43  Identities=30%  Similarity=0.577  Sum_probs=30.8

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCC
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPS  129 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~  129 (141)
                      .....|+-|-..+.+.+.+..   -+..||.+|        ..|-.|+.+|...
T Consensus        13 ~~~~~C~~C~~~I~~~e~v~a---~~~~wH~~C--------F~C~~C~~~L~~~   55 (82)
T 2co8_A           13 GAGDLCALCGEHLYVLERLCV---NGHFFHRSC--------FRCHTCEATLWPG   55 (82)
T ss_dssp             CSSCBCSSSCCBCCTTTBCCB---TTBCCBTTT--------CBCSSSCCBCCTT
T ss_pred             CCCCCCcccCCCcccceEEEE---CCCeeCCCc--------CEEcCCCCCcCCC
Confidence            344679999988876655542   578899998        5677777776544

>1vfy_A Phosphatidylinositol-3-phosphate binding FYVE domain of protein VPS27; endosome maturation, intracellular trafficking; 1.15A {Saccharomyces cerevisiae} SCOP: g.50.1.1

Probab=82.36  E-value=1.1  Score=25.38  Aligned_cols=33  Identities=18%  Similarity=0.278  Sum_probs=22.5

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHH
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDK  111 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~  111 (141)
                      ..|.+|...|..-..----..||.+|+..|-..
T Consensus        12 ~~C~~C~~~F~~~~RrHHCR~CG~v~C~~Cs~~   44 (73)
T 1vfy_A           12 DACMICSKKFSLLNRKHHCRSCGGVFCQEHSSN   44 (73)
T ss_dssp             SBCTTTCCBCBTTBCCEECTTTCCEECGGGSCE
T ss_pred             CcccCCCCccCCccccccCCCCCEEEcccccCC
Confidence            479999998864321111225999999999653

>1x4l_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=82.35  E-value=1.5  Score=24.26  Aligned_cols=42  Identities=26%  Similarity=0.536  Sum_probs=29.5

Q ss_pred             ccccccccccccc--CCceeecCCCCCcccHhhHHHHHcCCCccccccccccCC
Q 038049           78 SAGCAICLLDFID--GDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPS  129 (141)
Q Consensus        78 ~~~C~ICl~~~~~--~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~  129 (141)
                      ...|+-|-..+..  ++.+...  -+..||.+|        ..|-.|+.+|...
T Consensus         5 ~~~C~~C~~~I~~~~~~~~~~a--~~~~wH~~C--------F~C~~C~~~L~~~   48 (72)
T 1x4l_A            5 SSGCAGCTNPISGLGGTKYISF--EERQWHNDC--------FNCKKCSLSLVGR   48 (72)
T ss_dssp             SCSBTTTTBCCCCSSSCSCEEC--SSCEECTTT--------CBCSSSCCBCTTS
T ss_pred             CCCCcCCCccccCCCCcceEEE--CCcccCccc--------CEeccCCCcCCCC
Confidence            3669999988875  3333322  678899988        5688888887643

>2dj7_A Actin-binding LIM protein 3; LIM domain, Zn binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=82.20  E-value=1.7  Score=24.77  Aligned_cols=42  Identities=26%  Similarity=0.595  Sum_probs=31.3

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccC
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKP  128 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~  128 (141)
                      .....|+-|-..+.+++.+..   -+..||.+|        ..|-.|+.+|..
T Consensus        13 ~~~~~C~~C~~~I~~~~~v~a---~~~~wH~~C--------F~C~~C~~~L~~   54 (80)
T 2dj7_A           13 RGPSHCAGCKEEIKHGQSLLA---LDKQWHVSC--------FKCQTCSVILTG   54 (80)
T ss_dssp             SSCSCCTTTCCCCSSSCCEEE---TTEEECTTT--------CBCSSSCCBCSS
T ss_pred             CCCCCCcCcCCeeCCCeEEEE---CCccccccc--------CCcCcCCCCcCC
Confidence            345679999998876665543   568899988        668888888763

>1x4k_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=81.59  E-value=0.91  Score=25.10  Aligned_cols=41  Identities=22%  Similarity=0.538  Sum_probs=29.1

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCC
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPS  129 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~  129 (141)
                      ..|+-|-..+.+.+.+...  -+..||.+|        ..|-.|+.+|...
T Consensus         6 ~~C~~C~~~I~~~~~~~~a--~~~~~H~~C--------F~C~~C~~~L~~~   46 (72)
T 1x4k_A            6 SGCQECKKTIMPGTRKMEY--KGSSWHETC--------FICHRCQQPIGTK   46 (72)
T ss_dssp             CCBSSSCCCCCSSSCEEEE--TTEEEETTT--------TCCSSSCCCCCSS
T ss_pred             CCCccCCCcccCCceEEEE--CcCeecccC--------CcccccCCccCCC
Confidence            5699999888766544332  567899888        4577888777654

>2vnf_A ING 4, P29ING4, inhibitor of growth protein 4; acetylation, alternative splicing, anti-oncogene, cell cycle, coiled C nucleus, zinc, zinc-finger, ING4; HET: M3L; 1.76A {Homo sapiens} SCOP: g.50.1.2 PDB: 2k1j_A 2jmq_A 2qic_A*

Probab=81.44  E-value=0.48  Score=25.85  Aligned_cols=43  Identities=33%  Similarity=0.685  Sum_probs=25.8

Q ss_pred             CcccccccccccccCCceeecCC--CC-CcccHhhHHHHHcC----CCccccccc
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPK--CN-HRFHVACIDKWLLS----HSSCPTCRQ  124 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~--C~-H~Fh~~Ci~~wl~~----~~~CP~CR~  124 (141)
                      +...| ||.... .+ ....-..  |. .-||..|+.  +..    +-.||.|++
T Consensus         9 e~~~C-~C~~~~-~g-~mi~CD~cdC~~~wfH~~Cvg--l~~~p~g~w~C~~C~~   58 (60)
T 2vnf_A            9 EPTYC-LCHQVS-YG-EMIGCDNPDCSIEWFHFACVG--LTTKPRGKWFCPRCSQ   58 (60)
T ss_dssp             CCEET-TTTEEC-CS-EEEECSCTTCSSCEEETGGGT--CSSCCSSCCCCHHHHC
T ss_pred             CCCEE-ECCCcC-CC-CEEEeCCCCCCCceEehhcCC--CCcCCCCCEECcCccC
Confidence            34556 898753 23 3333334  44 579999998  433    234999865

>1wev_A Riken cDNA 1110020M19; structural genomics, PHD domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: g.50.1.2

Probab=81.43  E-value=0.16  Score=30.08  Aligned_cols=51  Identities=18%  Similarity=0.525  Sum_probs=34.2

Q ss_pred             Cccccccccccccc-CCceeecCCCCCcccHhhHHHHHcC--------CCcccccccccc
Q 038049           77 ASAGCAICLLDFID-GDEIRLLPKCNHRFHVACIDKWLLS--------HSSCPTCRQRLK  127 (141)
Q Consensus        77 ~~~~C~ICl~~~~~-~~~v~~lp~C~H~Fh~~Ci~~wl~~--------~~~CP~CR~~~~  127 (141)
                      .+..|.+|...-.. +..+..-..|...||..|+..=+..        .=.||.|+....
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            35679999865332 2344444469999999999865431        235999987654

>1x4u_A Zinc finger, FYVE domain containing 27 isoform B; phosphoinositide binding, zinc binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=81.34  E-value=1.1  Score=26.08  Aligned_cols=36  Identities=19%  Similarity=0.359  Sum_probs=23.5

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHH
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDK  111 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~  111 (141)
                      .+...|.+|...|..-..----..||.+|+..|...
T Consensus        12 ~~~~~C~~C~~~F~~~~RrHHCR~CG~vfC~~Cs~~   47 (84)
T 1x4u_A           12 NNFGNCTGCSATFSVLKKRRSCSNCGNSFCSRCCSF   47 (84)
T ss_dssp             CCCSSCSSSCCCCCSSSCCEECSSSCCEECTTTSCE
T ss_pred             CCCCcCcCcCCccccchhhhhhcCCCcEEChhhcCC
Confidence            344679999998854321111124999999999654

>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=81.27  E-value=1.2  Score=27.53  Aligned_cols=34  Identities=21%  Similarity=0.343  Sum_probs=22.6

Q ss_pred             cccccccccccc------CCceeecCCCCCcccHhhHHHH
Q 038049           79 AGCAICLLDFID------GDEIRLLPKCNHRFHVACIDKW  112 (141)
Q Consensus        79 ~~C~ICl~~~~~------~~~v~~lp~C~H~Fh~~Ci~~w  112 (141)
                      ..|.+|++.-..      ++.+..-..|+..||..|+...
T Consensus         2 ~~C~~C~~~~~~n~k~g~~~~Li~C~~C~~~~H~~Cl~~~   41 (114)
T 2kwj_A            2 SYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFT   41 (114)
T ss_dssp             CCCSSSCCBTTBCTTTCCCCCCEECSSSCCEECTTTTTCC
T ss_pred             CcCccCCCCccccccCCCCCCCeEeCCCCCccchhhCCCh
Confidence            459999875421      2233333359999999999754

>3asl_A E3 ubiquitin-protein ligase UHRF1; histone reader module, epigenetic regulation, LI binding protein complex; 1.41A {Homo sapiens} PDB: 3sou_A 3sow_A* 3sox_A 3zvy_A 2lgg_A 2lgk_A* 2lgl_A 3t6r_A 3zvz_B

Probab=80.67  E-value=0.28  Score=27.77  Aligned_cols=44  Identities=34%  Similarity=0.718  Sum_probs=27.2

Q ss_pred             cccccccccccCCceeecCCCCCcccHhhHHHHHcC-----CCccccccc
Q 038049           80 GCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-----HSSCPTCRQ  124 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-----~~~CP~CR~  124 (141)
                      .|.+|...- ++..+..-..|...||..|+..=+..     .=.||.|+.
T Consensus        20 ~C~~C~~~~-~~~~ll~CD~C~~~yH~~Cl~Ppl~~~P~g~~W~C~~C~~   68 (70)
T 3asl_A           20 ACHLCGGRQ-DPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECRN   68 (70)
T ss_dssp             SBTTTCCCS-CGGGEEECTTTCCEEEGGGSSSCCSSCCSSSCCCCTTTSC
T ss_pred             CCcCCCCcC-CCCCEEEcCCCCCceecccCCCCcCCCCCCCCcCCcCccC
Confidence            466777542 23334444458899999999854432     224888864

---

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	141
d1iyma_	55	g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sati	3e-17
d1chca_	68	g.44.1.1 (A:) Immediate early protein, IEEHV {Equi	5e-11
d1fbva4	79	g.44.1.1 (A:356-434) CBL {Human (Homo sapiens) [Ta	1e-09
d3dplr1	88	g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of S	2e-09
d1g25a_	65	g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapi	2e-09
d1bora_	56	g.44.1.1 (A:) Acute promyelocytic leukaemia proto-	3e-09
d1ur6b_	52	g.44.1.1 (B:) Not-4 N-terminal RING finger domain	6e-09
d1v87a_	114	g.44.1.1 (A:) Deltex protein 2 RING-H2 domain {Mou	1e-06
d1wima_	94	g.44.1.1 (A:) UbcM4-interacting protein 4 (KIAA016	2e-06
d1vyxa_	60	g.44.1.3 (A:) IE1B protein (ORF K3), N-terminal do	4e-06
d1rmda2	86	g.44.1.1 (A:1-86) V(D)J recombination activating p	5e-06
d1jm7a_	103	g.44.1.1 (A:) brca1 RING domain {Human (Homo sapie	9e-06
d1jm7b_	97	g.44.1.1 (B:) bard1 RING domain {Human (Homo sapie	6e-05
d2baya1	56	g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {	0.001

>d1iyma_ g.44.1.1 (A:) EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 4530]} Length = 55

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: EL5 RING-H2 domain
species: Rice (Oryza sativa) [TaxId: 4530]

 Score = 68.4 bits (167), Expect = 3e-17
 Identities = 25/46 (54%), Positives = 32/46 (69%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRL 126
           CA+CL +  DG+E R LP+C H FH  C+D WL SHS+CP CR  +
Sbjct: 8   CAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTV 53

>d1chca_ g.44.1.1 (A:) Immediate early protein, IEEHV {Equine herpesvirus 1 [TaxId: 10326]} Length = 68

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Immediate early protein, IEEHV
species: Equine herpesvirus 1 [TaxId: 10326]

 Score = 52.6 bits (126), Expect = 5e-11
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 3/53 (5%)

Query: 75  SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK 127
           ++ +  C ICL D  +     +   C H F   CI +W+  + +CP C+  ++
Sbjct: 2   ATVAERCPICLEDPSNYS---MALPCLHAFCYVCITRWIRQNPTCPLCKVPVE 51

>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 = 49.2 bits (117), Expect = 1e-09
 Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 5/54 (9%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSS-CPTCRQRLKPSDAMP 133
           C IC  +  D   +++ P C H    +C+  W  S    CP CR  +K ++ + 
Sbjct: 26  CKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPIV 75

>d3dplr1 g.44.1.1 (R:19-106) RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase complex
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.4 bits (117), Expect = 2e-09
 Identities = 16/61 (26%), Positives = 22/61 (36%), Gaps = 14/61 (22%)

Query: 81  CAICLLDFID--------------GDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRL 126
           CAIC    +D               +       CNH FH  CI +WL +   CP   +  
Sbjct: 24  CAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREW 83

Query: 127 K 127
           +
Sbjct: 84  E 84

>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 = 48.2 bits (114), Expect = 2e-09
 Identities = 14/59 (23%), Positives = 22/59 (37%), Gaps = 2/59 (3%)

Query: 81  CAICLLDFIDGDEIRLLP-KCNHRFHVACIDKWL-LSHSSCPTCRQRLKPSDAMPSLDE 137
           C  C         ++L+   C H    +C+D        +CP C   L+ S+    L E
Sbjct: 6   CPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNFRVQLFE 64

>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 = 48.0 bits (114), Expect = 3e-09
 Identities = 13/55 (23%), Positives = 19/55 (34%), Gaps = 7/55 (12%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPSL 135
           C  C  +       +LLP C H     C++        CP C+         P+L
Sbjct: 9   CQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGADTPAL 56

>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 = 47.0 bits (111), Expect = 6e-09
 Identities = 9/49 (18%), Positives = 16/49 (32%), Gaps = 1/49 (2%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWL-LSHSSCPTCRQRLKP 128
           C +C+      D       C ++    C  +     +  CP CR+    
Sbjct: 3   CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPE 51

>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 = 42.7 bits (99), Expect = 1e-06
 Identities = 10/48 (20%), Positives = 19/48 (39%), Gaps = 5/48 (10%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-----HSSCPTCR 123
             +     +    +  L KC+H FH+ C+     +        CP+C+
Sbjct: 42  SDMTDSKALGPMVVGRLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCK 89

>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 = 41.2 bits (96), Expect = 2e-06
 Identities = 14/74 (18%), Positives = 27/74 (36%), Gaps = 9/74 (12%)

Query: 75  SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS--------SCPTCRQRL 126
           SS S+GC +CL ++       +   C   F   C+ +++            SCP      
Sbjct: 2   SSGSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAACPK 60

Query: 127 KPSDAMPSLDEIVT 140
           +       ++ +V 
Sbjct: 61  QGHLQENEIECMVA 74

>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 = 39.8 bits (92), Expect = 4e-06
 Identities = 9/50 (18%), Positives = 15/50 (30%), Gaps = 3/50 (6%)

Query: 81  CAICLLDFIDGDEIRLLPK-CNHRFHVACIDKWLLSH--SSCPTCRQRLK 127
           C IC  +  +               H +C+  WL     ++C  C     
Sbjct: 9   CWICNEELGNERFRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYN 58

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.3 bits (94), Expect = 5e-06
 Identities = 17/54 (31%), Positives = 21/54 (38%), Gaps = 5/54 (9%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSS-CPTCRQRLKPSDAMP 133
           C IC     D     +   C H F   CI + L    S CP+CR    P+D   
Sbjct: 26  CQICEHILAD----PVETSCKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLES 75

>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 = 39.7 bits (92), Expect = 9e-06
 Identities = 16/64 (25%), Positives = 24/64 (37%), Gaps = 9/64 (14%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS---SCPTCRQRLKPSDAMPS--L 135
           C ICL    +     +  KC+H F   C+ K L        CP C+  +       S   
Sbjct: 24  CPICLELIKEP----VSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRF 79

Query: 136 DEIV 139
            ++V
Sbjct: 80  SQLV 83

>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 = 37.5 bits (86), Expect = 6e-05
 Identities = 14/61 (22%), Positives = 20/61 (32%), Gaps = 7/61 (11%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMP--SLDEI 138
           C+ C        E   L  C H F   C+   +   + CP C       D      LD +
Sbjct: 25  CSRCTNIL---REPVCLGGCEHIFCSNCVSDCI--GTGCPVCYTPAWIQDLKINRQLDSM 79

Query: 139 V 139
           +
Sbjct: 80  I 80

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 56

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 32.8 bits (74), Expect = 0.001
 Identities = 8/53 (15%), Positives = 18/53 (33%), Gaps = 3/53 (5%)

Query: 81  CAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMP 133
           CAI              PK    F  + +++++    + P   + L   + + 
Sbjct: 3   CAISGKVPRRPVLS---PKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIVE 52

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	141
d1iyma_	55	EL5 RING-H2 domain {Rice (Oryza sativa) [TaxId: 45	99.86
d1chca_	68	Immediate early protein, IEEHV {Equine herpesvirus	99.73
d1ur6b_	52	Not-4 N-terminal RING finger domain {Human (Homo s	99.73
d3dplr1	88	RIGG-box protein 1 (RBX1) of SCF ubiquitin ligase	99.7
d1g25a_	65	TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9	99.69
d1v87a_	114	Deltex protein 2 RING-H2 domain {Mouse (Mus muscul	99.68
d1fbva4	79	CBL {Human (Homo sapiens) [TaxId: 9606]}	99.67
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	99.61
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	99.61
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	99.57
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	99.54
d1vyxa_	60	IE1B protein (ORF K3), N-terminal domain {Kaposi's	99.48
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	99.42
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	99.39
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	99.38
d1wgma_	98	Ubiquitin conjugation factor E4A {Human (Homo sapi	99.24
d1wima_	94	UbcM4-interacting protein 4 (KIAA0161) {Human (Hom	99.06
d1wila_	89	Hypothetical protein KIAA1045 {Human (Homo sapiens	97.16
d1we9a_	64	PHD finger protein At5g26210 {Thale cress (Arabido	96.21
d1f62a_	51	Williams-Beuren syndrome transcription factor, WST	96.04
d1mm2a_	61	Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606	94.63
d1fp0a1	70	Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo	93.93
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	93.79
d1z60a1	59	TFIIH p44 subunit cysteine-rich domain {Human (Hom	93.73
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	92.07
d1wepa_	79	PHD finger protein 8 {Mouse (Mus musculus) [TaxId:	92.01
d1wesa_	71	PHD Inhibitor of growth protein 2, Ing2 {Mouse (Mu	91.54
d1weva_	88	PHD finger protein 22 {Mouse (Mus musculus) [TaxId	91.15
d1y02a2	51	Rififylin (FYVE-RING finger protein Sakura) {Human	90.82
d1wema_	76	Death associated transcription factor 1, Datf1 (DI	90.38
d1weea_	72	PHD finger protein At1g33420 {Thale cress (Arabido	89.79
d1dvpa2	72	Hrs {Fruit fly (Drosophila melanogaster) [TaxId: 7	86.85
d1joca1	64	Eea1 {Human (Homo sapiens) [TaxId: 9606]}	85.0
d2co8a2	36	Nedd9 interacting protein with calponin homology,	84.92
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	84.03
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	83.63
d1vfya_	67	vps27p protein {Baker's yeast (Saccharomyces cerev	82.79
d1weoa_	93	Cellulose synthase A catalytic subunit 7, IRX3 {Th	82.33
d1wewa_	78	Sumoylation ligase E3, SIZ1 {Thale cress (Arabidop	82.29
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	81.94

>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=99.86  E-value=5.7e-23  Score=113.61  Aligned_cols=51  Identities=49%  Similarity=1.152  Sum_probs=46.3

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCcccccccccc
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLK  127 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~  127 (141)
                      ++.+|+|||++|.+++.+..+|.|||.||.+||..|++++.+||+||+++.
T Consensus         4 d~~~C~ICl~~~~~~~~~~~l~~C~H~Fh~~Ci~~Wl~~~~~CP~CR~~i~   54 (55)
T d1iyma_           4 DGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVV   54 (55)
T ss_dssp             CSCCCTTTCCCCCTTSCCEECSSSCCEECTTHHHHTTTTCCSCSSSCCCSC
T ss_pred             CCCCCeEECccccCCCEEEEeCCCCCcccHHHHHHHHHhCCcCCCCCCEeE
Confidence            346799999999999999887669999999999999999999999999874

>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=99.73  E-value=5.3e-19  Score=101.69  Aligned_cols=48  Identities=33%  Similarity=0.847  Sum_probs=41.9

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccC
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKP  128 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~  128 (141)
                      .++|+||++.+.+  .++.+| |||.||.+||..|++.+.+||+||+++..
T Consensus         5 ~d~C~IC~~~~~~--~~~~~~-C~H~Fc~~Ci~~w~~~~~~CP~CR~~i~~   52 (68)
T d1chca_           5 AERCPICLEDPSN--YSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPVES   52 (68)
T ss_dssp             CCCCSSCCSCCCS--CEEETT-TTEEESTTHHHHHHHHSCSTTTTCCCCCC
T ss_pred             CCCCccCCcCccC--CcEEeC-CCCcCcHHHHHHHHHhCCcCCCCCcchHh
Confidence            4679999999854  456788 99999999999999999999999998853

>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=99.73  E-value=5.1e-19  Score=96.47  Aligned_cols=48  Identities=19%  Similarity=0.426  Sum_probs=40.6

Q ss_pred             cccccccccccCCce-eecCCCCCcccHhhHHHHHcCC-CccccccccccC
Q 038049           80 GCAICLLDFIDGDEI-RLLPKCNHRFHVACIDKWLLSH-SSCPTCRQRLKP  128 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v-~~lp~C~H~Fh~~Ci~~wl~~~-~~CP~CR~~~~~  128 (141)
                      +|+||+++|..++.+ ..++ |||.||.+|++.|+..+ .+||+||+++.+
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            799999999877654 4456 99999999999999864 569999999865

>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=99.70  E-value=5.5e-18  Score=102.09  Aligned_cols=50  Identities=32%  Similarity=0.683  Sum_probs=41.6

Q ss_pred             cccccccccccccCC---------------ceeecCCCCCcccHhhHHHHHcCCCccccccccccC
Q 038049           78 SAGCAICLLDFIDGD---------------EIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKP  128 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~---------------~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~  128 (141)
                      ++.|+||++++.+..               .+..++ |||+||.+||..||+.+.+||+||++..-
T Consensus        21 ~d~C~IC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-C~H~FH~~Ci~~Wl~~~~~CP~CR~~~~~   85 (88)
T d3dplr1          21 VDNCAICRNHIMDLCIECQANQASATSEECTVAWGV-CNHAFHFHCISRWLKTRQVCPLDNREWEF   85 (88)
T ss_dssp             SCCCSSSCSCTTSCCTTHHHHTTCC---CCCEEEET-TSCEEEHHHHHHHHTTCSBCSSSCSBCCE
T ss_pred             CCcCEEccchhhCccccccccccccccccCCeEEcc-ccCcccHHHHHHHHHHCCcCCCCCCcccc
Confidence            456999998885532               356677 99999999999999999999999998753

>d1g25a_ g.44.1.1 (A:) TFIIH Mat1 subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: TFIIH Mat1 subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.1e-17  Score=95.16  Aligned_cols=53  Identities=23%  Similarity=0.605  Sum_probs=41.8

Q ss_pred             CcccccccccccccCC--ceeecCCCCCcccHhhHHHHHcC-CCccccccccccCCC
Q 038049           77 ASAGCAICLLDFIDGD--EIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPSD  130 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~--~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~~  130 (141)
                      ++.+|+||++.+..+.  .+..++ |||.||.+||..|+.+ +.+||+||+++..++
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            3578999999875443  345566 9999999999999965 567999999986554

>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=99.68  E-value=1.2e-17  Score=105.15  Aligned_cols=52  Identities=25%  Similarity=0.581  Sum_probs=41.6

Q ss_pred             cccccccccccccC---------------CceeecCCCCCcccHhhHHHHHcCC-----CccccccccccCCC
Q 038049           78 SAGCAICLLDFIDG---------------DEIRLLPKCNHRFHVACIDKWLLSH-----SSCPTCRQRLKPSD  130 (141)
Q Consensus        78 ~~~C~ICl~~~~~~---------------~~v~~lp~C~H~Fh~~Ci~~wl~~~-----~~CP~CR~~~~~~~  130 (141)
                      +.+|+||++++..+               ..+.+++ |||.||.+||..|++.+     .+||+||+.+..+.
T Consensus        25 ~~~C~IC~e~l~~~~~~~~~~~~~~~~~~~~~~~~~-CgH~FH~~Ci~~Wl~~~~~~~~~~CP~CR~~~~~~~   96 (114)
T d1v87a_          25 EEDCIICMEKLAVASGYSDMTDSKALGPMVVGRLTK-CSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKT   96 (114)
T ss_dssp             SCEETTTTEETTSCCSTTTTCCCSSSCSSCCEEESS-SCCEECHHHHHHHHHHTCCSSCCBCTTTCCBSSSCS
T ss_pred             cccccchhheecccccccccccccccccccceEECC-CCChhhHHHHHHHHHhcCcCCCCccccccchhccCc
Confidence            45799999998542               2356677 99999999999999753     37999999887664

>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=99.67  E-value=2.2e-17  Score=97.44  Aligned_cols=50  Identities=30%  Similarity=0.779  Sum_probs=42.1

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcC-CCccccccccccCCCCC
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPSDAM  132 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~~~~  132 (141)
                      ..|+||++.+.+   .+.+| |||.||.+||..|+.. +++||+||.++...+.+
T Consensus        24 ~~C~IC~~~~~~---~~~~~-CgH~fC~~Ci~~wl~~~~~~CP~Cr~~i~~~~~i   74 (79)
T d1fbva4          24 QLCKICAENDKD---VKIEP-CGHLMCTSCLTSWQESEGQGCPFCRCEIKGTEPI   74 (79)
T ss_dssp             TBCTTTSSSBCC---EECSS-SCCEECHHHHHHHHHTTCCSCTTTCCCCCCCCCS
T ss_pred             CCCccCCCcCCC---eEEeC-CCCeeeHHHHHHHHHHCcCcCCCCCcCccCCcee
Confidence            569999998755   47788 9999999999999975 56799999999866543

>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=99.61  E-value=5.2e-17  Score=89.47  Aligned_cols=50  Identities=24%  Similarity=0.566  Sum_probs=42.6

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCCCCC
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPS  134 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~~~  134 (141)
                      ..+|+||++.+.++   +.+| |||.||.+||+.|   +.+||+||+++......++
T Consensus         6 ~l~C~IC~~~~~~p---~~lp-CgH~fC~~Ci~~~---~~~CP~Cr~~~~~~~~~~a   55 (56)
T d1bora_           6 FLRCQQCQAEAKCP---KLLP-CLHTLCSGCLEAS---GMQCPICQAPWPLGADTPA   55 (56)
T ss_dssp             CSSCSSSCSSCBCC---SCST-TSCCSBTTTCSSS---SSSCSSCCSSSSCCSSCCC
T ss_pred             CCCCcccCcccCCC---EEec-CCCHHhHHHHHcC---CCcCcCCCCcccCCCCCCC
Confidence            35899999999776   6788 9999999999865   6789999999988777665

>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=99.61  E-value=3.2e-17  Score=90.54  Aligned_cols=50  Identities=18%  Similarity=0.213  Sum_probs=42.6

Q ss_pred             cccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCCC
Q 038049           80 GCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAM  132 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~  132 (141)
                      .|+||++.++++   ..++.|||+||.+||.+|++++.+||+||+++..++..
T Consensus         2 ~C~Ic~~~~~~P---v~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~dLi   51 (56)
T d2baya1           2 LCAISGKVPRRP---VLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIEEIV   51 (56)
T ss_dssp             CCTTTCSCCSSE---EEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGGGCE
T ss_pred             CCccCCchHHhc---CccCCCCCcccHHHHHHHHhhccCCCccCCcCCHHhce
Confidence            499999998765   45545999999999999999999999999998876543

>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=99.57  E-value=4.8e-16  Score=92.68  Aligned_cols=53  Identities=34%  Similarity=0.571  Sum_probs=43.9

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcC-CCccccccccccCCCCCC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPSDAMP  133 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~~~~~  133 (141)
                      +..+|+||++.+.++   ..++ |||.||..||..|++. +..||.||.++...+..+
T Consensus        22 ~~l~C~IC~~~~~~p---v~~~-CgH~FC~~Ci~~~~~~~~~~CP~Cr~p~~~~~l~~   75 (86)
T d1rmda2          22 KSISCQICEHILADP---VETS-CKHLFCRICILRCLKVMGSYCPSCRYPCFPTDLES   75 (86)
T ss_dssp             HHTBCTTTCSBCSSE---EECT-TSCEEEHHHHHHHHHHTCSBCTTTCCBCCGGGCBC
T ss_pred             cCcCCccCCcchhcc---eecC-CCChhhHHHHHHHHhhCCCcCcccCCCCChhhccC
Confidence            346799999998765   6787 9999999999999974 568999999987666543

>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=99.54  E-value=1.6e-15  Score=93.63  Aligned_cols=52  Identities=29%  Similarity=0.556  Sum_probs=42.6

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcCC---CccccccccccCCCCCCC
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH---SSCPTCRQRLKPSDAMPS  134 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~---~~CP~CR~~~~~~~~~~~  134 (141)
                      -+|+||++.+.++   ..++ |||.||..||..|+.++   ..||.||+++..++..++
T Consensus        22 l~CpIC~~~~~~p---v~~~-CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~~~l~~n   76 (103)
T d1jm7a_          22 LECPICLELIKEP---VSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQES   76 (103)
T ss_dssp             TSCSSSCCCCSSC---CBCT-TSCCCCSHHHHHHHHSSSSSCCCTTTSCCCCTTTCBCC
T ss_pred             cCCCccCchhCCe---EEcC-CCCchhhHHHHHHHHHCCCCCcCcCCCCcCChhhCCcC
Confidence            5699999999766   5577 99999999999999764   379999999976654443

>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=99.48  E-value=1.2e-14  Score=81.10  Aligned_cols=51  Identities=18%  Similarity=0.447  Sum_probs=38.9

Q ss_pred             CCCcccccccccccccCCceeecC----CCCCcccHhhHHHHHc--CCCccccccccccC
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLP----KCNHRFHVACIDKWLL--SHSSCPTCRQRLKP  128 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp----~C~H~Fh~~Ci~~wl~--~~~~CP~CR~~~~~  128 (141)
                      +++...|.||++++.+..   ..|    +|+|.||..||..|+.  ++.+||+||+++..
T Consensus         3 ded~~~C~IC~~~~~~~~---~~~c~c~~c~h~~H~~Cl~~W~~~~~~~~CP~Cr~~~~~   59 (60)
T d1vyxa_           3 DEDVPVCWICNEELGNER---FRACGCTGELENVHRSCLSTWLTISRNTACQICGVVYNT   59 (60)
T ss_dssp             TCSCCEETTTTEECSCCC---CCSCCCSSGGGSCCHHHHHHHHHHHTCSBCTTTCCBCCC
T ss_pred             CCCCCCCccCCccCCCce---eEecccCCCCCEEcHHHHHHHHhhCCCCCCcccCCeeec
Confidence            345577999999876542   233    2569999999999995  45689999998754

>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=99.42  E-value=1.9e-14  Score=87.82  Aligned_cols=51  Identities=22%  Similarity=0.442  Sum_probs=41.6

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCCCCC
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPS  134 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~~~  134 (141)
                      .+|+||++.|.++  +..++ |||.||.+||..|+.  ..||.||.++...+..++
T Consensus        23 l~C~IC~~~~~~p--v~~~~-CgH~fC~~Ci~~~~~--~~CP~Cr~~~~~~~l~~n   73 (97)
T d1jm7b_          23 LRCSRCTNILREP--VCLGG-CEHIFCSNCVSDCIG--TGCPVCYTPAWIQDLKIN   73 (97)
T ss_dssp             TSCSSSCSCCSSC--BCCCS-SSCCBCTTTGGGGTT--TBCSSSCCBCSCSSCCCC
T ss_pred             CCCccCCchhhcC--ceeCC-CCCchhHHHHHHHHh--ccccccCCcCchhhCccc
Confidence            5799999999765  33445 999999999999984  459999999887665554

>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=99.39  E-value=1.2e-13  Score=80.83  Aligned_cols=56  Identities=21%  Similarity=0.442  Sum_probs=46.9

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC-CccccccccccCCCCCCCc
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH-SSCPTCRQRLKPSDAMPSL  135 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~-~~CP~CR~~~~~~~~~~~~  135 (141)
                      .++-.|+||++.|.++   .+++ |||.|+..||..|+..+ ..||.|+.++...+..|+.
T Consensus         6 P~~l~CpIc~~~m~dP---V~~~-cgh~fc~~ci~~~~~~~~~~cP~~~~~l~~~~l~pN~   62 (78)
T d1t1ha_           6 PEYFRCPISLELMKDP---VIVS-TGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNY   62 (78)
T ss_dssp             SSSSSCTTTSCCCSSE---EEET-TTEEEEHHHHHHHHTTTCCBCTTTCCBCSSCCCEECT
T ss_pred             CccCCCcCcCchhhCc---eEcc-CCCcchHHHHHHHHHHCCCCCCcccccCCcccccchH
Confidence            3457899999999776   5677 99999999999999864 6799999999887766653

>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=99.38  E-value=7.3e-14  Score=82.24  Aligned_cols=56  Identities=16%  Similarity=0.177  Sum_probs=46.5

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcC-CCccccccccccCCCCCCCch
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLS-HSSCPTCRQRLKPSDAMPSLD  136 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~-~~~CP~CR~~~~~~~~~~~~~  136 (141)
                      ++-.|+||++.|.++   ..++ |||.|+..||..|+.. +.+||.||.++...+..++..
T Consensus         6 ~~l~CpIc~~l~~dP---v~~~-cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~~~l~pN~~   62 (80)
T d2c2la2           6 DYLCGKISFELMREP---CITP-SGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLA   62 (80)
T ss_dssp             STTBCTTTCSBCSSE---EECS-SCCEEETTHHHHHHHHTCSSCTTTCCCCCGGGCEECHH
T ss_pred             ccccCcCcCchhhhh---cccC-CcCeecHHHHHHHHhcCCccCCCccccccccccccHHH
Confidence            446799999999776   5677 9999999999999975 567999999998777666643

>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=99.24  E-value=4e-12  Score=77.37  Aligned_cols=58  Identities=21%  Similarity=0.165  Sum_probs=48.8

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccccccCCCCCCCchh
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQRLKPSDAMPSLDE  137 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~~~~~~~~~~~~~~  137 (141)
                      ++-.|+||++.|.++   .+++.|||.|+..||..|+.++..||.||+++...+..|+...
T Consensus        21 ~~f~CPI~~~lm~dP---V~~~~~~~ty~r~~I~~~l~~~~~~P~~~~~l~~~~L~pN~~L   78 (98)
T d1wgma_          21 DEFLDPIMSTLMCDP---VVLPSSRVTVDRSTIARHLLSDQTDPFNRSPLTMDQIRPNTEL   78 (98)
T ss_dssp             TTTBCTTTCSBCSSE---EECTTTCCEEEHHHHHHHTTTSCBCTTTCSBCCTTTSEECHHH
T ss_pred             HHhCCcCchhHHHHH---HhcccccchhhHHHHHHHHHhcCCcccccccccchhhcchHHH
Confidence            357899999999887   6777344689999999999999999999999998887777543

>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=99.06  E-value=1.7e-11  Score=73.95  Aligned_cols=48  Identities=25%  Similarity=0.584  Sum_probs=38.2

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC--------Cccccccc
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH--------SSCPTCRQ  124 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~--------~~CP~CR~  124 (141)
                      .+..+|+||++++...+.+..++ |||.||.+|+..|++.+        -.||.|+.
T Consensus         3 ~~~~~C~IC~~~~~~~~~~~~~~-C~H~fC~~Cl~~~~~~~i~~~~~~~i~CP~~~C   58 (94)
T d1wima_           3 SGSSGCKLCLGEYPVEQMTTIAQ-CQCIFCTLCLKQYVELLIKEGLETAISCPDAAC   58 (94)
T ss_dssp             CSBCCCSSSCCCCBGGGEEEETT-TTEEEEHHHHHHHHHHHHHHCSCCCEECSCTTC
T ss_pred             CCCCcCccCCCcccCCceEEECC-CCCEeCCcCHHHHHHHHHhcCCccccCCcCCCC
Confidence            34578999999997777777776 99999999999999632        24998643

>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=97.16  E-value=0.00051  Score=38.77  Aligned_cols=62  Identities=21%  Similarity=0.447  Sum_probs=39.9

Q ss_pred             CCCCCCcccccccccccccCCceeecCCCCCcccHhhHHHH--HcCC--------------Cccccccc--cccCCCCCC
Q 038049           72 SSPSSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKW--LLSH--------------SSCPTCRQ--RLKPSDAMP  133 (141)
Q Consensus        72 ~~~~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~w--l~~~--------------~~CP~CR~--~~~~~~~~~  133 (141)
                      .++..++..|.|| +.+...+....- -|+-+||..|++.-  +...              =+|+.|-.  .+..++.|.
T Consensus         9 re~v~~D~mC~vC-~v~t~~~l~pCR-vCtRv~H~~CL~r~gyl~~e~a~e~~e~A~T~~GWSC~~C~nl~~LLtEeem~   86 (89)
T d1wila_           9 REPVVNDEMCDVC-EVWTAESLFPCR-VCTRVFHDGCLRRMGYIQGDSAAEVTEMAHTETGWSCHYCDNINLLLTEESGP   86 (89)
T ss_dssp             CCCCCCSCCCTTT-CCCCSSCCSSCS-SSSSCCCHHHHHHHTSCCCCCCCSCSCCCSSSSSCCCTTTCCCCSSSCCCCCC
T ss_pred             ccCCCcCcccccc-Ccccccceecce-eecchhhHHHHHHhcccccHHHHHHHHhhcCCCCcchhhhcchhhhhcHhhhh
Confidence            3445667889999 666655433222 38999999999986  2111              14999965  234556665


Q ss_pred             Cc
Q 038049          134 SL  135 (141)
Q Consensus       134 ~~  135 (141)
                      ++
T Consensus        87 sl   88 (89)
T d1wila_          87 SS   88 (89)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>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=96.21  E-value=0.00051  Score=37.24  Aligned_cols=50  Identities=20%  Similarity=0.468  Sum_probs=35.1

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHH---c--CCCcccccccc
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWL---L--SHSSCPTCRQR  125 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl---~--~~~~CP~CR~~  125 (141)
                      .++..|.+|.....+++....-..|+.-||..|+..=.   .  .+-.||.|+..
T Consensus         4 ~~~~~C~~C~~~~~~~~~~I~Cd~C~~w~H~~C~~~~~~~~~~~~~w~C~~C~~~   58 (64)
T d1we9a_           4 GSSGQCGACGESYAADEFWICCDLCEMWFHGKCVKITPARAEHIKQYKCPSCSNK   58 (64)
T ss_dssp             SSCCCCSSSCCCCCSSSCEEECSSSCCEEETTTTTCCTTGGGGCSSCCCHHHHTT
T ss_pred             CCCCcCcCcCCCCCCCCCEEEcCCCCccCCcccCCcChHHCCCCCeEECcCCcCc
Confidence            44578999998876666544555699999999986311   1  23459999864

>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=96.04  E-value=0.0012  Score=33.95  Aligned_cols=44  Identities=32%  Similarity=0.757  Sum_probs=30.4

Q ss_pred             cccccccccccCCceeecCCCCCcccHhhHHHHHcCCC----ccccccc
Q 038049           80 GCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS----SCPTCRQ  124 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~----~CP~CR~  124 (141)
                      .|.||...-.. +.+..-..|...||..|++.-+....    .||.||.
T Consensus         2 ~C~vC~~~~~~-~~~i~Cd~C~~~~H~~C~~p~~~~~p~~~W~C~~C~~   49 (51)
T d1f62a_           2 RCKVCRKKGED-DKLILCDECNKAFHLFCLRPALYEVPDGEWQCPACQP   49 (51)
T ss_dssp             CCTTTCCSSCC-SCCEECTTTCCEECHHHHCTTCCSCCSSCCSCTTTSC
T ss_pred             CCcCcCCCCCC-CCEEEcCCCCCCCCCCCCCCCCCcCCCCCEECcCCcC
Confidence            48889765433 33444446999999999988665432    3999975

>d1mm2a_ g.50.1.2 (A:) Mi2-beta (CHD4) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Mi2-beta (CHD4)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.63  E-value=0.0037  Score=33.30  Aligned_cols=47  Identities=21%  Similarity=0.516  Sum_probs=31.1

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhHHHHHcCC----Cccccccccc
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH----SSCPTCRQRL  126 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~----~~CP~CR~~~  126 (141)
                      ..+..|.+|.+.   ++ +..-..|.-.||..|+..-+...    -.||.|+...
T Consensus         7 ~~~~~C~~C~~~---g~-lv~Cd~C~~~~H~~C~~~~~~~~~~~~W~C~~C~~~~   57 (61)
T d1mm2a_           7 HHMEFCRVCKDG---GE-LLCCDTCPSSYHIHCLNPPLPEIPNGEWLCPRCTCPA   57 (61)
T ss_dssp             SSCSSCTTTCCC---SS-CBCCSSSCCCBCSSSSSSCCSSCCSSCCCCTTTTTTC
T ss_pred             CCcCCCcCCCCC---Ce-EEEeCCCCccCchhhcCCCcCcCCCCcEECCCCcCcc
Confidence            344569999742   33 33333589999999997655432    2499997643

>d1fp0a1 g.50.1.2 (A:19-88) Nuclear corepressor KAP-1 (TIF-1beta) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: Nuclear corepressor KAP-1 (TIF-1beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.93  E-value=0.0099  Score=32.47  Aligned_cols=49  Identities=24%  Similarity=0.529  Sum_probs=32.3

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCC----ccccccccccCC
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHS----SCPTCRQRLKPS  129 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~----~CP~CR~~~~~~  129 (141)
                      ....|.+|.+   .++ +..-..|...||..|+...+....    .||.|+..-..+
T Consensus         6 ~c~~C~~C~~---~~~-ll~Cd~C~~~~H~~C~~p~l~~~p~~~W~C~~C~~~~~~~   58 (70)
T d1fp0a1           6 SATICRVCQK---PGD-LVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLK   58 (70)
T ss_dssp             SSSCCSSSCS---SSC-CEECTTSSCEECTTSSSTTCCCCCSSSCCCCSCCCCCSSC
T ss_pred             CCCCCCCCCC---cCE-EEECCCCChhhccccCCCCcCcCCCCCEECcCCcCcCccC
Confidence            3456777763   244 344445999999999998765432    399997655433

>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=93.79  E-value=0.047  Score=29.56  Aligned_cols=57  Identities=18%  Similarity=0.336  Sum_probs=39.2

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHHHcCC-----CccccccccccCCCCCCC
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSH-----SSCPTCRQRLKPSDAMPS  134 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~-----~~CP~CR~~~~~~~~~~~  134 (141)
                      ...|.+|.+.+++..-|..-..=+|.||-.|-+..++++     -.||.-.+--.....+||
T Consensus         8 ~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr~sik~q~~~~evyCPSG~kCpL~gs~~PW   69 (80)
T d2cs3a1           8 PLCCTICHERLEDTHFVQCPSVPSHKFCFPCSRESIKAQGATGEVYCPSGEKCPLVGSNVPW   69 (80)
T ss_dssp             SCCCSSSCSCCSSTTSEECSSCSSCEECHHHHHHHHHHHHSSSCCCCTTSSCCBCSSSSSBC
T ss_pred             ceeeeeehhhhcCCceEeCCCCcCCceeccccHHHHHhcCCCCcEECCCCCccccCCCCCCh
Confidence            467999999998876665333346999999999998753     237766554444445555

>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=93.73  E-value=0.023  Score=29.78  Aligned_cols=45  Identities=27%  Similarity=0.424  Sum_probs=31.2

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccc
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTC  122 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~C  122 (141)
                      ....|--|..++.+. .+..-+.|++.|+.+|=.--=++-.+||.|
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            346799999888543 455666799999999933221234679988

>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=92.07  E-value=0.028  Score=25.44  Aligned_cols=29  Identities=14%  Similarity=0.431  Sum_probs=24.9

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhH
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACI  109 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci  109 (141)
                      ..|+-|...+...|.|+..  =+++||-+|+
T Consensus         3 g~Ca~C~~~I~~~e~VmRA--~~~VyHl~CF   31 (31)
T d1rutx3           3 GACSACGQSIPASELVMRA--QGNVYHLKCF   31 (31)
T ss_dssp             EECTTTCCEECTTSEEEEE--TTEEECGGGC
T ss_pred             cccccccCcCChhHhheec--ccceeeeccC
Confidence            4699999999999999886  5799999984

>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=92.01  E-value=0.21  Score=27.42  Aligned_cols=48  Identities=17%  Similarity=0.382  Sum_probs=31.3

Q ss_pred             cccccccccccCCceeecCCCCCcccHhhHH--HH-HcC--CCcccccccccc
Q 038049           80 GCAICLLDFIDGDEIRLLPKCNHRFHVACID--KW-LLS--HSSCPTCRQRLK  127 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~--~w-l~~--~~~CP~CR~~~~  127 (141)
                      .+.||...+..++....-..|.-=||..|+.  .. ...  +-.||.|+....
T Consensus        13 v~CiC~~~~~~~~~mI~Cd~C~~W~H~~C~g~~~~~~~~~~~~~C~~C~~~~g   65 (79)
T d1wepa_          13 VYCLCRQPYNVNHFMIECGLCQDWFHGSCVGIEEENAVDIDIYHCPDCEAVFG   65 (79)
T ss_dssp             CCSTTSCSCCSSSCEEEBTTTCCEEEHHHHTCCHHHHTTCSBBCCTTTTTTSC
T ss_pred             eEeECCCccCCCCcEEECCCCCCcEeccccCcchhcCCCCCEEECccCcCCcC
Confidence            3449987765555444444688889999985  22 122  356999987543

>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=91.54  E-value=0.065  Score=29.17  Aligned_cols=43  Identities=30%  Similarity=0.632  Sum_probs=24.8

Q ss_pred             ccccccccccccCCceeec-CCCCC-cccHhhHHHHHcC----CCcccccccc
Q 038049           79 AGCAICLLDFIDGDEIRLL-PKCNH-RFHVACIDKWLLS----HSSCPTCRQR  125 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~l-p~C~H-~Fh~~Ci~~wl~~----~~~CP~CR~~  125 (141)
                      ..| ||.... +++.+... ..|-+ -||..|+.  +..    +-.||.|+..
T Consensus        17 ~~C-iC~~~~-~~~~i~c~~~~C~~~wfH~~Cvg--l~~~p~~~w~C~~C~~~   65 (71)
T d1wesa_          17 TYC-LCNQVS-YGEMIGCDNEQCPIEWFHFSCVS--LTYKPKGKWYCPKCRGD   65 (71)
T ss_dssp             CCS-TTCCCC-CSSEECCSCTTCSCCCEETTTTT--CSSCCSSCCCCTTTSSC
T ss_pred             CEE-EeCCCC-CCCEEEEECCCCCCcCccCccCC--CCcCCCCcEECcCCccc
Confidence            445 998653 33333332 12444 49999985  332    2349999764

>d1weva_ g.50.1.2 (A:) PHD finger protein 22 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein 22
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.15  E-value=0.016  Score=32.88  Aligned_cols=50  Identities=16%  Similarity=0.487  Sum_probs=32.5

Q ss_pred             cccccccccccccC-CceeecCCCCCcccHhhHHHHH-----cC---CCcccccccccc
Q 038049           78 SAGCAICLLDFIDG-DEIRLLPKCNHRFHVACIDKWL-----LS---HSSCPTCRQRLK  127 (141)
Q Consensus        78 ~~~C~ICl~~~~~~-~~v~~lp~C~H~Fh~~Ci~~wl-----~~---~~~CP~CR~~~~  127 (141)
                      ...|.||....... ..+..-..|+..||..|+...+     ..   .-.||.|.....
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            45699998654332 3344444699999999987432     11   235999976544

>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=90.82  E-value=0.013  Score=30.05  Aligned_cols=45  Identities=18%  Similarity=0.448  Sum_probs=27.7

Q ss_pred             cccccccccccCCceeecCCCCCcccHhhHHHHHcCCCccccccc
Q 038049           80 GCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLLSHSSCPTCRQ  124 (141)
Q Consensus        80 ~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~~~~~CP~CR~  124 (141)
                      .|.+|..+|..-..-..-..||.+|+.+|....-.....|..|.+
T Consensus         2 ~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~~~~~RvC~~C~~   46 (51)
T d1y02a2           2 SCKSCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGPRLCLLCQR   46 (51)
T ss_dssp             CCTTTCCCCSSGGGCEECTTTCCEECGGGEEC----CCEEHHHHH
T ss_pred             CccccCCcccCCccCcccccCCcccCccccCCCCCCCeECHhHhh
Confidence            488888888543322222359999999997655444456877754

>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=90.38  E-value=0.25  Score=26.69  Aligned_cols=48  Identities=21%  Similarity=0.412  Sum_probs=30.0

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHH----HH-----HcCCCccccccccc
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACID----KW-----LLSHSSCPTCRQRL  126 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~----~w-----l~~~~~CP~CR~~~  126 (141)
                      +...| ||......+. ...-..|.--||..|+.    ..     ....-.||.|+..-
T Consensus        15 ~~~~C-iC~~~~~~~~-mi~Cd~C~~w~H~~Cvg~~~~~~~~~~~~~~~w~C~~C~~~~   71 (76)
T d1wema_          15 NALYC-ICRQPHNNRF-MICCDRCEEWFHGDCVGISEARGRLLERNGEDYICPNCTILS   71 (76)
T ss_dssp             TCCCS-TTCCCCCSSC-EEECSSSCCEEEHHHHSCCHHHHHHHHHHTCCCCCHHHHHHS
T ss_pred             CcCEE-ECCCccCCCe-EEEECCCCCcCCccccCCCcccccccCCCCCcEECCCCcCcC
Confidence            34557 8976654433 44444588889999983    11     12346799997643

>d1weea_ g.50.1.2 (A:) PHD finger protein At1g33420 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: FYVE/PHD zinc finger
superfamily: FYVE/PHD zinc finger
family: PHD domain
domain: PHD finger protein At1g33420
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=89.79  E-value=0.05  Score=29.55  Aligned_cols=47  Identities=23%  Similarity=0.349  Sum_probs=31.0

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHHHc----CCCccccccccc
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKWLL----SHSSCPTCRQRL  126 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~wl~----~~~~CP~CR~~~  126 (141)
                      ..| ||.....+++....-..|..-||..|+..-..    ..-.||.|+..-
T Consensus        17 ~~C-~C~~~~~~~~~mv~Cd~C~~w~H~~C~g~~~~~~~~~~~~C~~C~~~~   67 (72)
T d1weea_          17 VDC-KCGTKDDDGERMLACDGCGVWHHTRCIGINNADALPSKFLCFRCIELS   67 (72)
T ss_dssp             ECC-TTCCCSCCSSCEEECSSSCEEEETTTTTCCTTSCCCSCCCCHHHHHHC
T ss_pred             EEe-eCCCCcCCCCeEEEeCCCCCcCchhhcCCccccCCCCcEECcCCcCcC
Confidence            457 78876666655555556989999999764211    233599997653

>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=86.85  E-value=0.32  Score=26.25  Aligned_cols=35  Identities=20%  Similarity=0.395  Sum_probs=24.1

Q ss_pred             cccccccccccccCCceeecCCCCCcccHhhHHHH
Q 038049           78 SAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKW  112 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~w  112 (141)
                      +..|.+|..+|.--..-..-..||++|+.+|....
T Consensus        13 ~~~C~~C~~~F~~~~rrhhCr~CG~~~C~~C~~~~   47 (72)
T d1dvpa2          13 GRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTAKQ   47 (72)
T ss_dssp             CSBCTTTCCBCCSSSCCEECTTTCCEECSTTSCEE
T ss_pred             CCccccCCCcccCccccccccccCCeeChhhhCCc
Confidence            35699999988653322222359999999997543

>d1joca1 g.50.1.1 (A:1348-1411) Eea1 {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: Eea1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.00  E-value=0.32  Score=25.60  Aligned_cols=36  Identities=19%  Similarity=0.315  Sum_probs=23.9

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhhHHHH
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKW  112 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~w  112 (141)
                      +...|.+|-..|..-..----..||++|+.+|....
T Consensus         7 ~~~~C~~C~~~F~~~~rrHHCR~CG~v~C~~Cs~~~   42 (64)
T d1joca1           7 EVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKN   42 (64)
T ss_dssp             GCCBCTTTCCBCCSSSCCEECTTTCCEECGGGSCEE
T ss_pred             cCCcCcCcCCcccCCccccchhhhCCeecccccCCc
Confidence            345699999888653221122259999999996543

>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=84.92  E-value=0.21  Score=23.25  Aligned_cols=32  Identities=25%  Similarity=0.456  Sum_probs=21.3

Q ss_pred             CCCcccccccccccccCCceeecCCCCCcccHhhH
Q 038049           75 SSASAGCAICLLDFIDGDEIRLLPKCNHRFHVACI  109 (141)
Q Consensus        75 ~~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci  109 (141)
                      .+..+.|..|-...-.-+.+  . .=|+.||..|+
T Consensus         5 ~g~~~~C~~C~K~VY~~Erl--~-a~g~~yHk~CF   36 (36)
T d2co8a2           5 AGAGDLCALCGEHLYVLERL--C-VNGHFFHRSCF   36 (36)
T ss_dssp             CCSSCBCSSSCCBCCTTTBC--C-BTTBCCBTTTC
T ss_pred             CCCCCcccccCCEEeeeeEE--E-ecCcEeccccC
Confidence            34457899997655444433  2 26799999984

>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=84.03  E-value=0.072  Score=24.68  Aligned_cols=27  Identities=26%  Similarity=0.668  Sum_probs=19.9

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhH
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACI  109 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci  109 (141)
                      ..|++|...+.+.    ++...|-.||.+|+
T Consensus         9 EkC~~C~~~I~dr----iLrA~Gk~yHP~CF   35 (35)
T d2dloa1           9 EKCATCSQPILDR----ILRAMGKAYHPGCF   35 (35)
T ss_dssp             CBCTTTCCBCCSC----CEEETTEEECTTTC
T ss_pred             HHHHHhchHHHHH----HHHHhCCCCCCCCC
Confidence            5699998887553    33348888998884

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=83.63  E-value=0.34  Score=23.48  Aligned_cols=31  Identities=19%  Similarity=0.502  Sum_probs=22.6

Q ss_pred             CCcccccccccccccCCceeecCCCCCcccHhhH
Q 038049           76 SASAGCAICLLDFIDGDEIRLLPKCNHRFHVACI  109 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci  109 (141)
                      ...+.|+.|-...-..+.+..   =|+.||..|+
T Consensus        13 g~~~kC~~C~k~VY~~E~~~~---~g~~~Hk~CF   43 (43)
T d1b8ta3          13 GGSDGCPRCGQAVYAAEKVIG---AGKSWHKSCF   43 (43)
T ss_dssp             CCCEECTTTSCEECSSSCEEE---TTEEECTTTC
T ss_pred             CCCCcCccCCCEeeHHHHhhc---CCCccccCCC
Confidence            344779999877666665543   6899999984

>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=82.79  E-value=0.49  Score=25.06  Aligned_cols=34  Identities=18%  Similarity=0.238  Sum_probs=23.0

Q ss_pred             ccccccccccccCCceeecCCCCCcccHhhHHHH
Q 038049           79 AGCAICLLDFIDGDEIRLLPKCNHRFHVACIDKW  112 (141)
Q Consensus        79 ~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~Ci~~w  112 (141)
                      ..|.+|...|.--..----..||.+|+.+|...+
T Consensus         6 ~~C~~C~~~F~~~~rkhhCr~CG~~fC~~Cs~~~   39 (67)
T d1vfya_           6 DACMICSKKFSLLNRKHHCRSCGGVFCQEHSSNS   39 (67)
T ss_dssp             SBCTTTCCBCBTTBCCEECTTTCCEECGGGSCEE
T ss_pred             cccccCCCcccCcccccccccCCCEecccccCCc
Confidence            4699999988543221122259999999996544

>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=82.33  E-value=2.6  Score=23.30  Aligned_cols=58  Identities=21%  Similarity=0.336  Sum_probs=37.8

Q ss_pred             CCcccccccccccccCCc--eeec-CCCCCcccHhhHHHHH-cCCCccccccccccCCCCCC
Q 038049           76 SASAGCAICLLDFIDGDE--IRLL-PKCNHRFHVACIDKWL-LSHSSCPTCRQRLKPSDAMP  133 (141)
Q Consensus        76 ~~~~~C~ICl~~~~~~~~--v~~l-p~C~H~Fh~~Ci~~wl-~~~~~CP~CR~~~~~~~~~~  133 (141)
                      .+...|-||-++......  +.+. ..|+--.|..|.+-=. ..++.||.|++++..-+..|
T Consensus        14 ~~~q~CqiCGd~VG~~~~Ge~FVAC~eC~FPvCrpCyEYErkeG~q~CpqCkt~Ykr~kgsp   75 (93)
T d1weoa_          14 LDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRYKRLRGSP   75 (93)
T ss_dssp             CSSCBCSSSCCBCCBCSSSSBCCSCSSSCCCCCHHHHHHHHHTSCSSCTTTCCCCCCCTTCC
T ss_pred             cccchhhhcccccccCCCCCEEEEecccCCccchHHHHHHHhccCccCcccCChhhhhcCCC
Confidence            345779999988754332  2221 1366668899987544 34788999999886554443

>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=82.29  E-value=0.72  Score=25.03  Aligned_cols=49  Identities=22%  Similarity=0.433  Sum_probs=30.6

Q ss_pred             cccccccccccccCCceeec-CCCCCcccHhhHHH----H--Hc---CCCcccccccccc
Q 038049           78 SAGCAICLLDFIDGDEIRLL-PKCNHRFHVACIDK----W--LL---SHSSCPTCRQRLK  127 (141)
Q Consensus        78 ~~~C~ICl~~~~~~~~v~~l-p~C~H~Fh~~Ci~~----w--l~---~~~~CP~CR~~~~  127 (141)
                      ...| ||......+..+..- ..|..=||..|+.-    .  ..   .+-.||.|+..-.
T Consensus        16 ~~~C-~C~~~~~~~~~i~c~c~~C~~W~H~~Cvgi~~~~~~~~~~~~~~~~C~~C~~~~~   74 (78)
T d1wewa_          16 KVRC-VCGNSLETDSMIQCEDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTSG   74 (78)
T ss_dssp             CCCC-SSCCCCCCSCEEECSSTTTCCEEEHHHHSCCCTTTCSCSCSCSSCCCHHHHHCCS
T ss_pred             ccEe-ECCCccCCCcEEEEeCCCCCcCCCccccCccccccccccCCCCEEECCCCcCcCC
Confidence            4567 998876555444332 14888899999842    1  00   1245999987543

>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=81.94  E-value=0.46  Score=21.57  Aligned_cols=30  Identities=30%  Similarity=0.492  Sum_probs=23.9

Q ss_pred             CcccccccccccccCCceeecCCCCCcccHhh
Q 038049           77 ASAGCAICLLDFIDGDEIRLLPKCNHRFHVAC  108 (141)
Q Consensus        77 ~~~~C~ICl~~~~~~~~v~~lp~C~H~Fh~~C  108 (141)
                      ....|.-|-+-|.+.+++.-.  =|-++|.+|
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            346799999999998887654  578888887